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ArmedXpert Manual v3.0.7.x

1. Au Controls Base Pairs 9 All Indicate clipped data ps PN Px Zoom 100 Organize C Samples J RFUs J User View Fit Zoom Show Hide Windows all Alleles Samples ES Controls Base Pairs All 3N r A PS MS Zoom 10095 Samples RFUs C User View Zoom Headings 25 30 raise 6 7 8 6 7 8 12 13 4 5 8 9 10 5 8 9 15 16 9 10 11 34 6 7 7 9 10 XY 7 8 9 17 2 9 10 24 6 7 8 67 8 12 13 as 919 sas 15 16 9 10 11 31 e7 5 10 XY 2 8 9 17 10 74 6 7 8 67 8 12 13 As 8919 5 8 9 15 16 so 11 11 e7 7 10 X Y 2 8 9 17 pisse pesnipinis sais 6 9 iim inz iib s faut xv 213 fa LR E EE ER ERE ERE ERR ST 12 15 15 8 13 XY 11 20 ERREUR LEE EE E SC 14 13 30 0111 10 12 14 15 8 93 FIGURE 3 4 View Controls by Allele Indicate clipped data Organize Show Hide Windows DEMO 2 Component 4 Vict Mix Stains Analyst txt is 26 ioi 15 sss ini2 9 12 1925 14132 35 8 Le 1 1417 XY 912 22225 12 13 28 29 30 9 10 10 11 12 15 16 6 9 3 8 11 12 9 12 13 19 20 24 25 13 14 14 2 182 15 17 18 19 8 11 14 15 17 X Y 9 12 122 22 2 24 25 12 13 28 29 30 9 10 10 11 12 15 16 6 9 3 8 11 12 9 12 13 19 20 24 25 13 14 14 2 18 2 15 17 18 19 8 11 14 15 17 XY 9 1
2. 123 13 127 23 131 3 0 180 67 188 64 192 61 255 35 259 4 263 46 305 309 33 313 68 111 75 163 09 167 2 216 83 220 82 252 46 264 45 307 55 31 _ 144 22 148 69 204 27 210 18 271 52 275 53 322 09 123 85 127 77 171 23 228 78 232 78 276 42 280 45 311 8 E a 148 58 1 200 36 212 22 267 37 271 47 317 79 321 95 119 78 175 18 175 18 232 67 236 76 268 33 276 41 316 0 en eee aes eae MERE NENNEN ERE eee 139 56 144 16 208 21 275 37 279 43 321 66 132 132 179 14 186 18 228 62 236 65 280 31 236 65 315 8 aS MUERE Oe Ses S 144 01 208 24 271 27 275 32 321 74 329 93 119 73 123 76 179 14 186 16 228 55 276 18 280 25 324 2 g ji Ji Clear Selection FIGURE 3 7 View All Controls by Base Pair Q Alleles Samples R di M Headings gt Controls Base Pairs All Indicate clipped data e A Zoom 100 Organize e Samples C RFUs C User Mew j doom ShowiMde Windows DEMO 2 Component 4 Vict Mix Stains Analyst txt c D851179 D2 s D75820 CSFiPO 351358 mHor Di35317 D165539 025138 91 139 55 144 26 200 36 204 36 208 3 267 42 271 48 321 95 326 12 330 16 123 82 127 87 171 18 186 17 216 86 228 77 232 79 268 4 280 49 284 52 324 47 328 61 344 11 347 67 117 36 139 62 144 22 200 35 204 4 208 31 267 4 271 44 322 06 326 2 330 22 123 82 127 85 171 21 186 26 216 82 228 71
3. D75820 Lg ee 0 1478 0 2906 0 1571 0 3238 0 0479 0 3062 CSF1PO n 2537 n NNS n 3251 lt m ON tor 1Px 0 2 1 Set Numerator Reset Knows Fick viamouse gt x0167 99x9999K1 11 Blood Vict 06 06 20 602 9 Denominator Reset Unknowns FIGURE 7 50 Likelihood Ratio Page with Reference Applied 98 Tab Five Interpretation ARMEDXPERT USER S MANUAL The third type of frequency calculations is a Probability of Inclusion calculation It calculates both probability of inclusion PI and probability of exclusion PE for single source and mixture samples To obtain the Probability of Inclusion Calculation page click on the Probability of Inclusion button The Select Pick via mouse window will appear Select the sample you wish to perform the calculations on with your mouse or click on the W arrow and select from the drop down list FIGURE 7 51 Select Pick via Mouse Window The Probability of Inclusion Calculation page will appear All loci and their corresponding alleles are imported into the page and ArmedXpert will automatically perform the calculations The frequency calculations separated by ethnicity will be listed under each allele The probability of exclusion and probability of inclusion will be listed to the right of the screen also separated by ethnic group Probabitity of Inclusion XX0156 1 99XX999901 15 2F1 Shirt Vict 06 06 20 D01 c3 5 2s X
4. Modhed RMP Apply Rests For a 2 contributor radi of types AA amp BB 1 1 combination s Open For a 2 contributor 2 allele mixture of types AB amp AB 1 1 combination s Frequency Report 12 13Iphr 0 67 12 13 phr 0 67 v FIGURE 2 13 warning The sort loci by allele count option displays the loci with the largest number of alleles first in the Mixture Interpretation Window It is the same as checking Highest to Lowest in the Mixture Interpretation Window The List proportions as dilutions 1 X option displays the proportion as dilutions ratios in the mixture interpretation window Click on the box next to each to turn these features on or off This section also has two save options available for the Mixture Interpretation Window The Prompt to save on window close option will bring up a confirmation window asking you to save ot not when you close the Mixture Interpretation Window The Prompt to save on application close option will do the same thing if you close ArmedXpett and the Mixture Interpretation Window 1s open Confirmation c3 s 3 Save interpretation of 22472 2 9945678 Q1 2 F2 Yag Swab 06 07 14 D02 FIGURE 2 14 Confirmation Window 13 ArmedXpert Menu ARMEDXPERT USER S MANUAL The bottom section is the Profile naming scheme section It allows you to set up names for the profiles used in the Mixture Interpretation Window The l
5. Cancel FIGURE 2 22 Frequency Options 17 ArmedXpert Menu ARMEDXPERT USER S MANUAL Clicking on Delete Races or Delete Sources will permanently delete a Race or Source Make sure you actually would like to delete them before clicking on either of these buttons Click on the Add Frequencies button to add Frequencies Begin by typing in the source name Then manually enter in new frequencies paste in frequencies or import frequencies from a file Each of the three methods is explained below Once all frequencies have been added click on the Commit button b Note Make sure you enter in all the data correctly The Race and Locus cannot be edited later Therefore if either is incorrect they cannot be changed once you commit the frequencies to Armed Xpett Add Frequencies c3 5 5 Source Description Optional Commit Paste Import from file Allele Frequency Close FIGURE 2 23 Add frequency window Method One To manually enter new frequencies start at the first box under the Race column Enter in the correct race Then proceed by clicking on the tab key to each next column Type in the locus then the Allele and finally the Frequency amount Clicking on the tab key will take you to the next line Continue manually filling in all the data Once finished you are ready to commit the frequencies Paste Import from file Race Locus Allele Frequency Ca
6. X4 1 1 9 SD054 7 9 SS 2 9 1 8 50064 EE 9 1 8 50069 ou a 34a 2025 9 2 7 50074 11314 1821 ue 12522 9 2 7 SD083 3538 x immer eumd NEN 15 9 9 50092 3t 1x20 11 13 9 1 8 SD112 1416 7 810 a EN 1 2 9 9 50114 15 17 9 3 10 12 14 17520 1619 8 1216 9 1 8 50119 79 17 24 16518 15 26 9 9 50047 o Ree mee 3 1922 8 ja SD049 15 18 8 11 14 22 25 ih n 8 8 SD052 10 3 12 7 93 133 3520 31518 ea 8 FE 50055 37 T 16 10 zz 29 8 5 lt enns7 i amp 12 7 4n 44 13 31 jee 19 2n 23 Q In a M zd 7 lll 7 NNNM gt FIGURE 6 1 1 Match amp Compare Profiles Sample Table based on Find Included in the Reference 73 Tab Four Match amp Comparison ARMEDXPERT USER S MANUAL Sources The Sources section allows you to compare one table with another Select the table using the W arrow keys next to A box and another table using the V arrow keys next to the B box Once tables are selected click the Compare Tables button The two tables will be compared and a screen will appear
7. 12 13 phr 0 37 p 1 00 Ref 1 12 p 0 00 12 13 phr 1 00 p 054 Ref 1 13 p 0 46 For a 2 contributor 2 allele mixture of types AB amp AB 1 1 combination s 2 of 1 12 2 12 13 phr 0 37 3tphr 0 37 A FIGURE 7 9 Reference Selection Box with Reference Selected 79 Tab Five Interpretation ARMEDXPERT USER S MANUAL Settings The Peak Height Ratio PHr Minimum Peak Height mPH Minimum Proportion mP Homozygote threshold HT and Stutter are defaulted from the Mixture Interpretation Settings discussed in Chapter 2 You can change these values on the arrows next to each box to appropriate value in accordance with your individual lab validated thresholds The changed value will remain active as long as the Mixture Interpretation Window stays open or you manually change it to another value The default values set in your Mixture Interpretation Settings will appear when a new Mixture Interpretation Window is opened The Lock locus on report option allows you to lock in the settings for the current locus allowing settings to be changed without altering the final report Mixture Interpretation Quality Control Frequencies Frequency Mixture interpretation settings PH 0 30 3 Roemer 175 2 HT 100 5 Default peak height ratio PHr 0 3 Lock locus Default minimum peak height mPH IETL Ny 3 Default homozygote threshold HT 100 Default minimum proporition mP 0 me cx cx
8. 4 se Print gt Armedipert Options Exit Armedxpert FIGURE 2 35 View Menu X AC X Choose value Select an option below Staff bl Ok Cancel FIGURE 2 54 Chose value Window 36 ArmedXpert Menu ARMEDXPERT USER S MANUAL Print To print a page click on the print option The appropriate print window will open 4 Import e Print Export 55 View gt In the print window you can change between orientations choose what to print change sizes and enter FIGURE 2 55 Print Menu headers Make all appropriate selections and enter any necessary headers 4b Print Workbook Plot Print Print Preview Orientation Portrait Landscape Print What Sheet Selection Workbook Scaling C Zoom 100 Fittopages 1 Wide 1 lt Tal More Options Header Footer Sheet gt PESE Left Header Select saved page setup Save as default ide Sel Right Header d2 M3 y4 Save Setup Armedxpert allows you to use special formatting flags help make your printing process easier A DeleteSetup Flag Meaning Example N Product version Ammedxpert v3 0 7 773 Zt Data source file name if applicable MyDNAD ata txt un Username admin y i ra FIGURE 2 56 Print Options 37 ArmedXpert Menu ARMEDXPERT USER S MANUAL The ptint window allows you to make additional changes as well
9. Plugins Use a plugin to export samples gt Excel Workbook Save as a workbook or in a workbook friendly Format Image Save the entire worksheet or selected range as an image a a ki Print gt Frequency Analysis Save a Frequency analysis page so that it dia can be resumed later Mixture Interpretation Save mixture interpretation so that it can be resumed later Armedxpert Options Exit Armedxpert FIGURE 2 50 Export Menu 34 ArmedXpert Menu ARMEDXPERT USER S MANUAL To save a Frequency Analysis so that it can be resumed later in Armed Xpert click on Frequency Analysis The Save As window will appear You can change the file name to whatever name you would like and Save it in whichever folder you would like Click Save once you have the file name and folder chosen You also have an option to save a frequency analysis as an excel workbook by clicking on Excel Workbook when you have the Frequency page open You can then open the Frequency analysis in Excel Finally you can save the report as an image by clicking on Image Excel Workbook Save as a workbook or in 5 55 View gt a workbook Friendly format re et or cte gt Image 0 6358 0 8078 0 7687 0 8746 10 11 12 zx 0 2537 03005 03251 0 2268 02714 02048 03 0 3975 0 2536 0 2656 0 3923 0 1692 0 2463 02315 0 7717 0 2905 0 3071 0 6429 0 42
10. Samples FIGURE 4 2 Sample Section 49 Tab Two Data ARMEDXPERT USER S MANUAL When you click on New Sample the window shown in Figure 4 4 below will appear This allows you to manually enter in a sample to an open sample table or a new table To enter in a new sample first select source type by clicking on V arrow next to the Set Sample Source Type box then choose the correct type from the drop down list Set Sample Source Type Identifiler B i Identifile Y filer Profiler CO filer Profiler Plus SEfiler Plus SGM Plus GT Profiler COfiler Allele s PowerPlex 16 PowerPlex ESI 1 RFUls PowerPlex ESX 17 PowerPlex Size Std Base Pairs FIGURE 4 3 set Sample Source Type drop down list Next choose the sample table you would like to add the sample to Click on the V arrow next to the Send to box and choose from the available sample tables opened You also have the option to send it to a new blank table Note The sample table has to be opened to add a new sample to it Enter a sample name Under each locus type in the allele s RFU s and Base Pairs Use a comma to separate more than one number in each box If you need to enter a new locus click the Add Locus button Once you are finished click the Ok button in the upper right corner of the window The d button refreshes the list of destination tables 4 1 Set Sample Source Type Allele s RFU s
11. The first is the Highest to Lowest option By clicking on the box next to Highest to Lowest the locus will be arranged from the locus with the most alleles to the ones with the least Note Changes made to the alleles while making your interpretation like deleting an allele or adding stutter can change the order of the loci when using the Highest to Lowest option gt Highest to PHr 0 60 Lowest mPH 75 Ignore Alleles Below mPH UD FIGURE 7 27 Highest to Lowest Feature 87 Tab Five Interpretation ARMEDXPERT USER S MANUAL As you make each call the proportion average will be shown on the Mixture Interpretation Window It is located in the middle top portion of the screen Next to the proportions will be the dilution ratio if that option is selected in the Mixture Interpretation settings in the ArmedXpert Options window c3 5 53 i Mixture Interpretation Interpretation 0 Setup SRP PERT aT EIN Contributor 2 x IVA IIIS oper ont Vict Db Ub zu p Lu Operations i References Locus D851173 2 gt Major 18 13 P Avg 0 69 2 2 7 ee PH 0 60 5 Minor n a P Avg 0 31 1 0 75 2 HT 150 3 Alleles 12 13 Ignore Alleles a Below mPH 0 00 RFUs 1580 2345 BPs 140 144 Lock locus Popout Res call report FIGURE 7 28 Proportion Average Section To assist with your interpretation you can choose to visualize
12. 1 0 Example of a PHR Report with hidden locus 116 Tab Six Reporting ARMEDXPERT USER S MANUAL On the left hand side of the report is the PHR at each locus The average PHR can be seen at the end of each table as well as the standard deviation the minimum PHR the maximum PHR and the standard error PHR Report D851179 D21911 CSFIPO D351358 THO1 D195433 TPOX D18551 Amel D55818 FGA a EN D Ai 1 53 3 801 0966 0 9126 0 8438 0 8638 09324 09840 0 8093 06637 0 7957 0 9582 _ 0 9436 0 A2 15 3 B01 0 9692 0 9595 09817 0 9204 0 9667 0 9108 09452 08561 0 9530 09590 0 9353 Std Deviation 0 0568 0 0611 0 0707 0 0770 0 0906 0 0334 0 0679 0 1269 0 0788 0 0194 0 0136 Mim 0 8652 0 8369 0 8438 0 7841 0 7827 0 9067 0 8093 0 6037 0 7957 0 9246 0 9232 Max 0 9716 0 9629 0 9861 0 9570 0 9667 0 9840 0 9799 0 8561 0 9862 0 9710 0 9592 StdError 0 0254 0 0273 0 0316 0 0344 0 0405 0 0149 0 0304 0 0568 0 0352 0 0087 0 0061 Std Deviation 0 0183 0 1474 0 0849 0 0143 0 0915 0 0764 0 0328 0 1093 0 0915 0 0699 0 0682 Mm 0 9441 0 6411 0 8333 0 9112 0 7898 0 8045 0 9350 0 7603 0 7393 0 8511 0 7123 Max 0 9806 0 9160 0 9858 0 9390 0 9722 0 9535 0 9924 0 9781 0 9168 0 9894 0 8335 Stdtrror 00105 0 0851 0 0490 0 0083
13. 2024 13142 1719 811 1415 X 12 2224 1011 15 69 3 1 12 9 12 1925 14182 1518 11 1417 XY 912 22225 11 ae ani i 1 amp 2 ix 1516 8 18 xr 3 EE ee NES ERST ee ae eee See Ee Eee quail sce cun 10 12 14 15 8 93 11 11 12 1923 1415 17518 8 1519 11 23 24 XX0166 Reag Blank 06 06 20 F02 XX0167 99XX9999K1 11 Blood Vict 06 06 20 G02 XX0168 99XX9999K2 Blood Susp 06 06 20 H02 XX0169 QA026 QA 06 06 20 803 XX0170 Reag Blank 06 06 20 C03 H un ray Be H en Sie XX0171 Pos Con 06 06 20 D03 10 111 XX0172 Neg Con 06 06 20 E03 SS ee a a XX0153 99XX9999Q1 15 12F1 Shirt Vict 06 06 20 H02 910 1011 15 693 1 12 912 1925 14182 1518 11 1417 XY 912 22225 RFUs are off scale Adis Mu RFUS are both e ind off en below 300 FIGURE 5 6 Example of a RFUs Check screen 63 Tab Three QC Checks ARMEDXPERT USER S MANUAL CODIS QC There are six types of CODIS Quality Control checks They are CODIS Alleles Allele Count Check X OSD PHR and Check multi These quality control checks will evaluate the samples on the active sample table to allow you to know if they are ready to be accepted by CODIS HU 5 M CODIS Allele at OSD PHR Check Alleles Count x multi CODIS QC FIGURE 5 7 CODIS QC Commands To perform the checks click on each type of CODIS quality control check you wish to
14. 93 1213 123133 1822 1215 2 2 0 0 XX0170 Reag Blank 06 06 20 C03 EGENT NOMENIEN XX0171 Pos Con 06 06 20 D03 10 11 1 10 12 8 93 11 2 1 1 0 XX0172 Neg Con 06 06 20 E03 FIGURE 6 5 Find Where Reference is Included Example Find Included in the Reference is used to find loci that are included in the reference All loci that contain an exact match to the reference are highlighted orange All loci that contain the part of the reference and no other allele s are highlighted yellow 075820 CSF1PO D351358 THO1 D13S317 D165539 D251338 D199433 vwa 18551 Amel D5S818 Ladder Identifiler 06 06 20 A01 67 8 6 7 8 9 12 13 4 5 8 9 10 5 8 9 15 16 17 9 10 11 12 11 12 13 6 7 n 0 0 Ladder Identifiler 06 06 20 A03 6 7 8 6 7 8 9 12 13 4 5 8 9 10 5 8 9 15 16 17 9 101112 11 12 13 67 7 8 9 1 1 0 0 Ladder Identifiler 06 06 20 F03 6 7 8 6 7 8 9 12 13 4 5 8 9 10 5 8 9 15 16 17 9 10 11 12 11 12 13 6 7 1 n 0 0 XX0153 99XX9999Q1 15 12F1 Shirt Vict 06 06 20 H02 16 16 0 0 XX0156 1 99XX9999Q1 15 2F1 Shirt Vict 06 06 20 D01 8 11 4 4 0 0 XX0156 3 99XX9999Q1 15 2F3 Shirt Vict 06 06 20 E01 8 11 4 4 0 0 XX0159 1 99XX9999Q1 15 8F1 Shirt Vict 06 06 20 F01 8 11 4 4 0 0 XX0161 1 QAO03F1 06 06 20 H01 11 12 9 4113 1724
15. D165539 D251338 LAS D851179 D21S11 D7S820 csFipo__ D3S1358 95433 20 02 7403 6117 2224 2344 25842804 4063 2468 1997 2155 1827 2560225 23162427 23842157 2833 2655 201 1580 2345 916 1144 994 594 2480 2001 609 1157 1548 747 1337 1465 677 444 978 409 1355 944 1456 1141 1053 355 787 410 886 292 332 934 423 01 602 1632 1025 278 243 629 1264 992 669 438 1309 308 927 951 178 360 692 550 900 363 542 358 338 371 246 402 332 328 377 227 443 01 729 5216 3296 522 308 1613 2253 2379 1564 467 377 1146 1409 1679 2011 415 1653 413 571 1531 373 1284 455 1483 1640 511 1924 13711 4982 925 2307 2315 505 4032 2418 542 2356 2776 1886 2548 2738 1519 395 1716 358 2295 1936 704 2445 2058 378 2051 370 1653 359 397 2085 675 3915 4443 3448 3618 4644 2698 2497 2333 2426 2489 2309 2968 3302 7403 6117 2224 2344 2584 2804 4063 2468 1997 2155 1827 2560 2265 2316 2427 23842157 2833 2656 P FIGURE 3 11 view Samples by RFUs 42 Tab One Views ARMEDXPERT USER S MANUAL Fit The Fit section allows the user to determine the width of the columns Samples change the column width to fit all sample data only changes the column width to show all the data for both the samples and the controls User will keep t
16. Un Nic User Manual Software Version 3 0 x NicheVision Forensics LLC ArmedXpert User s Manual NicheVision Forensics LLC 526 S Main Street Suite 714G Akron OH 44311 Phone 330 252 2711 Fax 330 252 2713 The information in this document is subject to change without notice NicheVision Forensics LLC makes no warranty of any kind in regard to the contents of this document including but not limited to any implied warranties of merchantability quality or fitness for any particular purpose NicheVision Forensics LLC shall not be liable for errors contained in or for incidental or consequential damages in connection with the furnishing performance or use of this document All trademarks are the property of their respective owners Table of Contents INTRODUC TETN ener re eT 1 ch dete Oba a7 Cnr ne I reer errr Z DIODIDO tert rr E tr tee 2 Changing the Database in Aid X Pert reu rape 2 Using the Demo Database EL ele qamermer 5 ARMBDXPERI VIBINUL nens SEuER ERU CE EKRP aD DdubE 7 Ne OG T 8 sage erates sce ee dete teeny etn cnet ed 31 DIDO 34 26 loire 27 EE ILE GU E EA C E 39 bi c o
17. lt lt is E 4 lgnore Case Also select tables Title 156 1 33 253333 1 15 2F1 Shirt Vict 06 06 20 D01 lt 0159 1 33433330 1 15 SF1 Shirt Vict 06 06 20 FUT x Combine FIGURE 4 9 Combine Sources Window A new combined sample table will appear with the default or user defined title An example is shown in Figure 4 10 below In this example the three samples selected above were combined into a new sample table XX0156 1 99XX999901 15 2F1 Shirt Vict 06 06 20 D01 XX0159 1 99XX999901 15 8F1 Shirt Vict 06 06 20 F01 XX0156 3 99XX999901 15 2F3 Shirt Vict 06 06 20 E01 15h10m48s D851179 Dnsh osse csripo 0351358 m A ees 7 D165539 D251338 D195433 vwa TPOX D18S51 Amel D5S818 FGA 12 13 28 29 30 9 10 10 11 12 15 16 6 9 3 8 11 12 9 12 13 19 20 24 25 13 14 142 18215 17 18 19 8 11 14 15 17 X Y 9 12 22 22 2 24 2 12 13 28 29 30 9 10 10 11 12 15 16 6 9 3 8 11 12 9 12 13 19 20 24 25 13 14 14 2 18 2 15 17 18 19 8 11 14 15 17 X Y 9 12 22 22 2 24 2 12 13 28 29 30 9 10 10 11 12 15 16 17 6 9 3 8 11 12 9 12 13 19 20 24 25 13 14 14 2 18 2 15 17 18 19 8 11 14 15 17 X Y 9 12 22 22 2 24 2 XX0156 1 99XX9999Q1 15 2F1 Shirt Vict 06 06 20 D01 XX0156 3 99XX9999Q1 15 2F3 Shirt Vict 06 06 20 E01 XX0159 1 99XX9999Q1 15 8F1 Shirt Vict 06 06 20 F01 FIGURE 4 1
18. 0156 1 99 lt 999901 15 2F1 Shirt Vict 06 06 20 D01 Edit Locus Locus Locus Locus Locus Locus 1 Allele s 12 13 Allele s 28 29 30 Allele s 3 10 Allele s 10 11 12 Allele s 15 16 Allele s 6 3 3 RFU s 1580 2345 RFUf s 916 1144 994 RFU s 594 2480 RFU s 2001 609 1157 RFU s 1548 747 RFU s 1337 1465 Base Pairs 139 55 144 26 Base Pairs 200 36 204 36 20 Base Pairs 267 42 271 48 Base Pairs 321 95 326 12 33 Base Pairs 123 82 127 87 Base Pairs 171 18 186 17 Locus Locus Locus eee a ee O ee See Allele s 8 11 12 RFU s 677 444 978 Allele s 9 12 13 RFU s 408 1355 944 Base Pairs 268 4 280 49 284 Allele s 19 20 24 25 RFUfs 456 1141 1053 3 Base Pairs 324 47 328 61 34 Allele s 13 14 14 2 18 2 RFU s 787 410 886 232 Base Pairs 117 36 121 33 12 Allele s 15 17 18 18 RFU s 332 934 423 303 Base Pairs 171 04 178 38 18 Allele s 8 11 RFU s 970 2010 Base Pairs 216 86 228 77 23 Base Pairs 223 34 241 83 Locus Locus Locus Locus EN ee 2a _ RR RR Allele s 14 15 17 Allele s gt Y Allele s 9 12 Allele s 22 22 2 24 25 RFU s 1144 883 360 RFU s 1707 258 RFUl s 376 2105 RFU s 441 168 550 256 Base Pairs 290 93 295 08 30 Base Pairs 234 84 236 89 24 Add Locus Base Pairs 106 63 112 28 Base Pairs 142 61 155 75 FIGURE 4 6 Edit Sample Window To change the kit of your sample table click on the Change Ki
19. 100 iz Default stutter 100 iue mre Globally Do OF Sort loci by allele count 0 08 FIGURE 7 10 Mixture Interpretation Settings The Multi PHr button allows you to set a PHr range The PHR Range peak height ratio is for each separate locus A default range can be set up using the ArmedXpert options window See instruction in Chapter 2 under the Interpretation Quality Control options section to set up a default range To activate this feature click the box left of the Multi Phr button to activate this feature Note The default PHr value to the left of the Multi PHr will be used if the feature is not activated or no range is added to the Multi PHr feature jhest to FHr 0 50 vest 8 ih 4bk 4 mPH 75 ore cn 000 ck locus E View call report report cda MM FIGURE 7 11 Muti PHr Button 80 Tab Five Interpretation ARMEDXPERT USER S MANUAL If defaults have not been added or you want to change a range for a Locus click on the Mult PHr button The window show below will appear You can type a Minimum rfu value with an appropriate Phr and or a Maximum rfu value with an appropriate Phr Click on the button to add another range To delete a range click on the X next to the appropriate range Fj PH 050 Iu mPH 75 es PD 2 H k v Min Max Phr 1000 Max 5 Popout View call 0 0 6 i Lx cals Addon Min 1000 o4 x FIGURE 7 12 Multi PHr Window The
20. 15 16 17 9 101112 11 12 13 6 7 7 9 10 XY 7 8 XX0156 1 99XX9999Q1 15 2F1 Shirt Vict 06 06 20 D01 12 13 28 29 30 9 10 10 11 12 15 16 6 9 3 8 11 12 9 12 13 19 20 24 25 13 14 14 2 18 2115 17 18 19 8 11 14 15 17 X Y 8 XX0156 3 99XX9999Q1 15 2F3 Shirt Vict 06 06 20 EO1 9 XX0159 1 99XX9999Q1 15 8F1 Shirt Vict 06 06 20 F01 10 XX0161 1 QA003F1 06 06 20 H01 13 14 28 31 11 112 10 1418 6 amp 9 1113 17524 1314 1417 811 12 XY 11 XX0162 1 Reag BlankF1 06 06 20 802 ay a ETE EET CNN S Sheet1 XX0156 1 99XX9999Q1 15 2F1 XX0156 3 99XX9999Q1 15 2F3 159 1 99XX999901 15 8F1 FIGURE 8 1 0 Match and Compare additional worksheet example 110 Tab Six Reporting ARMEDXPERT USER S MANUAL CMF The CMF form is the CODIS upload file When you are ready to upload your data to CODIS click on CMF and the CMF window will open as shown in Figure 8 11 below Choose the CMF Version that is appropriate from the drop down list on the lower left hand side of the CMF window The CMF Attributes on the left hand bottom of the window will change based on the version selected Fill in the CMF Attributes Note If you filled in the default CMF Attributes in the Options Window they will be automatically filled in the appropriate boxes X CMF EN I3 Samples amp sources Selected samples amp sources ENNV 3 Component V 51 E and 52 274 1 35556
21. 1923 1415 1718 8 amp 8 151 RFUs are off scale above 6000 FIGURE 5 13 OSD Result Example 66 Tab Three QC Checks ARMEDXPERT USER S MANUAL The PHR command evaluates peak height ratios to see that they meet the threshold The PHR settings are set up under the Quality Control Section in ArmedXpert Options Menu Any sample s locus that has a PHR imbalance is highlighted pink Any sample s locus that is not valid for this check is highlighted dark grey VIEWS Data QU Match i Comparison Interpretation Keporting M Ma OPO 8 5 a Check Check Allele Stutter RFUs CODIS Allele ae OSD PHR Check Begin Clear Controls Ordering Alleles Count x muli Review Checks Standard Checks It _SODIS QC QCReview Clear C Program Files NicheVision Inc ArmedXpert data Saved_Profiles Page_Data MT Test Genotypes Table txt p13s317_pisssae _o2si938_ _pissa33_ 01 13 13 130301 1011 1012 1415 893 10 Poise sa p ws rae a p Col ola ola Y FOCOEEJNCENIRUUNEL CN O00 mi mop sn 1 0 Tessmann eu 2 30 5 9 10 1219 10 11 12 16 1 Riso nis mem pois ss i 2930 910 9191 16 17 E oo o a 29 30 8 9 10 12 9 10 11 16 17 8 9 93 11 12 11 12 17 18 20 26 12 14 2 15 16 17 18 19 8 8 ee oo 22 Nun us sls ues ee XC S Item was not v
22. Base Pairs Allele s RFU s Base Pairs Allele s RFU s Base Pairs SendTo Add Table Allele s Allele s Allele s Allele s RFU s RFL s RFU s Base Pairs Base Pairs Base Pairs Base Pairs Locus Allele s Allele s Allele s Allele s RFU s RFLl s RFL s RFU s Base Pairs Base Pairs Base Pairs Base Pairs Allele s Allele s Allele s Add locis RFUl s RFUl s RFUl s Base Pairs Base Pairs Base Pairs FIGURE 4 4 New Sample Window 50 Tab Two Data LOCH Allele s RFU s Base Pairs OCUS Allele s RFL s Base Pairs EN Add ARMEDXPERT USER S MANUAL To edit any sample on your sample table click the Edit Sample button The select pick via mouse window will appear as seen below in figure 4 5 You can use your mouse to select the sample you wish to edit or click on the V arrow and select the one you would like to edit from the drop down list Ein L Py o Change Combine Commit Samples Load Samples Connect Disconnect Sort Kit Sources to Data Source From Data Source Server Server Sort Pick via mouse FIGURE 4 5 Select Pick via mouse Window A window similar to the Enter new sample window will appear At each locus the allele s RFU s and Base Pairs can be added to or changed All fields that cannot be changed are grayed out Once you complete your edits click on the Edit button 51 Set Sample Source Type dentifiler Send To
23. Clear DEMO_I_2 Component_4_Vict_Mix_Stains_Analyst txt c 5 D851179 D21511 D7S820 CSFIPO D351358 THO1 D135317 D16 539 D251338 19645 018551 lh irt Vic a REIN 1233 28 29 30 9 10 10 11 12 15 16 16 93 8 11 12 9 12 1319 20 24 29 13 14 14 2 183 15 11 18 19 8 11 114 15 17 Xv 9 12 22 22 2 24 25 Pao aaaea anupsw enn ueuapsaac pce ais en pen er sar anas vul aa ofon sspe an ns ms mu m fanl is x 9 mx m 3 28 910 1011 15 693 1 12 912 1925 14182 1518 u 141 XY 912 22225 FIGURE 5 12 Check X Result Example The OSD off scale data command evaluates the RFU s for off scale values The OSDs settings are set up under the Quality Control Section in ArmedXpert Options Menu It highlights in yellow any sample s locus that contains RFUs that are off scale puer Ei EEEE E 4 Check Check Allele Stutter RFUs CODIS Allele Check OSD PHR Check Begin Clear Controls Ordering Alleles Count x muli Review Checks Standard Checks Ji CODIS QC QCReview Clear DEMO 2 Component 4 Vict Mix Stains Analyst txt s a esae 521511 fo7sszo _csraro_ p3s1358 THo4 DISSSUZ OIGSSIS 0291338 _D199433 0195433 v ETE 6 55 9 24 25 amp 7 5 57 85 12 15 45 amp 9 10 5 8 9 15 1617 9 10 1112 i112 13 6 7 7 9 1 8 519 24 24 2 6 7 8 6 7 8 9 12 13 4 5 8 9 10 5 a
24. Click on C D Form and the window shown in Figure 8 2 will appear CODIS Disposition Form for CODIS Administrator cts S 3 CODIS Disposition Form for CODIS Administrator 1 Category _ vo PROFILE for conis Reason DO _ l EVIDENCE PROFILE for the FORENSIC INDEX This profile is from crime scene evidence is attributable to a putative perpetrator and is not from an item owned used by the suspect The source of the EVIDENCE PROFILE for the FORENSIC INDEX has been identified L The source of the EVIDENCE PROFILE for the FORENSIC INDEX is unknown 1 gmowsomrmowcs wmm _ graver SOURCE D vo Yes Reason UU b a Correct results were obtained for all controls zi Jii gt Evidence Victim Define Alleles for Pick via mouse dam O Suspect Elim Y Evidence FIGURE 8 2 CODIS Disposition Form Window 105 Tab Six Reporting ARMEDXPERT USER S MANUAL Fill in the top portion of the screen by filling in all necessary boxes If the information filled in at the top portion of the screen will be used more than once click on the duplicate button found at the bottom of the page This will open up another CODIS Disposition Form Window with the top portion of the screen fill in exactly like the original one n CODIS Disposition Form for CODIS Administrator ca E 2s CODIS Disposition Form
25. Data ARMEDXPERT USER S MANUAL In the example shown in Figure 4 18 below an individual staff sample is being deleted from the staff profile Once you have selected the correct sample s or table click on the Delete button If you choose the entire table it will delete the entire profile Note It can cause an error to delete an entire QA profile so just delete the samples found in the QA profile not the QA profile itself A confirmation window will appear to confirm you want to delete Click Ok to confirm the delete pp y Q Datasour e Load c3 5 Samples amp sources Selected samples amp sources HECK SDO050 m 2 ALD gt vw vw The selected item s will be completely removed Are you sure you want to delete Ye Ne SD057 LM J Ignore Case Also select tables Search V Search Tables Search Profiles FIGURE 4 18 Deleting a Datasource sample To connect or disconnect from the server click on the appropriate command When you click on the Connect Server button the Login window appears This enables you to change between databases while in ArmedXpert The Login window instructions in chapter one Connect Disconnect Server Server FIGURE 4 19 Connect Disconnect Server buttons 58 Tab Two Data ARMEDXPERT Sort The final section is the Sort section There are two options Sort and Sort Sam
26. Match amp Compare Profiles button Click on the box to the left of the profile that you would like to compare to the sample Then click either the Find Where Reference is Included or Find included in the Reference The select pick via mouse window will appear to select the sample you would like to compare to your profiles The pick via mouse option will allow you to select the sample using your mouse Clicking the W arrow will provide a drop down list of all available samples from which you can select the appropriate sample _ E n Match Compare Profiles F co s XS Staff SRM Unknown Find Where Find Included Reference is in the Cancel Reference Included FIGURE 6 9 Match amp Compare Profiles Window 72 Tab Four Match amp Comparison ARMEDXPERT USER S MANUAL The profile table will open All locus cells will be highlighted based on the results The Key is found on the bottom of the page and to the right of the table Profis E 5 179 021511 D75820 CSF1PO D351358 D135317 D165539 0251338 0195433 vWA TPOX D18551 10 12 10 11 iE EN 0051 12 14 242 28 10 9 11 9 93 11 11 12 1520 15 17 19 11 12 14 15 12 13 21 23 50052 12 15 28 30 103 12 15 17931 11 12 11 13 1820 13 15 17 18 19 X 11 22 24 5
27. Samples amp sources Selected samples amp sources LADDERSANDCONTROLSCHECK_TABLE gt ss Ignore Case Also select tables Search J Search Tables Search Profiles Delete Load FIGURE 2 34 New Table Selection Window 24 ArmedXpert Menu ARMEDXPERT USER S MANUAL The fifth section is Reporting This section has three subsections Reporting Options CODIS and CMF Attributes The first subsection Reporting Option allows you to set ArmedXpert to automatically check all samples against the loaded selected profiles as soon as you import the table into ArmedXpert When checked ArmedXpert will generate a report when a table is imported into ArmedXpert It lists all the samples included on the imported table and indicate which ones are at equal to or above the minimum number set for exact and included matches compared to the selected profile types Note If this option is not checked you can manually check a staff profile against any sample table in ArmedXpert The sample comparison reporting directions can be found in Chapter 8 To enable automatic table and staff profile comparison check the box to the left of Compare table to profile types selected below upon opening Then enter the minimum number of total matches the minimum number of exact matches and the minimum number of included matches that you would like to show on the report To show all included set the minimum number of included
28. button only the controls will appear on the table To bring the samples back in view either click the F8 button once and just the samples will be shown twice and both samples and controls will be shown or go back to the View tab and click on All or Samples depending on what you want to view The Check Controls feature depends on the settings in the database If the Check controls feature is not working correctly check that the following four things are correct in ArmedXpert e You may need a few expressions added or changed to the Control qualifiers See Chapter 2 under Armed Xpert Options section for instructions You may need to add the correct table that is used to check the controls against See Chapter 2 under Armed Xpert Options section for instructions e You may need to add or correct the QA Profile used to check the QA Controls See Chapter 4 under Data Source section for instructions e You may need to change the thresholds for the Quality Controls See Chapter 2 under Armed Xpert Options section for instructions sare copo 55818 FGA DEROEXIEEENEA Ladder Identifiler 06 06 20 F03 89 10 24 67 8 678 12 13 45 8 9 10 5 89 15 16 9 10 11 11 6 7 Ladder Identifiler 06 06 20 A03 RII AE EE E AEA PEE E 6 7 8 67 8 12 13 4 5 8 9 10 5 8 9 15 16 9 10 11 1 13 14 pesnipiniz 10 1418 6 amp 9 1113 1724 13 14 1
29. button on the bottom of the Organize window This will allow you to perform commands for an entire group like bringing all windows in a specific group to the front or minimize maximize or close the entire group The commands are to the right of the group name If you move your mouse over any of the commands buttons a description of the command will be displayed To move a window to another group click on it and drag it to the appropriate group You can click on any of the Group names to rename them The number of windows in a particular group is listed under the group name Windows ad DIX J 5 Remowe Group FIGURE 3 22 Group Commands When the Top Most button appears yellow the Organize window will remain in the front of all other windows unless it is minimized Click on the Top Most button to toggle this feature on or off Click on the red X on the upper right hand corner of the Organize window to close it or the on the upper right hand corner to minimize the Organize window b Note The Organize window opens as an undocked window from ArmedXpert Organize e Group 1 Fa 3 Remove Group Bring To aae t DEMO 2 Component 4 Vict Mix Stains Analyst txt wt Undock Bring i Front Misture Interpretation DDA Interpretation Undock oe Te Bring To i 4 t mi RMP XX0156 3 99XX999901 15 2F3 Shit Viet 06 06 2
30. many samples as you wish to commit QQ Datasource Commit I i Select items to commit to the datasource DEMO 2 Component 4 Vict_Mix_Stains_Analyst tet A 220156 3 38 5433330 1 15 2F3 Shirt Vict 06 06 20 E01 Ladder Identifiler 06 06 20 F03 1 99 lt 999901 15 2F1 Shirt Vict 06 06 20 D01 Ladder Identifiler 06 06 20 403 Ladder Identifiler 06 06 20 401 220156 1 9 999901 15 2F1 Shirt Vict 2 gt 220156 3 9999990 1 15 2F3 Shirt Vict O6 06 20 E ERE 220159 1 996699990 1 15 8F1 Shirt Vict 06 06 20 F gt gt 220161 1 GA003F1 06 06 20 H01 a 220162 1 Reag BlankF1 06 06 20 B02 220162 2 Reag BlankF2 06 06 20 C02 2060164 99 lt 999901 2 LFS Vict 06 06 20 D02 xx0165 QA004 QA 06 06 20 E02 gt lt 0166 Reag Blank 06 06 20 F02 lt lt XXD157 994 lt 9999K1 11 Blood Vict 06 06 20 G02 y w ou me c mi A AP A gt 2 Ignore Case Also select tables i Commit items as Table _Individual Profiles S Table Name 2 Component 4 Vict Mix Stains Analyst txt Type kit Identifiler S Commit Done FI GURE 4 12 Datasource Commit Table Window 54 Tab Two Data ARMEDXPERT USER S MANUAL You can also use the Selection Filter box to enter in a specific name and all samples containing that name will be highlighted This is helpful in finding certain samples in a large sample table Click the gt button and all samples hi
31. 0 9 594 10 2480 For a 2 contributor 2 allele mixture of types AA amp BB 1 1 combination s Only combinations including the following reference profiles are included 10 12 nations have PHr gt 0 3 MPh gt 100 mP gt 0 UJ NJ N f m Biel EU ple I 2 Dn Qi 5 o FIGURE 7 32 Mix Interp Worksheet Tab These reports can be printed and or saved using the print and export features explained in Chapter 2 90 Tab Five Interpretation ARMEDXPERT USER S MANUAL You can add a comment s to the call report Click on Add Comment button A drop down list will appear to give you a choice to add comments to the Calls page or the Mixt Interp page or you can remove comments that you have already added If you select to add comment to either page the Add a comment window will open Type the comment you would like to appear on the page Click Ok This will add a comment to the specific page in the Call report Adi Comment FIGURE 7 33 Add Comment button Add comment to calls Add comment to Mix Interp Remove comments From calls FIGURE 7 34 Add Comment drop down list e o 5 T a u o e 2 5 2 a o a D8S1179 D21S11 D7S820 CSF1PO 035135 Profile OS 0 81 0 70 0 61 0 66 0 6 Profile 06 0 19 0 30 0 39 0 34 0 3 Profile OS Avg 0 69 NN 0 31 Comment made by admin Example of a comment to call report a Calls Mix Inte
32. 0 5553 0 4142 0 9528 0 4755 0 6362 0 6695 E FIGURE 7 54 cp only displayed 100 Tab Five Interpretation ARMEDXPERT USER S MANUAL The fourth type of frequency calculations is a RMP calculation It is used to perform frequency calculations on a two or three person mixture sample To obtain the RMP page click on the RMP button The Select Pick via mouse window will appear Select the sample you wish to perform the calculations on with your mouse or click on the W arrow and select from the drop down list The RMP page will display All loci and their corresponding alleles are imported into the page On the left half of the screen is each locus with each corresponding allele s with the calculations for each allele by ethnicity On the right half of the screen you can see the calculation of any allele combination If any of the locus has more than alleles then is possible for the number of indicated contributors it will be highlighted yellow to warn you that the number of contributors may be wrong The section on the bottom of the page is where you indicate the number of contributors Use the up and down arrow to alternate from 1 2 and 3 RMP XX72 2 99XX5678 01 2 F2 Vag Swab 06 07 14 D02 bogz 2 99xx5678 0112 F2 Vag Swab 06 07 14 D02 Locus Locus Profile 0851178 Add Comment Remove Locus D21511 29 30 30 2 32 2 dd Combo 29 30 302 322 D75820 8 9 10 12 g 9 1 12 ddCom
33. 10 FALSE 24 6 7 8 67 89 12 13 45 8 9 10 5 89 15 1617 9 101112 11 12 13 67 7 9 10 X Y 7 8 9 17 18 19 2 18 9 10 24 242 6 7 8 6 7 8 9 12 13 4 5 89 10 5 8 9 15 16 17 9 10 11 12 11 12 13 67 7 9 10 X Y 7 8 9 17 18 19 Ladder Identifiler 06 06 20 F03 8 9 10 24 24 2 6 7 8 6 7 8 9 12 13 45 8 9 10 5 8 9 15 16 17 9 10 11 12 11 12 13 67 7 9 10 XY 7 amp 9 17 18 19 1 153 99XX9999Q1 15 12F1 Shirt Vict 06 06 20 028 13 28 9 10 10 11 15 693 11 12 912 1925 14182 1518 11 1417 XY 9 12 XX0156 1 99XX9999Q1 15 2F1 Shirt Vict 06 06 20 001 8 12 13 126 29 30 9 10 10 11 12 15 16 6 9 3 8 11 12 9 12 13 19 20 24 25 13 14 14 2 18 2 15 17 18 19 8 11 14 15 17 XY 9 12 22 22 2 24 XX0156 3 99XX9999Q1 15 2F3 Shirt Vict 06 06 20 E01 12 15 28 29 30 9 10 10 11 12 15 Te 9 3 8 11 12 9 12 13 19 20 24 2 13 14 14 2 15 2 19 17 18 19 amp 11 14 15 X Y 9 12 22 22 2 24 1 aavvaaaan1 151 gE1 Shirt Viet 1 1 12 13 23 2a anl 9 10 lain 11 312 15 16 la Gale 11 12 9 12 12110 20 24 25 13 14 142 127115 17 13 1912 11114 15 171 x v a 12 FIGURE 3 19 Clipped Data Shown 45 Tab One Views ARMEDXPERT USER S MANUAL Organize The Organize section allows you to move a window to the top of all other windows
34. 16 16 0 XX0156 3 99XX9999Q1 15 2F3 Shirt Vict 06 06 20 E01 16 16 0 XX0164 99XX999901 2 LFS Vict 06 06 20 D02 16 16 0 XX0159 1 99XX999901 15 8F1 Shirt Vict 06 06 20 F01 XX0164 99XX9999Q1 2 LFS Vict 06 06 20 D02 XX0156 199XX9999Q1 15 2F1 Shirt Vict 06 06 20 D01 16 16 0 XX0156 3 99XX9999Q1 15 2F3 Shirt Vict 06 06 20 E01 16 16 0 XX0159 1 99XX9999Q1 15 8F1 Shirt Vict 06 06 20 F01 15 15 0 XX0153 99XX999901 15 12F1 Shirt Vict 06 06 20 02 16 16 0 XX0167 99XX9999K1 11 Blood Vict 06 06 20 G02 XX0168 99XX9999K2 Blood Susp 06 06 20 H02 XX0153 99XX999901 15 12F1 Shirt Vict 06 06 20 H02 Comparison Source XX0156 3 99XX9999Q1 15 2F3 Shirt Vict 06 06 20 E01 XX0159 1 99XX9999Q1 15 8F1 Shirt Vict 06 06 20 F01 XX0164 99XX9999Q1 2 LFS Vict 06 06 20 D02 0167 Qax xaaa IM 4 Sheeti XX0156 1 i USEI 99XX9999Q1 15 2F1 156 3 99XX999901 15 2F3 XX0159 1 99XX999901 15 8F1 XX0164 99XX994 lt ill FIGURE 8 9 Samples Comparison Report example Table comparison c3 E 3 1 D891179 D21S11 D7S820 CSFiPO D351358 THO1 D135317 D165539 0291338 195433 vWA TPOX D18551 Am 2 XX0156 1 99XX9999Q1 15 2F1 Shirt Vict 06 06 20 D01 Ladder Identifiler 06 06 20 F03 5 Ladder Identifiler 06 06 20 A03 6 Ladder Identifiler 06 06 20 A01 8 9 10 24 24 2 7 8 6 7 9 12 13 4 5 8 9 10 58 9
35. 2 30 2 30 2 1 30 2 Theta 0 01387226 0 01777886 0 00859452 0 0018352211 0 0053172 0 0050064 0 0019544 0 00033404 0 0130816 0 0211264 0 008672 0 00133376 2pq 2su p p 1 p Theta 2uv 2 8 9 2 9 12 9 9 1 9 Theta 2 9 10 0 04806456 0 04150224 0 0231043916 0 08590136 0 05460796 0 0284351 0 0260046059 0 10173796 0 00939798 0 01833612 0 0027504659 0 02933396 2pr 2 10 12 0 16495574 0 16284 0 19897456 p p 1 p Theta p 1 p Theta 2pq 2st 2tv p p 1 p Theta 15 15 1 15 Theta 17 17 1 17 Theta 2 15 16 2 16 17 2 15 17 16 16 1 16 Theta 0 0625200531 0 0465286476 0 1140369 0 0980634 0 10433268 0 0553713275 Freq Alli FIGURE 7 59 calculations Page 0 042 Je ojo ojojo ojo ojoje Em O N 5 ojojo 00 ul e iuo E Sir wi Sin Oo co to na O o 00 On min HB 9 Ml lt You can automatically add a sample to the Mixture Page Go the bottom of the window either click on the Pick via mouse button and select your reference or click on the W arrow and select the sample from the drop down list of samples This will automatically fill in the allele combinations for that sample and all calculations will be done automatically Pick via mouse Illi Contributors 2 FIGURE 7 60 Bott
36. 4 Match amp Compare Section of the General View options D851179 D21S11 D7S820 _CSF1PO D351358 _THO1 135317 Dit XX1747 99XX5678 K10 Susp 2 Ref 06 08 21 H03 XX1748 99XX5678 K11 Elim Ref 06 08 21 A04 XX72 1 99XX5678 Q1 2 Vag Swab 06 07 14 CO2 XX72 2 99XX5678 Q1 2 F2 Vag Swab 06 07 14 D02 XX74 1 99XX5678 Q1 F1 Gen Swab 06 07 14 A03 XX74 2 99XX5678 Q1 F2 Gen Swab 06 07 14 B03 10 13 10 11 1 18 67 mnr 12 14 29 32 2 wo a 11 101 12 11 13 30 30 2 10 12 XX95 99XX5678 K9 Susp 1 Ref 06 07 14 F07 FIGURE 2 5 Example of Reference at top option view oe re so XX74 1 99305678 Q1 F1 Gen Swab 06 07 14 A03 XX74 2 99XX5678 Q1 F2 Gen Swab 06 07 14 B03 10 11 12 11 13 30302 910 1012 XX95 99XX5678 K9 Susp 1 Ref 06 07 14 F07 FIGURE 2 6 Example of the Reference at the bottom if option is not checked 9 ArmedXpert Menu ARMEDXPERT USER S MANUAL The final section is for plug ins There is a separate guide on how to create a plug in located on our support website http www armedxpert com guides 2012 3 8 how to wtite a plugin export data html The buttons found in this section are used to enter your created plug in into ArmedXpert Plugins Run post import plugins Open Plugins Refresh Directory Plugins FIGURE 2 7 Plugins section First you use the Open Plugins Directory button to
37. 628 686 620 638 670 463 222 02 225 97 229 93 233 9 237 8 241 8 245 73 249 75 D18S51 7 9 10 10 2 11 12 13 13 2 14 14 2 15 16 17 18 2491 1483 1948 1006 1680 2404 1651 778 1128 261 9 270 06 274 16 276 18 278 27 282 4 286 47 19 20 21 22 23 24 25 26 27 731 902 1039 1051 835 762 661 774 1011 1038 288 5 290 62 292 66 294 79 298 97 303 35 307 77 871 934 1091 1147 312 22 316 53 320 8 325 1 329 19 333 33 337 42 341 34 344 99 055818 7 8 9 10 11 12 13 14 15 16 608 658 573 576 568 488 524 433 440 467 133 99 138 11 142 53 147 02 151 4 155 65 159 77 16393 16797 1724 Im FIGURE 8 7 Total Data Report 108 Tab Six Reporting 9 ll NE ARMEDXPERT USER S MANUAL Samples Comparison The Samples Comparison compares one table against another or itself It can compare one table to a profiles table like a staff profile It also can run match and compare reports This report is useful in comparing your staff profile table to a sample table to confirm that there was no contamination This can run the same report that runs automatically if you have Compare tables to profiles types selected below upon opening checked in the Reporting section of the ArmedXpert Options menu In the box marked reference click on the W arrow and a drop down list of all your open sample tables will appear Choose the sample table you would like to compare to
38. 7 9 11 12 11 12 20 14 15 17 18 SD055 312 32 10 12 16 17 7 1113 9 11 2425 14 16 9 10 13 14 x 11 12 20 SD058 28 30 10 11 10 11 17 93 8 11 11 12 17 19 1415 17 18 8 14 20 11 12 21 28 50059 11 16 29 30 10 11 11 12 1617 93 9 13 11 12 1626 12 14 14 17 10 12 20 24 50061 12 14 30 322 8 10 12 14 15 17 93 11 12 12 17 26 12 16 14 17 11 120 23 ie j en eS FIGURE 6 1 0 Match amp Compare Profiles Sample Table based on Find Where Reference is Included D21511 D7S820 5 D351358 THO1 D13S317 D16S539 D251338 D195433 _ vWA__ TPOX D18551 SD096 4522 911 16 u 0 SD110 Kaz j 50127 17 22 91 15 INN 1 ous 50053 p uk 20 0 10 50056 7 9 3 Sa 1618 10 12 16 10 0 10 SD058 see 1 8 1420 1 50060 15 33 1725 1 28 50066 7 9 3 10 0 10 50086 7 9 3 17523 12 16 10 10 M SD087 28 31 aa 11 15 1925 1 1 9 SD094 1820 EN 15 10 2 8 50102 14 16 9 93 1520 le jo 1 9 SD108 1820 5 1 2 8 50118 1416 9 9 3 N 0520 i 5 1 1 9 0121 7 9 aS SSS pe Ed 1 9 50125 ET 1820 1 28 50129 18 9 93 13 18 ANN 10 10 50133 14 16 9 9 3
39. 9 12 13 8 9 10 24 24 2 6 7 8 6 7 8 9 12 13 9 10 11 12 9 10 11 12 vWA TPOX D18551 Amel D55818 FGA 11 12 13 67 7 9 10 XY 7 8 9 17 18 19 20 9 10 11 12 11 12 13 67 7 9 10 xY 7 8 9 17 18 19 20 14 18 2 3 14 14 2 18 2 15 17 18 19 8 11 14 15 17 XY 9 12 22 22 2 24 25 13 14 14 2 182 13 14 14 2 18215 17 18 19 8 11 14 15 17 x Y 9 12 22 22 2 24 25 1314 1417 amp i 12 1213 2226 Eu 12 1925 5 15 16 3 2 19 20 24 2 3 2 14 18 SEEN ES ee MEER NE PEE NR HERR I 15 17 18 19 8 11 14 15 17 X Y 9 12 22 22 2 24 25 1416 amp 11 1618 XY 1 13 1923 TT pum 47 39 19 E 9 11 e E es eee 12 13 28 29 30 9 10 10 11 12 15 16 29 31 10 14 793 1214 12 17 20 pee 12 121 1 1 THO 4 5 4 5 4 5 6 9 3 6 93 6 9 3 6 9 3 EN gn 6 9 3 2 13 14 14 2 18 12 13 15 13 14 2 14 18 2 12 15 10 14 16 18 SS ee Ee Ss 12 15 16 6 9 3 812 12 13 20 24 9 10 6 9 3 1925 12 11 1416 93 12 13 12 13 1822 35 oes 15 19 _ MET 13 30 10 111 1012 1415 893 11 1 12 1923 1415 17 18 pup 11 1 FIGURE 3 3 view Samples amp Controls by Allele All Alleles Samples ze Headings
40. Begin Mixture Single Likelihood Probability RMP User Interpretation Source Ratio of Inclusion Defined Mixture Interpretation Frequency Calculations DEMO 2 Component 4 Vict Mix Stains Analyst txt E Th Pu s y Mixture Interpretation of XX0156 1 99XX999901 15 2F1 Shirt Vict 06 06 20 D01 c amp 0851179 021511 075820 CSFIPO D3s1358 THO1 D13S317 D16s539 _D 12 13 28 29 30 9 10 10 11 12 15 16 6 9 3 8 11 12 9 12 1319 iz13 29 30 10 10 12 15 16 693 812 12 13 13 28 910 1011 15 693 1 12 9 12 Mixture Interpretation DDA Interpretation c Seu a eer ae a fe ee Pick via mouse 040156 1 990 999901 15 2F1 Shirt Vict 06 06 20 D01 Conturi XX0156 1 99XX9999Q1 ET Locus D851173 2 7 Profils 10 12 13 P Avg 0 69 oe PHr 0 30 E Profile 11 13 P Avg 0 31 mPH If E HT 100 Alleles 12 13 iy Ignore alleles mP 0 00 Eu RFUs 1580 2345 BPs 19858 14426 m p Lock locus F on report 1 12 13 100 5 E Apply Ww Globally Apply Stutter Add Profile 0 08 0351358 0139317 D16S539 Mixture Information D851179 D21511 075820 CSF1PO 0351358 0135317 D165539 D He SL es Profile 10 0 81 0 70 0 61 0 66 0 65 0 60 0 70 For a 2 contributor 2 allele mixture of types AA amp AB 2 2 combination s Profile 11 0 19 0 3
41. Black 1 8501E 9 1 85 Billion Hispanic 2 9496E 8 294 Million 1Px 0 2Px 1 Known Sources FBI v lt gt Numerator Reset Knowns jo 2Px 1 set 9 Denominator Reset Unknowns Pick via mouse 28016 38 553333K1 11 Blood Vict 06 06 20 G02 FIGURE 7 48 Bottom of Likelihood Ratio Page To aid in the Likelihood Ratio calculations there are options at the bottom of the screen 1 Px is the number of unknown contributors for the prosecution and in this example is zero 2 Px is the number of unknown contributors for the defense and in this example is one Enter the correct numbers for each and click the Ser button Note The top tow of alleles at each locus 15 the Numerator or Prosecution and the bottom row of alleles at each locus is the Denominator or Defense The calculations change based on the values set You can add a reference contributor to either Numerator prosecution or Denominator defense Choose either Numerator or Denominator by clicking on the circle next to the wanted choice The circle will be filled in as shown below to indicate the chosen one Then either click on the Pick via mouse button and select your reference or click on the VW arrow and select the reference from the drop down list of samples If you have more than one sample to select use the Pick via mouse button hold down the Ctrl button on your keyboard and then select the samples with your mouse once sel
42. For a 2 contributor 2 allele mixture of types AA amp AB 2 2 combination s 12 13 phr 0 64 p 0 98 Ref 1 12 p 0 02 49 0 1 12 13fphr 1 00 p 0 81 Ref 1 13 p 2 0 19 4 3 1 For a 2 contributor 2 allele mixture of types AB amp AB 1 1 combination s 12 13 phr 0 67 Ref 1 12 13 phr 0 67 FIGURE 7 1 9 Three different ways to make calls The first way is to right click the combination you would like to call The Send to Profile 1 and Send to Profile 2 buttons will appear If you are doing a 3 contributor mixture interpretation a Send to Profile 3 button will appear also Right click on the genotype combination in the combination row you would like to call and select the particular profile by clicking the appropriate Send to Profile 1 2 or 3 button Then repeat for the next profile until all profiles have been chosen Once selected the information will be appear in blue as show in the example below Genotype 12 13 is applied to Profile 1 Victim and Genotype 13 13 is in process of being applied to Profile 2Guspect You can also add and view added comments by clicking on the Comment button The comments will also be added to the Mix Interp page of the Call Report see page 89 figure 7 36 for an example of the comment on the Mix Interp page 12 13 phr 0 64 p 0 98 Ref 1 12 p 0 02 49 0 1 12 13 phr 1 00 p 0 81 Victim Ref 1 For a 2 contributor
43. O 0 1219 0 0678 0 0421 sDiv O 0 0322 piv o 0 0480 0 0981 0 0478 0 0854 0 0924 88558 FEAF 8 8 M lt Jii gt FIGURE 8 18 Example of a PHR Report Any locus that does not contain data because there was only one allele at that locus can be hidden from the report to make the report easier to be read To hide a locus click on the locus title multiple loci can be selected by holding down the Ctrl key and clicking on each locus Then hit the F5 button All selected loci will be hidden from the report To redisplay the hidden loci hit the F6 button PHR Report D8s1179 021511 csrieo b3sisss mHor 0195433 TPOX biSssi Amel bSssi8 FGA a RSE average PHR 0 9276 0 9028 0 9070 0 8630 0 8880 0 9247 0 9279 0 7175 0 9351 0 9492 0 9387 std Deviation 0 0568 0 0611 90707 0 0770 0 0906 0 0334 0 0679 0 1269 0 0788 0 0194 0 0136 Mim 0 8652 0 8369 0 8438 0 7841 0 7827 0 9067 0 8093 0 6037 0 7957 0 9246 0 9232 ma 0 9716 0 9629 0 9861 0 9570 0 9667 0 9840 0 9799 0 8561 0 9862 0 9710 0 9592 std Error 0 0254 0 0273 0 0316 0 0344 0 0405 00149 0 0304 90568 0 0352 0 0087 0 0061 a0 ditution 0 9441 D8S1179 CSF1PO D3S1358 D19S433 1 0 dilution ID 8 2 LOng 4 02 0 9806 0 8708 0 9858 09390 0 8943 9535 09350 08860 0 9168 0989
44. allows the third profile to swap to the second position in a three person mixture This enables an elimination profile to move ahead of the suspect profile when applying references see note below Note References are added in order of profiles when using the auto call reference feature in the Mixture Interpretation Window For example the first reference is added to the first profile and the second reference is added to the second profile So make sure you keep this in mind when assigning custom naming Note All profile names can be manually renamed in the Mixture Interpretation Window regardless of these settings 14 ArmedXpert Menu ARMEDXPERT USER S MANUAL The second subsection is the Interpretation Quality Control options This section displays the thresholds used during the check controls It displays the stutter amount used for each Locus These can be changed by each locus Click in the cell you would like to change and type a new amount You can also add a MPH minimum peak height for each Locus separately You can use this feature for one specific Locus or all the Loci Just type in the appropriate MPH in the row for the appropriate Locus Proceed to the next Locus if necessary until you have added all appropriate MPH values If no amount is filled in the MPH the default values will be used Mixture Interpretation Quality Control Frequencies Frequency ptions 4b Interpretation quality control options D21511
45. as shown in Figure 6 13 below Any differences will be highlighted reddish A color key is found at the bottom of page indicating which table 1s which b Note This feature compares samples on one table with samples with the identical names on another table ARDET 5a A lable Reference A 4 B 3ble H ererence Compare Tables Sources FIGURE 60 12 sources Section DEMO 2 Component 4 Vict Mix Stains Analyst txt vs DEMO 2 Component 4 Vict Mix Stains Review txt Mine paisa f p7sszo D Amel D55818 FGA 06 06 20 H02 13 28 910 1011 15 693 1 12 912 1925 14 18 2 1518 11 1417 XY 912 22115 1215 30 1112 11 1416 93 10 1213 1213 18 22 1215 1518 8 13 XY u 20 1215 30 1 12 11 1416 93 10 12 13 1213 1522 12 15 1518 8 13 XY 11 20 3 30 1012 1415 893 11 1 12 1923 1415 17 18 8 15 19 23 30 1012 1415 893 11 1 12 1923 1415 1718 8 15 19 ee SE ee ie HEC XE 3E WECCHE C CIE dECNE GE CNUE C WE 3 13 28 910 1011 15 693 1 12 912 1925 14182 1518 11 1417 XY 912 22225 0 E03 on 06 06 2 8 t 06 06 20 H s No difference s at locus DEM MO 2 Component 4 Vict Mix Stains Analyst txt FIGURE 6 13 Example of a Compare Table Report 74 Tab Four Match amp Comparison ARMEDXPERT
46. change the default settings for the software The default settings can only be set through this window Mixture Interpretation Quality Control Frequencies Frequenc Mixture interpretation settings Default peak height ratio PHr 0 55 Default minimum peak height mPH 30 Default homozygote threshold HT 125 Default minimum proporition mF 0 Default stutter 2 100 FIGURE 2 12 Mixture Interpretation settings 12 ArmedXpert Menu ARMEDXPERT USER S MANUAL The Warn when specified contributors different than mixture setting when activated will give you a warning message anytime the number of contributors used in the mixture interpretation window is different than the number of contributors in the Mixture Interpretation Frequency Window 1 txt e 75 lixture Interpretation DDA interpret Mon e amp Tarne FFE yw 40 7 PF 0851 8 9 10 ee Tere 6 7 6 9 as a one Pickviamouse 290156 1 39559339 1 15 2F1 Shit Vict 06 06 20 D01 z Operations References Highest to 4 Locus D851178 2 foor nja PHI 055 wwe Minor nje Veram mPH50 HT 125 gt Below m PH Q Mixture Interpretation Freque Mixture Information All 5 MPh gt 50 mP gt 0 For a 2 contributor 2 allele mixture of types AA amp AB 2 2 combination s 12 1 3tpht 65 p 0 99 2 o 0 01 12 13 phr 1 00 p 0 81 13 p 0 19 AMP Method
47. errors are found on the check a message will appear at the bottom of the page that states Check completed with no errots as shown below in figure 5 2 Click on the Clear Checks button to clear the check results on the page Description of each standard check and examples of each check results are shown on the next two pages The key for each check 15 shown circled in red in each example 61 Tab Three QC Checks ARMEDXPERT USER S MANUAL XX0166 Reag Blank 06 06 20 F02 167 99XX9999K1 11 Blood Vict 06 06 20 602 12 13 29 30 1010 1012 1516 693 amp 12 12 13 2024 15142 17519 an i amp 15 XX iziz 2224 XX0168 99XX9999K2 Blood Susp 06 06 20 H02 XX0169 QA026 QA 06 06 20 803 12 415 3030 1 12 11 11 1416 93 12 13 12 13 18 22 1215 1518 8 8 13513 XY 1 11 2020 XX0170 Reag Blank 06 06 20 CO3 cemere n Pm XX0171 Pos Con 06 06 20 D03 13 13 3030 10111 10 12 14 15 89 3 1 11 1 12 1923 1415 1718 88 1519 1L 11 2324 XX0172 Neg Con 06 06 20 E03 p pues Check completed with no errors FI GURE 5 2 Example of a Check completed with no errors screen Check Controls evaluates ladders controls and QA profiles to determine if they are within established parameters The ladders controls and QA profiles that are within established parameters are highlighted green The ones that are not are highlighted pink Once you click on the Check Controls
48. feature will update your SQL database to your new upgraded Armed Xpert version The Reset QA feature will reassociate the profile type named QA with quality control checks When you upgrade ArmedXpert it is may be necessary to run the SQL updater Click on Run SQL updater command This will update SQL ArmedXpert Administration x Users Database Run SQL Reset Updater QA Database User Name First Name Last Name DateCreated Role 10 22 2010 1 38 PM 1 FIGURE 2 43 Database Window When you click on the Reset QA button will reset the QA profile This feature should only be used if there is a problem with your QA profile The QA Profile will have to be manually deleted before executing this command and then recommitted afterwards To delete a profile follow the instructions found in the Data chapter of the manual A warning message will appear after you click on the Rest QA button Click button to complete the action Warning Running this command will reassociate the profile type named QA with quality control checks samples should be manually deleted before executing this command and then recommitted afterwards This operation will update your database Continue OK Cancel FIGURE 2 44 Warning Message Window 30 ArmedXpert Menu ARMEDXPERT USER S MANUAL Import The Import command allows you to load a OSIRIS Plot files Click on Import and the l
49. figure 6 2 The pick via mouse option will allow you to select the sample using your mouse Clicking the V arrow will provide a drop down list of all available samples from which you can select the appropriate sample To select more than one sample as references click on the Pick via mouse button and click the Ctrl button on your keyboard Then select samples with your mouse while keeping the Ctrl button pressed down Once all samples have been chosen release the Ctrl button Find Where Find Included in Find Foreign Find Where Referei Reference is Included the Reference toReference X Includes j FIGURE 6 2 Set Reference Button 69 Tab Four Match amp Comparison ARMEDXPERT USER S MANUAL Once you are finished selecting your reference s click on the sample table that you would like to match and compare This does not have to be the same sample table as the selected reference s Then click on one the four compare buttons Find Where Reference is Included Find Included in the Reference Find Foreign to Reference or Find Where References Includes Foreign To clear the match from the page click the Clear Match button This also clears the reference from the page Note If your reference is on a separate page from your sample table you are comparing you have click on the Clear Match button for each page The Clear Match button on clears a match for the front page e Clear B ies Match FIGURE 6 3 Clear Match button All
50. first column The second column list all matched comparison samples The third column is the total number of matches The fourth column lists the number of exact matches equal to or greater than the user defined amount The final column lists the number of included matches The reference sample vs the comparison sample is shown first on the report If you compare the reference sample against a profile or profiles they will be shown next Any additional match and compare reports will be displayed on the additional worksheets shown at the bottom of the report Click on a tab to display each You can also click on any sample that it blue on the report and it will take you directly to the match and compare tab that includes that sample LIAE Reference Sample Comparison Sample Total No No Exact Matches gt 6 No Included Comparison Source DEMO I 2 Component 4 Vict Mix Stains Review txt XX0156 1 99XX999901 15 2F1 Shirt Vict 06 06 20 D01 XX0156 3 99XX9999Q1 15 2F3 Shirt Vict 06 06 20 E01 16 16 0 159 1 99XX9999Q1 15 8F1 Shirt Vict O6 06 20 F01 15 15 XX0164 99XX9999Q1 2 LFS Vict 06 06 20 D02 16 16 XX0156 3 99XX9999Q1 15 2F3 Shirt Vict 06 06 20 E01 156 1 99XX9999Q1 15 2F1 Shirt Vict 06 06 20 D01 16 16 XX0159 199XX9999Q1 15 8FlShirt Vict O6 06 20 F01 15 15 XX0164 99XX9999Q1 2 LFS Vict 06 06 20 D02 16 16 XX0156 199XX9999Q1 15 2F1 Shirt Vict 06 06 20 D01
51. for CODIS Administrator Case Category 8 E EVIDENCE PROFILE for the FORENSIC INDEX This profile is from crime scene evidence is attributable to a putative perpetrator and is not from an item owned used by the suspect fhe source of the EVIDENCE PROFLE forthe FORENSICINDEKasbecnidentifed fhe source of the EVIDENCE PROFUE forthe FORENSICINDEX unknown Correct results were obtained for all controls F FIGURE 8 3 Top Portion of the CODIS Disposition Form Window Four different samples can be added to the report Evidence Victim Suspect and Elim Suspect2 this can be changed to either type by clicking the arrow next to Elim and choosing from the drop down list To add a type first click on the circle next to the type you would like to add This will fill in the circle The select pick via mouse window is next to the type selections You can use your mouse to select the sample you wish to choose or click on the W arrow and select the one you would like to add from the drop down list This will fill in the information from the sample table Continue with the next type until you finished adding all the necessaty types The Loci Alleles and RFU s will appear for each selected type Note The different types of samples fill in the report in the order you add them Therefore if
52. load your plugin This will open your Plugin Directory as shown below Copy the Plugin in the correct folder For example if the plugin were a report plugin you would copy it in the reports folder Once the plugin has been copied to the correct folder click on the Refresh Plugins button This will activate the plugin in ArmedXpert f plugins eI File Edit View Favorites Tools Help ae l t Baci cA 3 25 Search gs Folders Gi Folder Sync Address C Documents and Settings All Users Application DatalNicheVision Forensics4rmedXpert plugins Go Name Size Type Date Modified File Version tm File and Folder Tasks events File Folder 12 11 2012 11 19 il 712013 10 53 C Make anew folder export File Folder 3 71201 3 AM import File Folder 3 7 2013 10 54 4M this Folder to the kits File Folder 3 7 2013 10 55 AM E Share this Folder lib File Folder 10 10 2012 3 45 PM reports File Folder 3 7 2013 10 55 bootstrap py 2KB File 11 13 2012 12 50 PM Other Places plugin_log txt SKB Text Document 3 7 2013 11 00 4M spreadsheet_helper py 4KB PY File 11 13 2012 12 50 PM c Armedxpert xdac py 2 PY File 10 10 2012 1 32 PM E My Documents i Shared Documents xj My Computer My Network Places Details plugins File Folder gt FIGURE 2 8 Plugins Directory 10 ArmedXpert Menu ARMEDXPERT USER S MANUAL The second main section is Data This section a
53. perform After clicking each command the check will be performed and your page will display the results of the check All errors will be highlighted A key will be displayed on the page to explain what the highlighted colors mean for the check being done If no errors are found on the check a message will appear at the bottom of the page that states Check completed with no errors as shown below in example 5 8 Click on the Clear Checks button after each check to clear the check results on the page Views Data QC Checks Match amp Comparison Interpretation Reporting a UY Check Check Allele Stutter RFUs CODIS Allele te OSD PHR Check Controls Ordering Alleles Count multi _ Standard Checks 01 Identifiler Kit Standard 10 10 04 01_ Mixture MFO Neat 10 10 04 Mix Mixture M_F_1_1 10 10 04 Mix Mixture M 1 10 10 10 04 2 Mix Mixture M F 1 100 10 10 04 2 Mix Mixture MF1 4 10 10 04 Mix Mixture M 10 1 10 10 04 2 Mix vue em eens m Mixture M F 100 1 10 10 04 2 Mix 0 11 13 14 29 30 8 9 10 12 9 10 11 12 16 17 8 9 9 3 11 12 11 12 17 18 20 26 12 14 2 15 16 17 18 19 8 8 1 18 XY 1091114 29 30 910 91011 16 17 8 9 9 3 10 14 12 1 12 17 18 20 12 142 15 16 1819 88 1418 XY Mixture M F 4 1 10 10 04Mix 10 11 14 29 30 8 9 10 12 9 10 11 1617 55 93 1 12 1 12 17 18 20 26 12 142 15 16 17 18 19 88 1 1
54. sep sen Wo ECT NE O Check Check Allele Stutter RFUs CODIS Allele Check OSD PHR Check Begin Clear Controls Ordering Alleles Count x multi Review Checks Standard Checks CODIS QC QCReview Clear DEMO 2 Component 4 Vict Mix Stains Analyst txt estapo pas1a58 Toi 10138817 0168539 _ 0251938 d 195433 v wc Hex one 51855 Nd 5 ee RN 9 10 EFEEIITIOETERUARCI l mar lae T anle sn 2z 064 p 1213 128 3 11 12 1516 6 938 xv 9 12 222 9 mus 12 13 28 1215 9 10 9 10 9 10 15 16 16 93 15 16 6 9 3 t 15 16 6 93 per Y EX 12 xy 9 12 22 xy 9 12 22 JP m e Ee 10 10 10 12 ese lesa an um ms nio ms fenf mis opus ns Russ osos 9 10 10 11 1515 693 1 12 9 12 1925 14182 1518 j 1L 11 1417 XY 9 12 22225 FIGURE 5 11 Allele Count Result Example 65 Tab Three QC Checks ARMEDXPERT USER S MANUAL The Check X command checks for samples that only have a single X displayed at amelogenin It will highlight in pink a sample s locus that contains a single X Tem Views Data QC Checks Match amp Comparison Interpretation Reporting amp ly RE OEFUWES Check Check Allele Stutter RFUs CODIS Allele Check OSD PHR Check Begin Clear Controls Ordering Aleles Count X multi Review aks Standard Checks CODIS QC j QCF Review
55. the right hand bottom of the CMF window will appear Several of the attributes have drop down lists Click on the arrow next to those and make the appropriate choice All other boxes can be filled in directly Note If you would like to add additional packet attributes go to the ArmedXpert options window to make any additions or edits to the attributes The instructions on how to make additions or edits can be found in Chapter 2 of this manual 111 Tab Six Reporting ARMEDXPERT USER S MANUAL If you scroll down through the Packet Attributes you will see all of the loci and the allele s at each locus All checked loci are included If a Locus contains a Partial add a checkmark to box located under the Partial column next to the appropriate Locus Proceed to the next sample until finished with all Samples If the attributes are the same for all selected samples click on the Copy to All button after you complete the attributes for the first selected sample All attributes will be copied to all other selected samples X CMF ca 5 Samples amp sources Selected samples amp sources NV 3 Component 51 E and 52 ox 4 2 9905678 Q1 F2 Gen Swab 06 07 14 B03 74 1 9925678 Q1 F1 Gen Swab 06 07 14 403 2874 1 9925678 Q1 F1 Gen Swab 06 07 14 403 AX74 2 9905678 Q1 F2 Gen Swab 06 07 14 B03 2081748 995678 K11 Elim Ref 06 08 21 404 872 1 9925678 Q1 2 F1 Yag Swab 06 07 14 C02 95 9925679 KI Susp 1 Ref 06 07 14 F07 AX 2 2 99567
56. to 1 as shown below In the Profile Type box add a checkmatk to all the profile types you would like the tables to be compared against To disable this reporting option click on the box with the check mark and it will be removed Next to the Profile Type box are three options that can be used to customize what appears on your report If the Only compare other samples option is checked the profile will not be compared against controls and ladders The List unmatched samples option will list all samples whether they are a match or not If not checked only matched samples will appear on the report The Create match compare report option will show the actual match and compare reports per sample on separate tabs on your report if checked ArmedXpert Options c3 5 General Reporting Options CODIS CMF Attributes Data Interpretation Reporting options Quality Control Compare tables to profile types selected below upon opening Hieporting Min no total matches 5 4 Values are inclusive Use 1 Min no exact matches to match any amount Admin Console Min no included matches Only compare other samples Profile Type List unmatched samples Staff SRM Create match compare reports C Unknown QC Ok Cancel FIGURE 2 35 Reporting Options window 25 ArmedXpert Menu ARMEDXPERT USER S MANUAL Old Profi ID o s 0851179 02151 079820 CSF1PO D351358 THO1 0
57. you wish to remove a sample table or sample from the Selected samples amp sources box click on the sample table or sample and then click on the lt button By default the names of all selected samples will automatically fill in as the title of the combined report You can keep the default title or you can type in a new name for the combined report that is being created Click the Combine button to create the combined report Combine Sources c3 s Select items to combine Samples amp sources Selected samples amp sources H DEMO 2 Component 4 Vict Mix Stains Analyst twt 220156 1 3355838331 15 2F1 Shirt Vict 06 06 20 D01 DEMO I 2 Component 4 Vict Mix Stains Review tt 220159 1 994 lt 999901 15 8F1 Shirt Vict 06 06 20 F01 Ladder Identifiler 06 06 20 F03 2 lt 0156 3 9999990 1 15 2F3 Shirt Vict 06 06 20 E01 Ladder Identifiler 06 06 20 403 Ladder Identifiler 06 06 20 401 gt 1 99 lt 999901 15 2F1 Shirt Vict 06 06 20 220156 3 9999990 1 15 2F3 Shirt Vict 06 06 20 E gt gt 220159 1 3855533331 15 8F1 Shirt Vict 06 06 20 F 220161 1 GA003F1 06 06 20 H01 2 1 Reag BlankF1 06 06 20 602 0162 2 Reag BlankF2 06 06 20 C02 280164 994999901 2 LFS Vict 06 06 20 D02 20165 QADO4 QA 06 06 20 E02 20166 Reag Blank 06 06 20 F02 20167 99 lt 9999K1 11 Blood Vict 06 06 20 G02 20168 99 X9999K2 Blood Susp 06 06 20 H02 280169 04026 QA 06 06 20 B03 20170 Reag Blank 06 05 20 C03 S liil gt aig
58. 0 039 034 035 040 0 30 12 13 phr 0 63 p 0 97 Ref 1 12 p 0 03 12 13 phr 1 00 p 0 81 Profile 10 Ref 1 13 p 0 19 Profile 11 For a 2 contributor 2 allele mixture of types AB amp AB 1 1 combination s 12 13 phr 0 67 Ref 1 12 13 phr 0 67 Profile10 0 69 Profile 11 COFTUETUS ER OCT UT ER 07 99 wo a A FIGURE 7 30 cai report Example Mixture Interpretation of XX0156 1 99XX999901 15 2F1 Shirt Vict 06 06 20 D01 s ce ossiiz9 021511 D7s820 csrieo 0391358 0135317 0169539 251338 195433 vwa rPox 018951 Amel D5S818 s 12 13 28 29 30 9 10 10 11 12 15 16 6 9 3 8 11 12 9 12 13 19 20 24 25 13 14 142 18 2 15 17 18 19 8 11 14 15 17 XY 9 12 22 22 2 24 25 12 13 29 30 10 10 12 15 16 6 93 8 12 12 13 20 24 13 1142 1719 811 1415 X 12 2224 13 28 910 1011 15 69 3 11 12 912 1925 14182 1518 11 1417 XY 912 22225 L 4 35 9 3 32 9 1392 31512 saua 17 9 22225 XX0156 1 99XX9999Q1 15 2F1 Shirt Vict 06 06 20 D01 J M B M NM m profile10 8B m m Profile 11 eo eo co e e 5 e 5 E D 9 8 i 9 m N T a a a a a 0851179 D21511 075820 CSF1PO 0351358 D135317 D165539 D251338 D195433 _TPOX D18551 Amel 55818 FGA Profile 10 0 81 0 70 0 61 0 66 0 65 0 60 0 70 0
59. 0 0529 0 0441 0 0189 0 0631 0 0528 0 0403 0 0394 ID D 3 0 25ng 7 DO3 0 6719 _0 9185 0 5904 0 9539 08543 _0 9382 _0 8536 05661 0 8384 0 9604 0 9639 0 7260 0 8461 0 9295 0 9154 0 7885 0 6404 0 8671 0 8119 0 7817 Std Deviation 0 1533 0 0805 0 2111 0 1174 0 0730 0 0558 0 0832 0 1699 0 0827 0 1478 0 1601 Mim 0 6719 0 7668 0 5904 0 7211 0 8543 0 8519 0 6947 0 5204 0 8025 0 6647 0 6633 Max 0 9716 0 9185 0 9693 0 9539 1 0000 0 9561 0 8536 0 8348 0 9604 0 9604 0 9639 StdError 00885 O 0465 0 1219 0 0678 0 0421 0 0322 0 0480 0 0981 0 0478 0 0854 0 0924 FIGURE 8 20 Example of the left hand side of the PHR Report A graph appears to the right of the loci that displays the average PHR for each locus by Dilution table PHR Average 1 5 Dilution 1 2000 1 0000 0 8000 0 6000 0 4000 0 2000 0 0000 D8S1179 D21S11 CSF1PO D3S1358 THO1 D19S433 TPOX D18S51 Amel D5S818 FGA PHR Average 1 0 dilution D8S1179 D3S1358 D19S433 PHR Average 25 Dilution 021911 CSF1PO 0351358 0195433 D18S51 Amel D5S818 FGA eo uo co a FIGURE 8 21 Example of the right hand side of the PHR Report 117 Tab Six Reporting ARMEDXPERT USER S MANUAL TemplateReport The Template Report allows you to create your own customized template r
60. 0 Combined Sample table Example 53 Tab Two Data ARMEDXPERT USER S MANUAL Data Source The four commands in the Data Source Section are Commit Samples to Data Source Load Samples From Data Source Connect Server and Disconnect Server The Commit Samples to Data Source allows you to save commit a sample to your database and the Load Samples to Data Source allows you to retrieve it One example of a use for this is to commit your staff profiles to the Database so they can be retrieved for use later to comparte against Any sample can be saved or committed to your database Connect and Disconnect Server commands allow you to connect or disconnect to the server 9 88 Commit Samples Load Samples Connect Disconnect to Data Source From Data Source Server Server Data Source FIGURE 4 11 Data Source Section To commit a sample or a table as a table to the ArmedXpert Database click on the sample table so it is open and active on the screen One example of this is to commit a ladder and controls check table to the Datasource so that you can use it to check controls Click on the Commit Samples to Data Source button The Datasource Commit window will appear Click on the next to the Sample Table and all the samples on the sample table will appear on the left hand side of the window Click on the sample or table you wish to commit click the gt button and the sample or table will be move to the box on the right Repeat this for as
61. 001 Undock FJ ol x ot Remove Group Bring To Front w Group 2 2 DEMO 2 Component Vict and 5 Susps D3 Extra Allele bt Undock J Add Group FIGURE 3 23 Organize Window with Groups 47 Tab One Views ARMEDXPERT USER S MANUAL 48 Tab One Views ARMEDXPERT USER S MANUAL Tab Two Data samples and sort samples It is also where you can connect or disconnect to a server There are three main sections Samples Data Source and Sort T he Data tab is used add new samples edit samples combine samples commit samples load New 4 LU Combine Commit Samples Load Samples Connect Disconnect Sort Sort Sample Sample Sources to Data Source From Data Source Server Server Samples Samples Data Source Sort FIGURE 4 1 Data Tab Samples There are four commands in the Samples Section New Sample Edit Sample Change Kit and Combine Sources The New Sample option allows you to enter manually a new sample onto your current sample table ot to a new table The Edit Sample option allows you to edit any sample on your sample table The Change Kit option allows you to change the kit that is shown for the sample Finally the Combine Sources option allows you to combine specific samples or entire tables into one new sample table Tp pape pay New Edit Change Combine Sample Sample Sources
62. 0060 11 13 28 30 11 1617 9 11 11 13 1725 14 15 17 11 12 19 21 4 4 0074 10 13 29 30 11 15 18 12 1114 18 21 12 13 16 15 10 11 19 22 4 a soosa 9 11 30312 12 12 12 11 12 18 20 14 14 18 15 12 13 24 25 4 4 5108 9 11 30312 12 12 12 11 12 18 20 14 14 18 15 12 13 24 25 4 4 50125 9 11 30 312 12 12 12 11 12 1820 14 1418 15 NN 12 13 24 25 4 4 0069 29 30 9 11011 15 17 12 1011 17 18 14 15 11 19 12 13 X 9 11 20 25 3 3 5008 9 14 291 333 1114 14 910 10 12 10 13 1617 8 1517 13 20 11 13 19 23 3 3 SD087 14 28 31 1012 14 6 8 amp 9 11 12 1925 12 13 18 19 14 15 11 13 29 23 3 3 SD090 14 16 29 30 11 12 13 12 14 22 13 20 24 3 3 spo 14 322 16 11 12 25 3 3 5099 10 12 28 32 2 10 11 20 24 3 3 5D103 12316 X 12 13 23 2 24 3 3 SD106 13 x 11 12 20 21 3 3 50110 16 32 12 25 3 3 50115 14 19 ROI 10 11 20 24 3 3 50127 16 12 25 3 3 50130 14 19 10 11 20 24 3 3 50045 13 14 12 13 20 25 2 2 50047 15 x 12 23 19 22 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 D053 11 13 29 30 10 11 10 11 171 93 8 9 13 20 25 13 14 15 16 11 121 14 15 11 12 19 20 0054 11 28 332 11 1012 15
63. 09 0 1083 0 2222 0 10923025 0 1207 0 3251 0 19873764 D21511 28 29 30 PO 928 29 30 P1 p 28 29 30 0 1658 0 335241 0 2151 0 1899 0 1788 0 34082244 0 069 0 2044 0 3301 0 36421225 D75820 ER ia ES 230754 9 10 1 5 9 19 0 1478 0 2906 0 19219456 0 1571 0 3238 0 23126481 0 0479 0 3062 0 12538681 CSF1PO 10 11 12 ES ae P0 9 10 11 12 P1 g 10 11 12 0 2537 03005 0 3251 0 77316849 0 2714 0 2048 0 60248644 0 2536 0 3923 0 83083225 0351358 15 16 32s 16 15 16 PO p 15 16 P1 p 15 16 0 2463 0 2315 0 22829284 0 2905 0 3071 0 35712576 0 4258 0 2656 0 47803396 lt il 1Px 0 2Px 11 Set Numerator ResetKnowns Pick via mouse Denominator Reset Unknowns FIGURE 7 47 Likelihood Ratio Page 96 Tab Five Interpretation ARMEDXPERT USER S MANUAL a Likelihood Ratio XX0156 1 99XX999901 15 2F1 Shirt Vict 06 06 20 D01 om XX0156 1 99XX9999Q1 15 2F1 Shirt Vict 06 06 20 D01 ZI Locus Allele 1 a Allele 2 b Allele 3 c Allele 4 d Likelihood 0 0308 0 3539 0 14799409 0 0139 0 3556 0 13653025 0 0542 0 2906 0 11888704 FGA 22 22 2 24 25 22 222 24 3 i 3 azz 4 35 PO g 22 22 2 24 25 P1 22 22 2 24 25 0 1888 0 0128 0 1378 0 0689 600 0 16670889 0 225 0 0139 0 1861 0 275625 0 1773 0 0123 0 1256 0 1379 0 20529961 i 1 Caucasian 3 9534E47 39 5 Million
64. 1314 1417 amp 1 12 3 1 2 0 XX0162 1 Reag BlankF1 06 06 20 B02 TEST e SS S RES ERR ERES ERR ERES ERR ee XX0162 2 Reag BlankF2 06 06 20 C02 Eee E iussum XX0164 99XX9999Q1 2 LFS Vict 06 06 20 D02 4 4 0 0 XX0165 QA004 QA 06 06 20 E02 9 12 910 14 7 93 12 14 2 2 0 0 XX0166 Reag Blank 06 06 20 F02 ERE eee ae CE ERR eas eee RN REESE Fc EE REEL XX0167 99XX9999K1 11 Blood Vict 06 06 20 G02 2224 3 1 3 0 16 16 0 0 XX0169 QA026 QA 06 06 20 03 11 12 14 16 93 12 13 12 13 1822 1215 5 13 NE 239 3 2 1 0 XX0170 Reag Blank 06 06 20 C03 TS e ERR Em PRA RN c XX0171 Pos Con 06 06 20 D03 10 111 10 12 14 15 8 9 3 15 12 139 3 1415 1718 8 1519 11 22324 2 1 1 0 XX0172 Neg Con 06 06 20 03 ege ape p p 1 0 1 0 FIGURE 6 6 Find Included in the Reference Example Find Foreign to Reference is used to find loci that contain allele s that do not match the reference All loci that contain allele s that do match the reference are highlighted red X Y Ladder Identifiler 06 06 20 A01 0 0 0 15 Ladder Identifiler 06 06 20 A03 0 0 0 15 Ladder Identifiler 06 06 20 F03 ERA 0 0 0 15 XX0153 99XX9999Q1 15 12F1 Shirt Vict 06 06 20 H02 9 10 10 11 15 69 11 12 9 12 1925 14182 15 18 11 14 17 XY 9121 22225 9 10 6 9 3 XY 9 12 0 0 0 12 0 0 0 12 0 0 0 12 0 0 0 13 0 0 0 1 0 0 0 12 0 0 0 14 0 0 0 12 0 0 0 1
65. 135317 D165539 D251338 D195433 TPOX 018551 Ladde Le ain tleveon lezo 1113 lac l o a 4n soo lac 46 la 1n 44 11 3 3 9 10 X Y 7 8 9 17 18 Table comparison 9 10 17 18 Old Profi IDvs QA Comparison Sample Total No gt 12 No Exact Matches No Included 9 10 17 18 Comparison Source QA 3 19 INE 1 faz 11 23 24 17 18 X Y 11 12 22 23 24 i 4 15 12 13 22 26 No matches above the specified thresholds were found for 6 sample s in 4 15 12 13 23 26 01 L Table comparison zz Old Profi ID vs Staff Comparison Sample Total No gt 12 No Exact Matches No Included Comparison Source Staff 0985 1 Item 3 swab of Victim Epi 09 11 25 D01 M gt MhSheeti 098S 1Ttem3swabofVitim dR FIGURE 2 36 Sample of the reports that will open when you load a Sample table based on options chosen The second subsection CODIS allows you to add defaults to the CMF Report in ArmedXpert All data filled in here will be displayed with you open the CMF report In the top portion enter in the default information for your Lab ArmedXpert Options o s 2s General Reporting Options CODIS CMF Attributes Data Common Messaging Format CMF Default CMF Attributes Source Lab 123456
66. 171 Pos Con 06 06 20 D03 ee 0172 Neg Con 06 06 20 E03 0162 1 Reag BlankF1 06 06 20 B02 0170 Reag Blank 06 06 20 C03 940166 Reag Blank 06 06 20 F02 FIGURE 4 22 sort Samples Window 60 Tab Two Data ARMEDXPERT USER S MANUAL Tab Three QC Checks he QC Checks tab is used to do quality control checks on your data There are four sections under the QC Checks They are Standard Checks CODIS QC QC Review and Clear The quality control settings for the checks are set up using the ArmedXpert Options Menu discussed in Chapter 2 gt p pm views Data QCChecks Match amp Comparison Interpretation Reporting amp g AUT Ev a 0 Check Check Allele Stutter RFUs CODIS Allele Check OSD PHR Check Begin Clear Controls Ordering Alleles Count x multi Review Checks Standard Checks CODIS QC QCReview Clear FIGURE 5 1 QC Checks Tab Standard Checks There are four types of standard quality control checks They are Check Controls Check Allele Ordering Stutter and RFUs The standard checks will evaluate the samples on your active sample table for quality control issues Click on each type of standard check you wish to perform After clicking each command the check will be performed and your page will display the results of the check All errors will be highlighted A key will be displayed on the page to explain what the highlighted colors mean for the check being done If no
67. 2 22 22 2 24 25 12 13 28 29 30 9 10 10 11 12 15 16 6 9 3 8 11 1219 12 13 19 20 24 25 13 14 142 182 15 17 18 19 8 11 14 15 17 XY 9 12 22 22 2 24 25 28 29 30 9 10 10 11 12 15 16 6 9 3 8 11 12 9 12 13 19 20 24 25 13 14 14 2 182 15 17 18 19 8 11 14 15 17 XY 9 12 22 22 2 24 25 42 13 2930 10 1012 15 16 693 812 1213 2024 15142 1719 amp 11 1415 X 12 2224 13 28 910 1011 15 693 1 12 9 12 1925 14182 1518 11 14 17 XY 912 22225 D1 A D851179 021511 D75820 CSFIPO D351358 THO2 D135317 0165539 FIGURE 3 5 View All Samples by Allele 40 Tab One Views ARMEDXPERT USER S MANUAL gt Alleles Samples R pa Headings gt Controls Base Pairs All 3 Indicate clipped data I Be Zoom 100 Organize _ Samples RFUs User E View JL RS em Show Hide Windows DEMO 2 Component 4 Vict Mix Stains Analyst txt D851179 Dais D75820 CSFIPO D351358 Thon D135317 D165539 123 04 127 11 131 15 184 64 186 68 188 64 192 56 255 16 259 14 263 2 304 72 309 04 313 3 11161 16604 216 68 22069 25226 2642 26828 309 26 123 04 127 14 131 22 184 66 186 65 188 64 192 53 255 15 259 21 263 29 30475 30909 11164 16308 2167522067 2523426431 30736 123 13 127 23 131
68. 2 15 3801 0 9692 0 9595 0 9817 0 9204 09667 0910 09452 0 8561 0 9530 09590 0 9353 60 ID A 3 L5ng 5 CO3 0 8656 0 8422 08567 07841 0 797235 0 9799 0 6117 0 9690 0 9333 09592 9 4909 0 9492 0 2000 Std Deviation 0 0568 0 0611 sDIV O 0 0707 0 0770 0 0906 sDIV O 0 0334 0 0679 0 1269 0 0788 0 0194 0 0136 0 0000 Min 0 8652 0 8369 0 0000 0 8438 0 7841 0 7827 0 0000 0 0000 0 0000 0 9067 0 0000 0 8093 0 6037 0 7957 0 9246 0 9232 goSztoS2ZzXzz Max 0 9716 0 9629 0 0000 0 9861 0 9570 0 9667 0 0000 0 0000 0 0000 0 9840 0 0000 0 9799 0 8561 0 9862 0 9710 0 9592 raS E gg SERRE Stdtror 0 0254 0 0273 piv o 0 0316 0 0344 0 0405 Div o 0 0149 sDIV O 0 0304 0 0568 0 0352 0 0087 0 0061 28688 F AS 6 PHR Average 1 0 dilution 1D_B 1_1 0ng 5 COl 09441 0 6411 08333 09191 0 9722 oss 09924 0 7603 07393 0 9373 _ 0 7186 1D_B 3_1 0ng 1 A03 0 9607 0 9160 0 8447 0912 07898 19 09363 09781 07893 0 8511 07123 Std Deviation 0 0183 0 1474 piv o 0 0849 0 0143 0 0915 0 0764 Div o 0 0328 0 1093 0 0915 0 0699 0 0682 Mim 0 944 0 6411 0 0000 0 8333 0 9112 0 78
69. 2 allele mixture of types AB amp AB 1 1 endo Xem 12 13 phr 0 67 Ref 1 12 13 phr 0 67 Send to Suspect zip 0 19 14 3 11 Comment FIGURE 7 20 Calls made from Mixture Information Section 84 Tab Five Interpretation ARMEDXPERT USER S MANUAL The second way is to manually select alleles in the middle section of the Mixture Interpretation Window Click on the Profile you would like to make a call for and then click on the boxes under the allele s you would like to select A check mark will appear in the boxes selected If you would like to make one of the alleles as an Any ot an Obligate right click on the checkmark box and a drop down list will appear You can also use this feature to remove or ignore an allele Select the appropriate option As shown in Figure 7 23 the word Any will appear right of the chosen allele if any is selected and a will appear right of the chosen allele if an obligate is selected id qd 1580 2345 Victim e FIGURE 7 21 Calls made from Middle Section 12213 1580 2345 12 Any Obligate 2 q r Ignore Allele Remove Allele 1111 Pat Sc FIGURE 7 22 Calls made from Middle Section 12 13 12 13 1580 231345 4590 12345 FIGURE 7 23 Examples of an 12 Any called and a 12 Obligate Called The final way is to click on the Popout calls button A window will appear as s
70. 232 77 268 29 280 46 284 46 324 57 328 68 344 13 347 63 117 38 1 139 62 144 22 200 35 204 34 208 26 267 42 271 46 322 01 326 15 330 24 123 85 127 89 171 17 186 2 216 86 228 77 232 77 268 31 280 48 284 48 324 52 328 62 344 13 347 63 117 39 139 55 144 17 200 36 204 36 208 3 267 4 271 45 321 97 326 1 330 18 1123 82 127 89 171 17 186 21 216 79 228 75 232 75 268 3 280 4 284 48 324 47 328 57 344 13 347 63 117 38 139 54 144 22 204 3 20826 2715 3220533025 12377 12783 171 23 186 21 216 83 232 79 280 5 284 51 32863 3441 14423 200 4 267 51 271 56 322 09 326 18 12386 171 23 186 25 228 78 232 85 268 42 280 55 324 58 347 65 H02 14423 200 4 267 51 271 56 322 09 326 18 123 86 171 23 186 25 228 78 232 85 268 42 280 55 324 58 347 65 Clear Selectic FIGURE 3 8 view Samples by Base Pair 41 Tab One Views ARMEDXPERT USER S MANUAL e All Alleles Samples M Headings Sen le le Xu 3 _ Controls Base Pairs All Indicate clipped data E IPS Zoom 10095 Organize _ Samples RFUs User View Fit Zoom Show Hide Windows DEMO 2 Component 4 Vict Mix Stains Analyst txt c adder Identifiler 06 06 20 A01 1818 3132 2384 1574 1274 1999 776 688 859 818 949 773 695 860 993 954 1253 1380 9
71. 3 0 180 67 188 64 192 61 255 35 259 4 263 46 305 309 33 313 68 11175 163 09 167 2 216 83 22082 2524626445 30755 324 47 328 268 29 280 46 284 46 324 57 328 324 52 328 139 62 144 22 200 35 204 34 208 26 144 22 148 69 204 27 210 18 271 52 275 53 32209 123 85 127 77 171 23 228 78 232 78 276 42 280 45 311 139 55 144 17 200 36 204 36 208 3 267 4 271 45 321 97 326 1 330 18 123 82 127 89 171 17 186 21 216 79 228 75 232 75 268 3 280 4 284 48 324 47 328 148 58 200 36 212 22 267 37 271 47 317 79 321 95 119 78 175 18 175 18 232 67 236 76 268 33 276 41 316 Ail FIGURE 3 6 view All Samples amp Controls by Base Pair O Al Alleles Samples R F Headings 5 2 Controls Base Pairs OAI Ar Indicate clipped data a Zoom 100 Organize L Samples _ RFUs User View Ft Zoom Showde Windows DEMO 2 Component 4 Vict Mix Stains Analyst txt 5 2s D851179 Dasi 7 D75820 CSFiPO D3s1358 THO Di35317 Di65539 D2 123 04 127 11 131 15 184 64 186 68 188 64 192 56 255 16 259 14 263 2 304 72 309 04 313 3 111 61 216 68 220 69 252 26 264 2 268 28 309 26 31 123 04 127 14 131 22 184 66 186 65 188 64 192 53 255 15 259 21 263 29 304 75 309 09 111 64 163 08 216 75 220 67 252 34 264 31 307 36 31
72. 3 0 0 0 13 FIGURE 6 7 Find Foreign to Reference Example 71 Tab Four Match amp Comparison ARMEDXPERT USER S MANUAL Find Where Reference Includes Foreign is used to find loci that do not contain the reference All loci that do not contain the reference are highlighted red 075820 csriPO 3s1358 THO1 D13S317 D16s539 0251338 _p19s433_ vwA__ TPOx D18ss1 Amei psse18 Fea Ladder Identifiler 06 06 20 A01 6 7 8 67 89 12 13 45 8 9 10 5 8 9 15 1617 0 0 0 2 Ladder Identifiler 06 06 20 A03 0 0 0 2 i 6 7 8 6 7 8 9 12 13 4 5 8 9 10 5 8 9 15 16 17 0 0 0 2 XX0153 99XX9999Q1 15 12F1 Shirt Vict 06 06 20 02 XX0156 1 99XX9999Q1 15 2F1 Shirt Vict 06 06 20 D01 XX0156 3 99XX9999Q1 15 2F3 Shirt Vict 06 06 20 E01 XX0159 1 99XX9999Q1 15 8F1 Shirt Vict 06 06 20 FO1 Y XX0161 1 QA003F1 06 06 20 H01 8 11 0 0 0 12 XX0162 1 Reag BlankF1 06 06 20 B02 0 0 0 XX0162 2 Reag BlankF2 06 06 20 C02 XX0164 99XX9999Q1 2 LFS Vict 06 06 20 D02 XX0165 QA004 QA 06 06 20 E02 Ix Y 0 0 0 13 XX0166 Reag Blank 06 06 20 F02 XX0167 99XX9999K1 11 Blood Vict 06 06 20 G02 9 0 0 0 12 XX0169 QA026 QA 06 06 20 803 1518 0 0 0 14 0 0 0 13 XX0172 Neg Con 06 06 20 E03 a as 0 0 0 FIGURE 6 8 Find Where Reference Includes Foreign Example The Match amp Compare Profiles button compares profiles in your database against a sample on an open sample table To use this feature click on the
73. 309 04 313 3 317 6 321 78 325 91 329 99 1448 334 04 338 05 341 83 D351358 12 13 14 15 16 17 18 19 622 560 592 1278 1177 617 542 490 111 61 115 75 119 66 123 61 127 75 131 95 136 04 140 2 THO1 4 5 5 7 8 9 9 3 10 17 13 33 717 679 816 800 739 638 508 561 480 541 166 04 167 11 171 16 175 2 179 16 183 18 186 24 187 11 191 03 201 83 D135317 8 9 10 11 12 13 14 15 791 637 571 715 564 692 567 681 216 68 220 69 224 63 228 73 232 62 236 52 240 52 244 52 D165539 5 8 9 10 11 12 13 14 15 706 827 795 1350 694 664 573 592 551 252 26 264 2 268 28 272 22 276 33 280 3 284 35 288 42 292 51 D251338 15 16 17 18 19 20 21 22 23 24 25 26 27 28 1032 1144 802 1146 919 987 846 889 766 696 831 309 26 311 64 315 87 320 06 324 29 328 39 332 46 800 639 63 336 48 340 49 344 08 347 64 351 24 354 92 358 7 D195433 9 10 11 12 12 2 13 13 2 14 14 2 15 15 2 16 16 2 1489 1352 1456 1109 1246 1078 1110 929 1081 101 73 105 62 109 49 113 4 115 4 117 35 119 38 911 972 827 856 802 803 121 48 123 34 125 25 927532 129 27 131 29 133 53 135 38 11 12 13 14 15 16 17 18 19 20 21 22 23 24 637 727 748 932 744 1012 1037 868 518 580 629 154 42 158 63 162 74 166 96 170 87 174 91 178 94 918 745 701 182 89 186 82 190 74 194 66 198 49 202 34 206 59 TPOX 6 7 8 9 10 11 12 13 730 732
74. 33 14 16 17188910 1292141161818 12 12 SESE DESO 11312 Ma po M mq p amem m3 X qe FIGURE 5 A Example of a Check Control screen Stutter checks for potential stutter It confirms that the threshold is met locus by locus If the threshold is not met it will indicate that there is potential stutter The stutters settings are set up under the quality control subsection of the Interpretation section in the ArmedXpert Options Menu All alleles that should be evaluated for stutter are highlighted in pink amp o Re x Check Check Allele Stutter RFUs CODIS Allele Check OSD PHR Check Begin Clear Controls Ordering Alleles Count X multi Review Checks Standard Checks CODIS QC QCReview Clear LLL ozis eme creo vastase mm Di3s317 ness asrse isses wa reox Diss Ame GA 1052904 Known standard of suspect Be me cn E Y cec c pecca e cue v ec ec ect ae ag escena 052904 Known standard of victim uns moe rem pnr oss espuma pmspss nx usw enpws apret nz 52904 No stutter filter DESIREE 12 IEICE 1QS2904_Stutter filter applied EDUHEXOCmEG ee FIGURE 55 Example of a Check Control screen Finally RFUs indicates all RFU s that are below scale off scale or both The RFU s settings are set up under the Quality Control Section in the ArmedXpert Options Menu The alleles with RFUs below scale are highlighted pink and all that are off scale are highlig
75. 3578 1923 2310 1306 1299 1577 1483 1652 162 pra e ceres SS m p ey FIGURE 3 9 view Samples amp Controls by RFUs T C e Fi i E Q all Alleles 5 Samples R pr Headings 5 Controls J Base Pairs C All A ndicate clipped data le es F Zoom 10095 Organize C Samples 4 RFUs User view Ft JL zem Show Hide Windows DEMO I 2 Component 4 Vict Mix Stains Analyst txt 7 1818 3132 1574 1274 776 688 859 949 773 860 55 2 de r 06 06 20 F03 1505 2601 1315 1066 622 560 717 791 637 706 827 1032 1489 6 0 1463 1057 1531 1411 1183 2333 1517 104 a aia aa ee pl 8761 4886 3028 3462 5470 7758 2441 3528 ee i XB NU E 3264 e w D 5 un D N co w M Ww co 5396 3394 2582 3317 5361 2776 2162 5373 3694 ee NEN ae ee ee 3811 4250 1814 2316 1473 1319 3578 1923 1306 1577 FS RT ENS EN ERU Ln ERR EE CRT ERR FIGURE 3 10 view All Controls by RFUs C2 all Alleles 9 Samples A j Headings m Controls Base Pairs All A Indicate clipped data PX PX Zoom 10095 Organize e Samples RFUs User View Fit Zoom Show Hide Windows DEMO 2 Component 4 Vict Mix Stains Analyst txt D135317
76. 38 D195433 918551 14 15 17 Amel XY 1705258 Ame X a FGA 22 22 2 24441 168 550 256 FGA 22 24 1495 1497 FIGURE 8 5 Define Alleles for Evidence On the bottom of the form is a place for the analyst to initial and date as well as a place for the tech reviewer to initial and date COONS Disi iio Form for CODIS Administrator Oo Ev Source Category NO PROFILE for CODIS Reason EVIDENCE PROFILE for the FORENSIC INDEX This profe is from crime scene evidence is attributable to a putative perpetrator and is mot from an ite owned used by the suspect x The source of the EVIDENCE PROFILE for the FORENSIC INDEX has been identified tvidence XX72 2 99XX5678 Q1 2 F2 Vag Swab 06 07 14 002 D165539 Suspect XX95 9905678 K9 Susp 1 Ref 06 07 14 F07 0851179 1 13 45474746 021511 30 30 2 3725 3575 075820 2943 2891 CSF1PO 10 12 3043 2797 D351358 15 17 3192 3051 THO1 4031 4198 0138317 9 12 3213 2604 D165539 5592 0251338 20 25 2889 2772 0195433 14 15 2 _ 3396 3420 VWA 17 18 3018 2803 TPOX u 6357 D18551 16 17 2608 2186 Amel 2136 2339 D55818 11 6377 FGA 2003 1744 Analyst initials date FIGURE 8 6 CODIS Disposition Form filled out 107 Tab Six Reporting ARMEDXPERT USER S MANUAL Total
77. 4 8335 1D_B 3_1 0ng 1 A03 0 9607 0 9160 0 8447 0912 0 7898 0 8045 0 9363 0 9781 0 7893 08511 071231 AveragePHR 0 9618 0 8093 0 8879 0 9231 0 8855 0 8692 0 9546 0 8748 0 8151 0 9261 0 7548 Std Deviation 0 0183 0 1474 0 0849 0 0143 0 0915 0 0764 0 0328 0 1093 0 0915 0 0699 0 0682 0 9441 0 6411 0 8333 0 9112 0 7898 0 8045 0 9350 0 7603 0 7393 0 8511 0 7123 0 9806 0 9160 0 9858 0 9390 0 9722 0 9535 0 9924 0 9781 0 9168 0 9894 0 8335 0 0851 0 0490 0 0083 0 0529 0 0441 0 0189 0 0631 0 0528 0 0403 0 0394 6719 PHR Average 1 0 dilution o o e a N eo q gt e ve o o o o eo co e a o a a PHR Average 25 Dilution Mac StdError 0 0105 25Dilution 0 971 0 9639 AveragePHR 0 8031 0 8583 0 7260 0 8461 0 9295 0 9154 0 7885 0 6404 0 8671 0 8119 0 7817 Std Deviation 0 1533 0 0805 0 2111 0 1174 0 0730 0 0558 0 0832 0 1699 0 0827 0 1478 0 1601 0 6719 0 7668 0 5904 0 7211 0 8543 0 8519 0 6947 0 5204 0 8025 0 6647 0 6633 Max 0 9716 0 9185 0 9693 0 9539 1 0000 0 9561 0 8536 0 8348 0 9604 0 9604 0 9639 StdError 0 0885 0 0465 0 1219 0 0678 0 0421 0 0322 0 0480 0 0981 0 0478 0 0854 0 0924 D8S1179 CSF1PO D3S1358 D19S433 FIGURE
78. 58 0 2656 0 5220 gt FIGURE 2 51 Frequency Analysis page with Export Menu To save a Mixture Interpretation page so that it can be resumed later in Armed Xpert click on Mixture Interpretation The Save As Window will appear You can change file name to whatever name you would like and Save it in whichever folder you would like Click Save once you have the file name and folder chosen ww Reperting Page a a Phugie Ex Ar Ex Loca 0169510 e o Pto haor 1415 P Avgib69 Pur OSS Minor 14 17 P Avg 031 y p rms 125 zl ueste 17 men S e 000 RFUs 1144 833 Lock our Be 29125 34 Popo vier el reponi gt Armeddicert Options Ext medger 14 15 phr 0 92 p 0 71 Major Ref 1 14 1 7 phr 0 92 p 0 29 Minor 14 15 phr 0 59 1 76 Ret 1 15 17ipt 59 0 24 ih For a 2 contributor 3 allele mixture of types AB amp CC 1 3 combination s 14 15ih 85 Ret 1 17Ir 15 FIGURE 2 52 Mixture Interpretation page with Export Menu 35 ArmedXpert Menu ARMEDXPERT USER S MANUAL View Click on View to view your stored profiles To initially add the profiles see the instructions under the Data Source section in chapter 4 Click on Profiles and the Chose value window will open Select the type of profile you would like to view Click the Ok button The profile type table will open EP Import es Profiles Y Export
79. 63 1749 1583 1707 755 879 921 ro 1950 34721486 1806 1454 2288 839 758 961 904 1083 861 773 976 1115 1428 1597 1101 1887 1752 1881 853 967 10 1505 26011111 1315 1066 1657 622 560 717 679 791 637 571 706 827 795 1032 1144 802 1489 1352 1456 637 727 748 02 7403 6117 2224 2344 25842804 4063 2468 1997 21551927 2560 2265 23162427 23842157 2833265 20 332 934 423 1 602 1632 1025 278 243 629 1264 992 669 438 1309 308 927 951 178 360 692 550 900 363 542 358 338 371 246 402 332 328 377 227 443 26 20 F01 373 1284 455 1483 1640 511 192 1463 1498 1057 983 1531 1281 1411 1183 1104 2333 15171622 12121001 1363 1063 11041027 1263 120 a n r 1 E 3711 4982925 2307 2315 505 4032 2418 542 2356 2776 1886 2548 2738 1519 395 1716 358 2295 1936 704 2445 2058 378 2051 370 1653 359 397 2085 675 4886 4163 3028 3146 3462 3751 7758 6758 2441 1948 3743 3440 4068 3903 3528 3185 4532 403 3448 3618 2698 2497 2333 2426 2489 2309 2299 2202 2328 2316 2449 2410 2734 2721 2968 330 6117 2224 2344 2584 2804 4063 2468 1997 2155 1827 2560 2265 2316 2427 2384 2157 2833 265 3394 2582 2439 3317 5361 5361 2776 2916 2162 2181 5373 2181 3694 3181 32643526 3252 31 4250 1814 1757 2316 2138 1473 1662 1319 1318
80. 67 12 13 phr 0 67 FIGURE 7 4 Example of screen once sample is selected Note You can click on the highlighted cell and detailed information about that locus displays Click on the detailed information to make it disappear For Example in Figure 7 4 above D8S1179 is highlighted By clicking on the highlighted cell the details for D8S1179 for the selected sample appear as shown below in Figure 7 5 Alleles 12 13 RFUs 1580 2345 BPs 139 55 144 26 FIGURE T 5 Detailed information displayed for highlighted locus 77 Tab Five Interpretation ARMEDXPERT USER S MANUAL Select number of Contributors Select the number of contributors using the Contributor selection box in the upper right corner The default number of contributor is 2 Click on the V arrow to change the number Contributor 2 he Refi 3 FIGURE 7 6 Number of contributors section Apply Reference s optional Next select any available references as permitted by your individual lab s mixture interpretation protocol Click on the Reference button under the Contributor selection box and the References Selection box will appear Click the V arrow in box 1 A drop down list of all your available samples will appear Click the one you would like to set as Reference 1 Once you select a reference the button next to the reference will change from Apply Reference to Remove Reference To set more than one reference proceed to Box 2 etc and
81. 73 0 70 0 71 0 65 0 71 074 0 70 0 70 Profile 11 0 19 030 039 034 035 040 0 30 0 27 0 30 029 035 0 29 026 0 30 0 30 Profile10 0 69 Profile 11 0 31 FIGURE 7 31 call report Example 89 Tab Five Interpretation i as d ARMEDXPERT USER S MANUAL The Call Report includes additional worksheet to document each of your interpretation parameters and results locus by locus If you click on the Mix_Interp Worksheet tab at the bottom of the report you will see a Mixture Interpretation Detail Report Le Mixture Interpretation Details for XX0156 1 99XX9999Q1 15 2F1 Shirt Vict 06 06 20 D01 Comment Only combinations including the following reference profiles are included 12 13 All combinations have PHr 0 3 MPh 100 mP 0 12 1580 13 2345 For a 2 contributor 2 allele mixture eof es AA amp AB 2 2 combination s je Only combinations including the following reference profiles are included 29 30 All combinations have PHr gt 0 3 MPh gt 100 mP 0 28 916 29 1144 30 994 For a 2 contributor 3 allele mixture of T types AA amp BC 1 3 combination s Ff ls a M m u am A AS 3U ph m 37 p 70 28 p 0 2 Fora 2 contributor 3 allele mixture of types AE i BC C 2 2 combination s Only combinations including the following reference profiles are included 10 All combinations have PHr gt 0 3 MPh gt 100 mP gt
82. 78 Q1 F1 Gen Swab 06 07 14 403 ox 4 2 9945678 Q1 F2 Gen Swab 06 07 14 B03 72 1 9945678 Q1 2 F1 Vag Swab 06 07 14 C02 E XX72 2 9945678 Q1 2 F2 Vag Swab 06 07 14 D02 gt 294 995678 K1 5 Vict Ref 06 07 14 E07 zx 295 995678 K9 Susp 1 Ref 05 07 14 F07 2041748 9925678 K11 Elim Ref 06 08 21 404 4 21747 9425678 K10 Susp 2 Ref 06 08 21 H03 lt lt CMF Version CMF Version CMF 3 2 F CMF32 7 Ignore Case Also select tables opy to All CMF 1 0 CMF Attributes Packet Attributes CMF 2f SOURCELAB 123456 CMF 3 1 DESTINATIONORI 456789 SUBMITBYUSERID TDBO1 Drom SUBMITDATETIME 2013 11 20T09 45 49 BATCHID KIT Identifiler z vV Save to file Ok Cancel FIGURE 8 11 CMF Window Click the Next to the Sample Table to expand to a detailed list of all samples Choose the Samples you would like to upload by clicking on them and clicking the gt button The samples will move to the box on the right as seen in Figure 8 12 below You can also use the Selection Filter box to enter in a specific name and all samples containing that name will be highlighted This is helpful in finding certain samples in a large sample table Click the gt button and all samples highlighted will move to the right hand box Continue these steps until all necessary samples have been moved to the right box Once all samples have been selected click on one of your selected samples The Packet Attributes section on
83. 8 xy Mixture MF Neat 0 10 10 04 Mix 1114 2929 910 910 1616 89 1 11 1 12 1718 14215 1819 88 1414 xy i Check completed with no errors FI GURE 5 5 Example of a Check completed with no errors screen 64 Tab Three QC Checks ARMEDXPERT USER S MANUAL The CODIS Alleles command checks the alleles at each locus against CODIS formatting rules It highlights in pink any sample s locus that contains alleles not accepted by CODIS musu Mirasa i REE A T n pne Bi wa CTS Check Check Allele Stutter RFUs CODIS Allele Check OSD PHR Check Begin Clear Controls Ordering Alleles Count X multi Review Checks Standard Checks CODIS QCReview Clear C Program Files NicheVision Inc ArmedX pert data Saved_Profiles Page_Data MT Test H txt paee mau ws ss ase xx zu m maspuu mas p wise meses xx amp amp ea fee UL OE a o FIGURE 5 9 CODIS Alleles Result Example The Allele Count command highlights in pink any sample s locus that contains a number of alleles above the user defined amount An Allele Count window appears after clicking on the Allele Count command Enter the maximum number of alleles that is accepted and click Ok Allele Count c s 23 Maximum number of alleles Cancel FIGURE 5 10 Allele Count Window a jew
84. 8 O1 2 F2 Vag Swab 06 07 14 D02 Ax 72 2 335578 01 2 F2 Vag Swab 06 07 14 D02 2894 332808 K1 5 Vict Ref 06 07 14 E07 2895 985578 KI Susp 1 Ref 06 07 14 F0 2081748 332808 K11 Elim Ref 06 08 21 404 281 747 99485678 K10 Susp 2 Ref 06 08 21 H03 d 4 aug s E CMF Version CMF 32 Selection filter V Ignore Case Also select tables Copy to All CMF Attributes j Packet Attributes SOURCELAB 123456 SPECIMENID 0495 99045678 K9 Susp 1 DESTINATIONORI 456789 SPECIMENCATEGORY Convicted Offender SUBMITBYUSERID TDBOT SOURCEID SUBMITDATETIME 2013 11 20T09 45 49 CASEID BATCHID PARTIAL KIT Identifiler SPECIMENCOMMENT DESCRIPTION Locus Partial Allele 1 Allele 2 v D21511 E 302 Mose O ls fo mermo 0 12 Mosse OF hs v v THON D Missi lE 2 V Save to file J FIGURE 8 12 CMF Window Example Click Ok when you are ready to save the file The Save As Window will appear In the File Name box type in the appropriate file name Then save it in the appropriate folder Click the Save button 112 Tab Six Reporting ARMEDXPERT USER S MANUAL PHR Report The PHR Report shows all the peak height ratios PHR as well as the average PHR for selected table s or sample s This is useful to determine thresholds The first step in running your PHR Report is to create dilution tables for the report Import your dilution sample table into A
85. 938935 0 2894 0 22717787 0 196066805 0 16284 0 43356 0 2857 0 22427 0 193555 0 19897456 0 46121864 0 32295 0 26096228 0 22996842 D351358 15 16 13 36 0 2463 0 231 0 1140369 0 397959225 0 2389 0 17646845 0 145252675 3 0 2315 0 2905 0 3071 0 1784251 0 444006275 0 2988 0 23861255 0 208518825 0 4258 0 2656 0 22618496 0 47939624 0 3457 0 28594248 0 25606372 0 13840728 0 41760182 0 266 0 20220364 0 17030546 0 0229512 0 3093128 0 10715 0 0650506 0 0440009 V Unrelated Y Full Siblings Parents amp Offspring Y Half Siblings Uncles Nephews Y First Cousins FIGURE 7 44 Single Source Calculation Page U 3239 U 325359 U 1Z 231 28 U 428Z013UZ U 3239 U Z392 Z20U U LB Z4UBYUGS 0 3556 0 3556 0 128742846 0 45941284 0 3556 0 24102568 0 18373852 0 2906 0 2906 0 086509876 0 41641209 0 2906 0 18752418 0 13598627 5A 22 24 22 24 0 1888 0 1378 0 05203328 0 34465832 0 1633 0 10766664 0 07984996 0 225 0 1861 0 083745 0 37371125 0 20555 0 1446475 0 11419625 0 1773 0 1256 0 04453776 0 33685944 0 15145 0 09799388 0 07126582 Caucasian Tin 6 2505E 416 1 4661bE 6 5 8512bE 9 1 7116E 12 1 0258E 14 Black Lin 5 2802E 18 2 9528E 6 5 5722E 10 2 8928E 13 3 0922E 15 Hispanic 1in 2 3643E 17 1 8021E 6 1 695E 10 5 4585E 12 3 7263E 14 Caucasian Lin 62 5 Quadrillion 1 46 Million 5 85 Billion 1 71 Trillion 102 Trillion Black Lin 5 28 Quintillion 2 95 Million 55 7 Billion 28 9 Trillion 3 09 Quadrillion Hispani
86. 98 0 0000 0 0000 0 0000 0 8045 0 0000 0 9350 0 7603 0 7393 0 8511 0 7123 Max 0 9806 09160 0 0000 0 9858 0 9390 0 9722 0 0000 0 0000 0 0000 0 9535 0 0000 0 9924 0 9781 0 9168 0 9894 0 8335 OST SES SSS SER ERE Stdtror 0 0105 0 0851 sDIV O 0 0490 0 0083 0 0529 sDIV O sDIV O 0 0441 0 0189 0 0631 0 0528 0 0403 0 0394 25688 FEAS g 25Dilution PHR Average 25 Dilution ID D 1 O 25ng 9 01 0 9716 0 8896 06182 0 8634 0 9341 9951 081 0 8348 0 8025 0 6647 6633 ip D 3 025ng 7 D03 0 6719 0 9185 0 5904 09539 ossaa 1 ooss2 ossse 0566 05384 0 9604 0 9639 1 0000 ID D 2 0 25ng 8 DO2 0 7659 0 7668 098693 07211 1000 08519 0 6947 0 5204 0 9604 0 8107 0 7181 98090 Average PHR 0 8031 0 8583 sDIV O 0 7260 0 8461 0 9295 sDIV O sDIV O sDIV O 0 9154 0 7885 0 6404 0 8671 0 8119 0 7817 0 4000 0 0000 Mim 0 6719 0 7668 0 0000 0 5904 0 7211 0 8543 0 0000 0 0000 0 0000 0 8519 0 0000 0 6947 0 5204 0 8025 0 6647 0 6633 Ma 0 9716 0 9185 0 0000 0 9693 0 9539 1 0000 0 0000 0 0000 0 0000 0 9561 0 0000 0 8536 0 8348 0 9604 0 9604 0 9639 SSSreessestes es ce StdError 0 0885 0 0465 sDiv
87. D75820 CSFIPO D351358 THOI D135317 D165539 0251338 185433 VW A TPOX Stutter mix Stutter Ranges tool earam 0 08 N 4 0 08 N 4 0 08 0 09 N 4 0 09 N 4 0 09 0 08 N 4 0 08 N 4 0 08 0 09 Ne 0 09 N 4 0 08 on N 4 0 11 N 4 0 11 0 05 N 4 0 05 N 4 0 05 0 08 N 4 0 08 N 4 0 08 01 N 4 0 1 N 4 0 1 on N 4 0 11 N 4 0 11 0 13 N 4 0 13 N 4 0 13 013 N 4 0 13 N 4 0 13 6 006 4 0 06 Ranges 4000 35240107 4 00 35240107 400 0 35 401 0 7 lt 400 0 35 gt 401 0 7 lt 400 0 35 gt 401 0 7 lt 400 0 35 gt 401 0 7 lt 400 0 35 gt 401 0 7 lt 400 0 35 gt 401 0 7 lt 400 0 35 gt 401 0 7 lt 400 0 35 gt 401 0 7 lt 400 0 35 gt 401 0 7 lt 400 0 35 gt 401 0 7 PROT TEE EPI AP RC PIN FIGURE 2 17 Interpretation Quality Control Options You can set up stutter intervals that determine stutter in the sample table and egrams Add the appropriate amounts for each Locus Used the sign to add additional values Click on the X to delete a value An example is shown below Add stutter intervals using the format N Margin DecimalPercentage separating multiple intervals with a semicolon eg N 4 06 N 4 08 Or use the controls below Margin Filter decimal 4 0 05 Lx 4 005 x FIGURE 2 18 Stutter Ranges Window Example 15 ArmedXpert Menu ARMEDXPERT USER S MANUAL If you have multiple Phr Armed Xpert has a
88. Data The Total Data report is a report that gives you all of the information from a sample table It lists the alleles RFU values and Base Pairs values for each sample on the sample table by locus To run the report have the sample table that you want to see the total data for open and in front of all open windows and click on the Total Data button DEMO 2 Component 4 Vict Mix Stains Analyst txt cJ DEMO 1 2 Component 4 Vict Mix Stains Analyst Locus Alleles RFUs Base Pairs Ladder Identifiler 06 06 20 F03 D851179 8 9 10 11 12 13 14 15 16 17 18 19 1505 1372 1682 1830 1043 955 960 1370 931 887 123 04 127 11 131 15 135 31 139 48 144 13 148 63 1043 781 153 03 157 26 161 48 165 56 169 62 021511 24 24 2 25 26 27 28 28 2 29 29 2 30 30 2 31 31 2 2601 1111 1946 1448 1698 2501 1792 1890 1211 184 64 186 68 188 64 192 56 196 46 200 37 202 27 32 32 2 33 33 2 34 34 2 35 35 2 36 37 38 1162 1224 1150 1194 1574 1114 1199 1436 1082 204 24 206 22 208 2 210 19 212 18 214 1 216 09 1415 1743 1132 1626 2386 867 218 09 220 09 222 02 224 11 225 97 228 06 230 232 02 236 239 91 D7S820 6 7 8 9 10 11 12 13 14 15 1315 1115 1257 1310 1198 845 1002 1142 1103 255 16 259 14 263 2 267 2 271 3 275 32 279 44 1017 283 49 287 56 291 64 CSF1PO 6 7 8 9 10 11 12 13 14 15 1066 1657 1479 1568 1030 1690 1083 727 1209 304 72
89. Destination Lab 456783 User CODIS ID TDBOT Interpretation Quality Control Admin Console Imaging System Organization Imaging System _ Specimen Category Convicted Offender Alleged Father Alleged Mother Biological Child Biological Father Biological Mother Biological Sibling CO Duplicate Double click an item to edit FIGURE 2 37 CODIS Option Window 26 ArmedXpert Menu ARMEDXPERT USER S MANUAL In the bottom portion the Specimen Categories are displayed There is several default ones already entered into ArmedXpert You can add additional categories by clicking on the Add Category button and entering in the appropriate category on the next available line You can also delete any category by clicking on it and then clicking on the Delete Category button You can edit any of the categories by double clicking on it and then typing in the edit Specimen Category Detainee Deceased Deduced Suspect Juvenile Staff Volunteer lt gt Double click an item to edit Add Category Delete Category FIGURE 2 38 copis Specimen Category Section The third subsection CMF Attributes allows you to add to enter CMF Attributes used in the CMF report in ArmedXpert All data filled in here will be displayed with you open the CMF report You can change the order of all the attributes by double clicking in the cell containing the number order and then clicking in a new number The A
90. Function Keys Clear Match Print the selected Page 000000000000 Hide selected Rows or Columns Show all Rows and Columns Show Controls Show Samples Show Alleles Show RFUs 0 0 0000 F11 Show Base Pairs Alt Keys Alt then left click mouse iN Increase Column Width CUT Decrease Column Width 000000000 Increase Row Height DeceaseRowHeight Displays Headings Opens the Organize Window 00 SIES Opens the Sort Samples Window Misc Keys Ctrl 7 Ctrl Moves to First Row and First Locus Position Home Ctrl End Esc Clears pick via mouse option ab Shift Moves to Previous Cell in Row Tab T 121 ARMEDXPERT USER S MANUAL Appendix B Contact Information If you have questions about ArmedXpert that this manual does not answer be sure to visit the Armed Xpert online support site at http www armedxpert com The online support site offers additional information about ArmedXpert including e A PDF version of this ArmedXpert User s Manual e Specific guides about different features and options in ArmedXpert e Frequently Asked Question You can also contact NicheVision Customer Support by sending email to support nichevision com or by calling 1 866 840 3758 or 330 252 2711 122 ARMEDXPERT USER S MANUAL Index About ArmedXpert 8 Admin Console 28 Armedxpert Options 7 8 61 63 66 67 88 109 Change Kit 51 CMF Form 111 CODIS Disposition Form 105 Combine Source 52 Commit Sa
91. HR Report c3 s 3 Description Table 1 5 Dilution 1 5 Dilution 1 0 dilution 1 0 dilution 25 Dilution 25 Dilution Remove Double click an item to change Add a table selected its description Dk Cancel FIGURE 8 16 PHR Report Window with selections If you would like to change any of the table s description names before you run the report click on the table from the list shown An Enter a description Window will open Type in the new description and click on the Ok button PHR Report Description Table 1 5 Dilution 1 5 Dilution 1 0 dilution 1 0 dilution 25 Dilution 25 Dilution Enter a description c s 24s Ok Cancel L Remove Double click an item to change Add a table selected its description Ok Cancel FIGURE 8 17 Entera description Window Once finished click the Ok button to run the PHR report 115 Tab Six Reporting ARMEDXPERT USER S MANUAL The PHR report shows the PHR at each locus for each sample chosen PHR Report o ES 851179 21511 D75820 CSF1PO D351358 THO1 D13S317 D165539 D251338 D195433 vwa TPOX 18551 Amel D5S818 FGA 1 5 Dilution PHR Average 1 5 Dilution ID A3 15ng 6 HO2 8652 0836 08669 07897 073 091581 90922 0 6037 098602 09246 09320 ID A2 15ng 2 A02 097161 0 9629 099861 0 9570 0 9609 09067 09029 0852 09716 0 9710 09232 S 8000 ID A
92. In the next box choose the table you would like to compare against Enter the minimum number of total and exact matches you would like to show on the report and the minimum number of included matches To show all included set the minimum number of included to 1 as shown below Then select the options you would like to run as well The Only compare other samples option will only compare samples not controls The Create match compate reports option runs match and comparison reports that can be retrieved by clicking on the different worksheets at the bottom of the report The List unmatched samples option will allow you to either list all samples whether matched or not ot only list matched samples to condense the report Finally the Compare references with profile option allows you to compare the reference against one or more of the chosen profiles Click on the Match button to run the report A report like the one in Figure 8 9 will appear Samples Comparison c E Thresholds Min no total matches 1 Values are inclusive Use 1 Min no exact matches 6 to match any amount Min no included 1 Options Only compare other samples J Create match compare reports List unmatched samples Compare references with profiles e vV Staff Match Cancel FIGURE 8 8 Samples Comparison command window 109 Tab Six Reporting ARMEDXPERT USER S MANUAL The Report lists the Reference Samples in the
93. MEHM Anayzed Raw Ladder MinRFU 0 gt HT 100 V Markers 5 Labels FIGURE 7 40 Virtual Electropherogram 93 Tab Five Interpretation ARMEDXPERT USER S MANUAL Frequency Calculations The Frequency Calculation section allows you to perform different frequency calculations ArmedXpert includes frequency calculations for Single Source Likelihood Ratio Probability of Inclusion RMP and User Defined The User Defined option allows you to run a custom plug in calculation 92 Lp 4 Y f Single Likelihood Probability RMP User Source Ratio of Inclusion Defined Frequency Calculations FIGURE 7 41 Frequency Calculations b Note When closing each page a confirmation window will open to ask if you would like to save the report or not if the option to prompt to save on application close or window close is turned on The first type of frequency calculations is a Single Source calculation To obtain Single Source Frequency Calculations click on the Single Source button The Select Pick via mouse window will appear Select the single source sample you wish to perform the calculations on with your mouse or click on the Warrow and select from the drop down list Fick via mouse y FIGURE 7 42 Select Pick via Mouse Window The Frequency Single Source page will appear as in Figure 7 44 shown on the following page All loci and their corresponding alleles are imported into the page On the bottom o
94. PHR Range feature The PHR Range peak height ratio is for each separate locus To add a range click on the PHR Range cell next to the appropriate Locus The window show below will appear You can type a Minimum rfu value with an appropriate Phr and or a Maximum rfu value with an appropriate Phr Click on the button to add another range To delete a range click on the X next to the appropriate range An example is of the PHR window filled out is shown below In this example we ate saying that alleles that have an rfu value over 1000 have a Phr of 60 and ones that are under 1000 have a Phr of 40 This would be reflected for the appropriate Locus in the Mixture Interpretation window Add ranges using the available formats Min Max Phr Min Phr Max Phr separating multiple ranges with a semicolon Or use the controls below iln Min Max zi S 1000 A RY 1000 8 x FIGURE 2 19 Multiple PHR Range Window Example You can add loci from a sample table by clicking on the Add Loci from Table button The sample table needs to be opened in ArmedXpert Samples amp sources Selected samples amp sources Aag B dg gt E n T LS 4 Ignore Case Also select tables Ok ancel FIGURE 2 20 Select Table Window A window with all the Loci from the table will open A check mark is shown next to each Locus Click on any of the boxes next to a Locus to remove a check mark for any L
95. This is a useful tool if you have several windows open at the same time Click on the Organize button and the window shown in Figure 3 21 will appear All opened windows including tables mixture interpretation windows frequency calculations and reports will appear Organize Windows FIGURE 3 20 Organize Section Choose from the list the window you want to bring to the front and click on the Bring to Front button Your selected window will now be brought to the front of all other windows You can also undock a window from ArmedXpett by clicking on the Undock button next to the appropriate window To return the window back to ArmedXpert click on the Undock button again and the window will be moved back into Armed Xpett Organize BAR Windows LF mar oa 5 Remove Group Bring To F 2 Component Vict Mix Stans amp nalyst t t sa LL Bring To Ser VS Front Mixture Interpretation DDA Interpretation Undock Bring To ded XX0156 3 99XX9999Q1 15 2F3Shirt Vict 06 06 20 Front Undock Bring To re Front weewerw DEM I 2 Component Vict and 5 Susps D3 Extra Allele tst ire qoe a px Undock Bring To bea Front ro 88 Add Group FIGURE 3 21 Organize Window 46 Tab One Views ARMEDXPERT USER S MANUAL You can sort the windows by Groups by clicking on the Add Group
96. USER S MANUAL Tab Five Interpretation he Interpretation tab is used to perform interpretation and frequency calculations of your samples It has two main sections Mixture Interpretations and Frequency Calculations The mixture interpretation section contains the Mixture Interpretation tool It allows Deconvolution of both two and three person mixtures into individual DNA profiles The frequency calculations section allows you to perform statistical analysis such as RMP and CPE CPI m Views Data QC Checks Match amp Comparison Interpretation Reporting V Highlight j 7 9 53 y Begin Mixture Single Likelihood Probability RMP User Interpretation Source Ratio of Inclusion Defined 7 Mixture Interpretation Frequency Calculations FIGURE 7 1 Interpretation Tab Mixture Interpretation The Mixture Interpretation section is used to interpret mixtures for any selected sample It gives you the information to aide you in making the appropriate calls It lists all available combinations at each locus based on your settings It keeps track of the proportions for each profile as well as gives you a graphical visualization of the proportions as you choose each combination The Mixture Interpretation tool can be used for a 2 or 3 contributor mixture It allows you to set references and apply stutter when appropriate To start using the Mixture Interpretation Tool click on the Begin Mixture Interpretation butto
97. VAd44 Ss EC palaifl pna 2 1 914155 1 4 1 0 9 01 50 amp A Fa f0 8 4 3M A Fa f0 9 43 5 3d a z A 2 1 8 15 Letters numbers and hyphens Date e g 21 3 2006 jpg aif or png image Any number from 1 to 50 inclusive Valid hexadecimal colour code 8 to 15 character string with at least one upper case letter one lower case letter and one digit useful for passwords w r a zA Z X a zA Z 12 6 eU N HA Email addresses HTML Tags Note These patterns are intended for reference purposes and have not been extensively tested Please use with caution and test Hiaraughly before usa Quantifiers 0 or more Ey or more ungreedy 1 more a b 7 1 or more ungreedy D Oorl 15 2 7 or 1 ungreedy abc 3 Exactly 3 4 abc 13 3 or more a q 3 5 3 401 53 A Q 5 221 3 4 or 5 ungreedy 0 7 a Special Characters Escape Character n New line Ar Carriage return x Tab Ww Vertical tab F Form feed g la Alarm i b Backspace m ig Escape 5 Niname Named Character String Replacement Backreferences n nth non passive group 2 xyz in abc xyz 1 xyz in abc xyz Before matched string After matched string 4 Last matched string 5 Entire matched string _ Entire input string Literal FIGURE 2 32 List of Regular Expressions 23 Ar
98. X0156 1 99XX9999Q1 15 2F1 Shirt Vict 06 06 20 DO1 amp Locus D85179 4 D21511 28 29 30 D75820 e 10 CSF1PO D351358 15 16 6 93 0 9541 0 0459 v gt FIGURE 7 52 Probability of Inclusion Page 99 Tab Five Interpretation ARMEDXPERT USER S MANUAL The calculations by ethnicity for the entire profile will appear at the bottom of the page The calculations are shown in both exponential and alphanumeric form 9 8 0 0139 03556 0 0542 0 2906 22 222 24 25 0 8333 0 1667 01773 0 0123 0 1256 0 1379 0 7947 0 2053 Caucasian Lin 3 9534E 7 39 5 Million Black Lin 1 8501E 9 1 85 Billion Hispanic Lin 2 9496E 8 294 Million Sources ec FIGURE 7 53 Bottom of the Probability of Inclusion Page If you would like the CPI to show only click on the column contained the CPE Hit the F5 key The CPE column will be hidden Hit the F6 key to make the column to reappear The image below 15 an example of the page displaying the CPI only Probability of Inclusion XX72 2 991065678 Q142 F2 Vag Swab 06 07 14 002 eens XX72 2 9913X5678 Q1121 F2 2 Vag Swab 06 07 14 DO2 cus Prof Aiei Ahe Allele 3 Allele 4 Alicie S Allele 6 Loos o0se7 01454 03393 02015 0 0128 oons 0 0361 o108 02222 0 3333 0 0444 05749 0 0323 0 0616 01207 03251 0 2463 0 0246 0 6250 Gere 0 2048 0 4928
99. Y 12 13 XX0162 1ReagBlankFl 06 06 20 802 ESSE EE XX0162 2 Reag BlankF2 06 06 20 C02 BL o ee ee ee ee ee Ee Se L XX0164 99XX9999Q1 2 LFS Vict 06 06 20 D02 XX0165 QA004 QA 06 06 20 E02 XX0166 Reag Blank 06 06 20 F02 NES iis po wem LN EE NENNEN XX0167 99XX9999K1 11 Blood Vict 06 06 20 G02 XX0168 99XX9999K2 Blood Susp 06 06 20 H02 XX0169 QAO26 QA 06 06 20 803 100170 Reag Blank 20 003 menn eed mere emm 90171 Pos Con 06 06 20 003 1513 3036 honi on i amp is lesa ini ini 92 ms wie amp 8 i amp i9 mul 232 100172 Neg Con 06 06 20 03 L EL L fe d FIGURE 2 47 File opened in ArmedXpert Click on Frequency analysis to import in a previously exported Frequency analysis calculation page All exported Frequency analysis will have an axf extension The Frequency analysis calculation page will import in with all the information that was exported out You can now continue using the Frequency analysis calculations page Click on Mixture Interpretation to import in a previously exported Mixture Interpretation All exported Mixture Interpretations will have an axm extension The Mixture Interpretation window will open along with a 32 ArmedXpert Menu ARMEDXPERT USER S MANUAL copy of the sample table that contains the sample that the mixture interpretation window was using All calls made before the Mixture In
100. a Aki C fisol CODIS quality control options OSD off scale data PHA Imbalance Ok Cancel FIGURE 2 30 Quality Control Options window 21 ArmedXpert Menu ARMEDXPERT USER S MANUAL The second subsection Ladder and Controls contains the settings that are used during the Check Controls Quality Control Check The top portion has the Control qualifiers These can be changed by clicking on the Expression column in the row that you would like to change and then change to the correct expression The expressions are using regular expressions This allows all controls to be picked up during the quality control check For example Ladder will pick up any control that contains the word Ladder no matter what characters are before or after the word ArmedXpert Options c3 5 2s General Options Ladders and Controls i Data Interpretation Ladders and controls options Control qualifiers Jualty Lontro Qualifier Description Expression All Controls Pas ConlNeg ConlReag Blank LadderlAJQ T Positive Control Pos Con JI POSCON Negative Control NEGCON Reagant Blank Reag Blank I E amp GBLA amp NK Ladder Ladder Quality Assurance S ample E wt3 Reporting Admin Console 4 Select the table to use when checking controls Identifiler Y Select Table a Ok Cancel FIGURE 2 31 Ladder and Controls Su
101. a x A Zoom 10095 Organize _ Samples _ RFUs _ User View JL Fk 15 Show Hide Windows DEMO 2 Component 4 Vict Mix Stains Analyst txt D7S820 CSFIPO D351358 1 135317 0165539 D251338 D195433 vwa TPOX D18551 Amel DSS818 FGA FALSE 24 6 7 8 6 7 8 9 12 13 45 8 9 10 5 8 9 15 16 17 9 101112 11 12 13 6 7 7 9 10 17 18 19 20 8 9 10 67 8 67 89 12 13 45 8 9 10 5 8 9 15 16 17 9 101112 11 12 13 67 7 9 10 XY 7 89 17 18 19 20 8 9 10 67 8 6 7 8 9 12 13 4 5 8 9 10 5 89 15 16 17 9 10 11 12 11 12 13 6 7 7 9 10 X Y 7 8 9 17 18 19 20 13 9 10 1011 15 693 11 12 9 12 1925 14182 1518 11 1417 XY 9 12 222 25 12 13 28 29 30 9 10 10 11 12 15 16 6 9 3 8 11 12 9 12 13 19 20 24 25 13 14 14 2 18 215 17 18 19 8 11 14 15 17 XY 9 12 22 222 24 2t 12 13 28 29 30 9 10 10 11 12 15 16 6 93 8 11 12 9 12 13 19 20 24 25 13 14 14 2 18 2115 17 18 19 8 11 14 15 17 XY 9 12 22 22 2 24 2t 12 13 28 29 30 9 10 10 11 12 15 16 6 9 3 8 11 12 9 12 13 19 20 24 25 13 14 14 2 18 2 9 12 22 222 24 2 1514 28 311 3412 10 1418 6 39 1 13 1724 1314 1417 8 11 12 xv 1213 RES MEER GCSCENE
102. a GMID_Tables Identifiler Datasource Commit D x __ p8s1179 D21511 75820 CSF1PO 351358 THO1 D2393 Select items to commit to the datasource SD041 SD043 E Staff Profile new xls SD044 SD041 j SD045 pup L soose 1415 30 322 1 131 11 12 1417 68 121 50047 5D046 0048 5006 5 50049 7 8 pies 05 SD050 50051 S051 0052 5D052 50053 pena B S0054 SOEs 0055 snare 55056 Selecti Ignore Case Also select tables 50057 0058 sp059 SD060 Type 50061 55062 14 15 30 322 10 11 11 12 14 17 6 8 Sauce iii SD063 50064 s00ss 30066 50067 9 10 10 12 16 17 8 9 11 1 SNNAR 7 9 9 1 11 13 142 16 7115 17 FIGURE 4 1 5 Datasource Commit Individual Profiles Window Click on the Individual Profiles tab Choose type of profile you are adding from the drop down menu next to the Type box The options are shown below in Figure 4 16 Source is optional to be filled in Click Commit button When finished with the window click the Done button to close the window L ommit items as Table Individual Profiles Type Staff Source QA SRM Unknown Staff Demo n Agents New profile type FIGURE 4 16 Drop down list 56 Tab Two Data ARMEDXPERT USER S MANUAL To Load a sample table or sample that you committed from your database click on the Load Samples From Data Source button The Datasource Load w
103. ag Blank 06 06 20 F02 AXXD157 83 243333K1 11 Blood Vict 06 06 20 G02 20168 33 243333K 2 Blood Susp 06 06 20 H02 260169 G4026 QA 06 06 20 B03 20170 Reag Blank 06 06 20 C03 v RIT Ll J Ignore Case Also select tables Title Combine FIGURE 4 8 Combine Sources Window The Sample amp sources box displays all open sample tables By clicking on the next to the Sample Table name the list will expand to show all available samples on the sample table Click on the entire sample table or the specific sample you wish to combine and then the arrow gt button The sample table or sample will move to the selected samples amp sources box on the right Repeat for the next sample table or sample The gt gt button will move all samples at once You can also use the Selection Filter box to enter in a specific name and all samples containing that name will be highlighted This is helpful in finding certain samples in a large sample table Click the gt button and all samples highlighted will move to the Selected samples amp sources box The Ignore Case next to the selection filter box should be checked if you would like the selection filter choice to include all samples containing the filter regardless of upper or lower case The Also select tables option should be checked if you would like the selection filter to choose tables as well as samples that contain the filter 52 Tab Two Data ARMEDXPERT USER S MANUAL If
104. alid for this check FIGURE 5 14 PHR Result Example The Check Multi command checks samples with identical names and confirms that they are identical at each locus Any locus that is not identical is highlighted pink For example in Figure 5 15 below at D3S1358 alleles 15 16 are showing for XX0159 1 99XX9999Q1 15 8F1 Shirt Vict 06 06 20 F01 Sample but alleles 15 16 17 are showing for the identical sample right below it VIEWS Data Qt CNeCKS macniscomp March amp Comparison Interpretation amp PROV EH Check Check Allele Stutter RFUs CODIS Allele oe PHR Check Begin Clear Controls Ordering Alleles Count x multi Review Checks Standard Checks Standard checks 1 COIS j QC Review Clear 7773777737367 13531 Shi 06 20 E01 28 29 30 9 10 10 11 12 15 16 6 9 3 8 11 1 06 20 E01 2 29 20 9 10 Bo naf ey ss 8 11 1 6 20 F0 1516 p 9 3 8 11 1 28 29 9 10 10 11 14 15 16 17 9 3 8 11 1 28 29 30 9 10 10 11 12 TS Te 6 9 3 8 11 1 28 29 30 9 10 10 11 12 15 16 6 9 3 8 11 1 1213 2530 10 10 10 12 15 16 6 93 8 12 12 13 29 30 10 10 10 12 15 16 6 9 3 8 12 13 13 28 28 9 10 10 11 15 15 953 151 FIGURE 5 15 Check Multi Result Example 67 Tab Three QC Checks ARMEDXPERT USER S MANUAL QC Review The QC Review section only has one command It is Begin Review This command gives you de
105. as saving setups To make additional changes to the way the page is printed click on the More Option button If you would like to save all the print setups click on the Save Setup button once all appropriate settings have been completed A Give the setup a name window will open Type in a user defined name Then click the Ok button When you want to use a saved set up select from the drop down list All saved changes will appear More Options Load Save Select saved page setup Save Setup DeleteSetup FIGURE 2 57 Print More Options Once you have made all print setups click Print or Print Preview 4 Print Print Preview FIGURE 2 58 Print Options If you have an OSIRIS Plot file open the Plot tab will open instead for the Workbook tab Choose the appropriate orientation and fit option Once you have made all selections click Print or Print Preview Print IB Workbook Plot 4h Orientation Print Portrait Landscape Print Preview Fit All on one page Charts per page 1 FIGURE 2 59 Plot Options 38 ArmedXpert Menu ARMEDXPERT USER S MANUAL Tab One Views Show Hide and Windows This tab s commands allow you to choose how the data appears on your screen It also has an organize tool which allows you to choose which window you would like to view T he first tab in ArmedXpert is Views There are five main sectio
106. aui filer eit 2 cx a rte ett ae a IR 12 29 31 9 12 910 14 7 9 3 12 14 9 12 17 20 13 15 14 8 11 E IEN E 8 15 e 1215 30 11 12 11 1416 93 1213 12 13 18 22 12 15 15 sees sspe p mean Fee ey ee eS eee as ee e pen een ed paramet elis XX0170 Reag Blank 06 06 20 C03 XX0171 Pos Con 06 06 20 D03 XX0172 Neg Con 06 06 20 E03 Ewe 16 18 X E 13 X pem 1519 Cohtrol LADDERSANDCONTROLSCH ECK _ TABLE FIGURE 5 29 Example of a Check Control screen 62 Tab Three QC Checks ARMEDXPERT USER S MANUAL Check Allele Ordering confirms that the alleles are all in correct order Any allele not in correct order will be highlighted pink amp dj we x Check Check Allele Stutter RFUs CODIS Allele Check OSD PHR Check Begin Clear Controls Ordering Alleles Count x multi Review Checks Standard Checks CODIS QC QC Review Clear uL amus onau we D mor NENNT 1 jg cstiro pas1ase Toi _ _Dasssa9_ 1D_2_GH_1 0ng_R1 1_V1 1_009_1 9 11 12 Cena Due man manana me iens e sa ID 2 GH 10ng RLA V1 1 005 1 9 11 12 20 21 26 ID 2 GH 10ng R19 Vl 2 003 1 9 11 12 10 10 151 15 141415 93 93 9 12 ID 3 EGJ 20ng R1 1 2 V1 1 006 1 12 13 14 15 11 12 13 14 16 17 18 8 9 10 12 02 31 es 0 910 11 12 ID 3 EG 1 3 00 52 34 VLI O10 i 8 33 15 1 12
107. bo V B CSF1PO 10 11 12 13 a0 11 12 13 dd Combo FIGURE 7 55 Adding a combination to the Mixture Frequency Page Unrestricted RMP jUnrestricted RMP any 0351358 15 16 17 dd Combo v isi At the first allele click the arrow next to Add Combo box to bring down the available allele combination drop down list Select the appropriate combination and ArmedXpert will automatically fill in the calculations for that allele combination The drop down list gives you all possible combinations as well as various RMP Random Match Probability and 2p options as well as a remove locus and add comment option Note If a RMP or 2p option is chosen no other combinations can be added for that locus When completed the Add Combo box will appear in the next column Add all combinations that are necessary to perform the calculation Continue this process for each locus listed 101 Tab Five Interpretation ARMEDXPERT USER S MANUAL b Note The Sum of column will change with each added combination M 4 Frequencies Calculations Diak in FIGURE 7 56 An Example of different choices made in an RMP report n A72n RMP XX0156 3 99XX999901 15 2F3 Shirt Vict 06 06 20 E01 15 y XX0156 3 99XX9999Q1 15 2F3 Shirt Vict 06 06 20 E01 Locus D851179 12 13 a i a2 aw 13 Any 12 13 add Com
108. bo v 0 2709 0 2058 0 2279 D21511 28 29 30 28 29 30 add combo 28 29 30 s 13 Cue Ix me CSF1PO 10 11 12 Add Combo 212 122 0351358 15 16 15 ae Add Combo 15 16 NA252 0 2656 To remove a combination place your mouse over the combination The combination will appear gray and will have a red line through it as shown below Double click on the box and it will be removed It can be added back at any time When either one of the RMP combos or the 2p combos are chosen the math used will appear in blue next to the combo when you have your mouse over the combo as shown below Click on any of the left of the FIGURE 7 57 Removal of Combination ethnicity and the math for that type will be shown i Add Combo YW Combo W Add Combo v 28 29 30 p q r 28 29 30 E Caucasian 0 1658 0 1811 0 2321 Black Hispanic FIGURE 7 58 Math shown 102 Tab Five Interpretation ARMEDXPERT USER S MANUAL You can also see the math calculations for all combinations by clicking on the calculations tab on the bottom of the page RMP XX72 2 99XX5678 Q1 2 F2 Vag Swab 06 07 14 D02 D j XX72 2 99XX5678 Q1 2 F2 Vag Swab 06 07 14 D02 25 2 11 13 0 03983382 0 01604284 0 04005232 2pr 2st 2vw p p 1 p Theta 2 29 30 2 2 30 30 2 2 30 2 32
109. bsection On the next page is a list of regular expressions These should only be changed if necessary This is an advanced user form and should only be changed by those who understand regular expressions 22 ArmedXpert Menu ARMEDXPERT Jmm regularexpressions A VA 5 Wb AB Y gt Start of line Start of string End of line End of string Word boundary Not word boundary Start of word End of word Character Classes bi 5 MS Md AD Mw xhh VOSKE Control character White space Not white space Digit Not digit Word Not word Hexadecimal character hh Octal character xxx POSIX Character Classes upper slower alpha alnum digit xdigit punct blank 5pace cntrl graph print word Assertions cc m tas 712 or l 15 rt PEJ 78 Upper case letters Lower case letters All letters Digits and letters Digits Hexadecimal digits Punctuation Space and tab Blank characters Control characters Printed characters Printed characters and spaces Digits letters and underscore Lookahead assertion Negative lookahead Lookbehind assertion 4 Negative lookbehind Once only Subexpression Condition if then Condition if then else Comment Items marked should work in mast regular expression implementations USER S MANUAL A Za z0 9 d 1 2 VAd 1 2 9
110. c lin 236 Quadrilion 1 8 Million 16 9 Billion 5 45 Trillion 372 Trillion Database Size 1 Theta 0 01 Sources V Unrelated Y Full Siblings V Parents amp Offspring V Half Siblings Uncles Nephews First Cousins FIGURE 7 45 Bottom Portion of the Single Source Calculation Page 95 Tab Five Interpretation Al ARMEDXPERT USER S MANUAL The second type of frequency calculations is a Likelihood Ratio calculation It is used to calculate likelihood ratios for mixture samples obtain the Likelihood Ratio Calculations click on the Likelihood Ratio Button The Select Pick via mouse window will appear Select the sample you wish to perform the calculations on with your mouse ot click on the V arrow and select from the drop down list FIGURE 7 46 Select Pick via Mouse Window All loci and their corresponding alleles are imported into the page and Armed Xpert will automatically perform the calculations The combined likelihood ratio for each ethnicity is listed under the Likelihood column The prosecution s results are listed under the C1 column and the defense s results are listed under the C2 column Likelihood Ratio XX0156 1 99XX999901 15 2F1 Shirt Vict 06 06 20 D01 c3 s 2 amp 8 XX0156 1 99XX9999Q1 15 2F1 Shirt Vict 06 06 20 D01 e Locus Allele 1 a Allele 2 b Allele 3 c Allele 4 d Likelihood D851179 12 13 Eee EE n PO o 12 13 1 12 13 0 3393 0 234934
111. d 82 Tab Five Interpretation ARMEDXPERT USER S MANUAL The mixture interpretation tool also has a feature to removes alleles that are below the mPH setting If you click the box next to Ignore alleles below mPH a check mark will appear in the box Click on it again to remove the check mark and disable the feature Once checked no alleles below the prescribed mPH s will be considered in the mixture combinations and show as grayed out As shown in the example below Allele 9 3 has a value of 81 which is below the 100 setting for mPH Allele 9 3 has been grayed out and all combinations including Allele 9 3 are excluded from the possible mathematical options shown in the mixture interpretation results PF ICI CI CIIM Co owest Locus THU 4 lt E Profile 03 n a Profile 04 n a Alleles 6 7 8 9 3 3 Profile 05 n a RFUs 204 241 296 2716 81 BPs 0 0 0 0 0 mPH 100 Ignore alleles below mPH mP 0 00 4b 4b Lock locus on report 100 x Appl Globally Apply Stutter Profile 03 0 05 Mixture Information 12 All combinations have PHr gt 0 MPh gt 100 mP gt 0 For a 3 contributor 4 allele mixture of types AA amp AB amp CD 12 1 2 combination s F 8 9 phr 0 11 p 0 87 6 phr2 0 43 p 0 10 6 p 0 03 t J AAA m A eR AR AN BR ATAA a Rin ANANA FIGURE 7 17 Remove Alleles below mPH Feature Any combi
112. e Value column across from any of the rows in the Template Report Window Type in or copy the appropriate name from the sample table that you want to use Fill in the rest of the rows respectively Click Ok to generate the report Template Report C Documents and Settings KPICS SpermFinder My Documents Custom Report Template xlsx Potential issues Issue Steps Detail Template variables Name Value Item1 Name Victim ltem2 Name Unknown ltem3 Name Suspect Item4 Name Item5 Name Item Mixture 1 1 10 10 04 Mix ltem2 Mixture M F 1 100 10 10 04 2 Mix Mixture_M_F_Neat_0 10 10 04 Mix ltem4 Item5 Report evaluation errors eno Template evaluation errors select an item to activate the cell Error Cell Error Test Reevaluate Issues Ok Chose FIGURE 8 24 Template Report Window filled in The right box on the Template Report Window displays the errors Since Items 4 amp 5 were not used there is an error for each empty cell nplate Report Documents and Settings KPICS SpermFinder Desktop BRITTNEY Custom Reports Guide Custom Report Template xls tential issues ssue Steps Detail nplate variables lame Value eml Name Victim em2 Name Unknown em3 Name Suspect em4 Name emS Name eml Mixture 1 1 10 10 04 Mix em2 Mixture M F 1 100 10 10 04 2 Mix em3 Mixture M F Neat 10 10 04 Mix em4 ems Report evaluation errors ego Template evaluation errors
113. eS eas ee ee ee ee ee ERR eee eee eee ES ee ee ee 12 13 28 29 30 9 10 10 11 12 15 16 6 9 3 8 11 12 9 12 13 19 20 24 25 13 14 14 2 18 2 15 17 18 19 8 11 14 15 17 XY 9 12 22 22 2 24 2t 12 29 31 912 910 14 793 1214 9 12 17520 1315 1416 81 1618 XY 1 13 19 23 22 26 22 FIGURE 3 14 Column widths are changed to fit just the Sample amounts 4 Tab One Views ARMEDXPERT USER S MANUAL Zoom The Zoom section allows you to change to size the page 1s displayed in Click the Zoom button to bring up the Zoom window which allows you to change to a specific size Click 100 to change it back to original size A Zoom 100 Zoom FIGURE 3 15 Zoom Section lype in user defined percentage Ok Cancel FIGURE 3 16 Zoom Window 44 Tab One Views ARMEDXPERT USER S MANUAL Show Hide The Show Hide section allows headings and clipped data to either be shown or hidden The Headings option is for viewing the headings for each column You can change the size of the column to a user defined width by displaying the headers and using your mouse to change the size of a specific column The Indicate clipped data option outlines in red all cells that are not shown completely so you know there is more information in that cell If a check mark is in the box next to either option it means headings and or clipped data w
114. ected release the Ctrl button The reference s alleles will appear in green at each locus as shown in figure 7 50 on the next page Numerator ResetKnowns 1Px O 2 1 Set Pick viamouse 0167 95 9999K1 11 Blood Vict 06 06 20 G02 Denominator Reset Unknowns FIGURE 7 49 Bottom of Screen of the Likelihood Ratio Page The Reset Knowns button resets all unknowns red back to known green for either the Numerator or Denominator for either the Numerator or Denominator depending on which is chosen The Reset Unknowns resets all knowns green to unknown red for either the Numerator or Denominator depending on which is chosen 97 Tab Five Interpretation ARMEDXPERT USER S MANUAL Double click on any allele to change from Green Known to Red unknown or vice versa All calculations will automatically recalculate with all changes done to the page At the bottom of the page are the calculations by ethnicity for the entire profile The calculations are shown in both exponential and alphanumeric form An example of the bottom of a Likelihood report can be seen in Figure 7 48 on the previous page Likelihood Ratio XX0156 1 99XX999901 15 2F1 Shirt Vict 06 06 20 D01 XX0156 1 99XX9999Q1 15 2F1 Shirt Vict 06 06 20 D01 Locus Allele 1 a Allele 2 b Allele 3 c Allele 4 d D851179 p 42 0 319 12 23 5 021511 O
115. edXpert is a complete case management DNA analysis software It allows users to perform Mixture Deconvolution for two or three contributors with the Mixture Interpretation Tool which considers all possible combinations at each locus using lab defined thresholds It automatically generates statistics such as CPE CPI RMP and Likelihood ratio It allows the user to perform quality control checks perform matching between evidence samples and references check for potential contamination with staff profiles and run a number of reports Any page can be saved viewed or printed ArmedXpett consists of six tabs and an ArmedXpert menu The ArmedXpert Menu is used to set default options and perform basic functions such as importing exporting and printing The tabs are used to navigate through the different functions of Armed Xpert Chapters 2 through 8 go through each of these in detail x g ArmedXpert views Data QC Checks Match amp Comparison Interpretation Reporting E o FIGURE 1 1 ArmedXpert Tabs i Armedxpert Options Exit Armedxpert KT FIGURE 1 2 ArmedXpert Menu 1 Introduction ARMEDXPERT USER S MANUAL ArmedXpert Specifications Imports ABI Genemapper ID or ID X Genemappet or Data Files GeneScan Tables Imports OSIRIS oer projects Excel CSV or XML formats Passwotd Protected with User roles in Microsoft SQL 32bit or Database 64bit Easily manage multiple databases Comb
116. eft hand side of the section is to set up default names Add a check mark next to each item that you would like to appear in the name The Preview section will show you an example of what your profile name will look like The text can be changed to any text that you wish Profile is shown as an example Auto number will just add another number to last number used during the time the software is opened The numbers will start at 01 and proceed up from there The Date and Time field add the current date or time to the profile name at the time the mixture interpretation window was opened The Sample Name will add the sample used for the mixture interpretation to the profile name ee Oe eer Profile naming scheme J Text Profile Custom Naming Auto number Sample Name 1 Date 2 Time Preview Profile 01 Custom Naming 1 Victim Suspect n2 FIGURE 2 15 Profile naming scheme Window Elimination Profile 38 9 16 Profile 39 12 14 Profile 40 11 13 ictim 9 15 Elimination 12 14 Suspect 11 13 FIGURE 2 16 Examples of what the Profiles look like in the Mixture Interpretation Window The right hand side is for custom naming To enable Custom Naming place a check mark in the box next to Custom Naming and turn off all check marks on the left hand side Enter a name in each profile box These profile names will appear each time the mixture interpretation window is opened The Swap 3P order
117. eport It allows you to create a template in Excel and then incorporate data from ArmedXpert into that customized template There is a specific guide on the Armed Xpert com website to explain how to create a template in Excel To open the Template report first make sure the sample table that you want to use for the report is open in ArmedXpertt Click on the Template Report button E Views Data QC Checks Match amp Comparison Interpretation Reporting c Wm a 4 D ay C D Total Samples CMF PHR 1 Template User Form Data Comparison Repor Defined Reports FIGURE 8 22 Template Report Button The Select the excel workbook to use as a template for the report Window appears Click on the previously saved custom spreadsheet and click open The Template Report Window will appear with the cell names you labeled on the custom spreadsheet X Template Report 1 sg 58 C Documents and Settings KPICS SpermFinder My DocumentsNsCustom Report Template xlsx Potentialissues ers Issue Steps Detail Reevaluate Issues Template variables Template evaluation errors select an item to activate the cell Name Value Error Cell Error Text Item Name Item2 Name ltem3 Name ltem4 Name ltem5 Name Item Item2 Item3 Item4 Item5 Report evaluation errors k Close FIGURE 8 23 Template Report Window 118 Tab Six Reporting ARMEDXPERT USER S MANUAL Double click on the cell in th
118. equencies Frequency Options Data Single source frequency calculation options int erpretatiar Quality Control Database Size 1 Reporting J Use theta Admin Console RMP calculation options J Use theta Include Locus Details in Report General frequency options No significant digits 4 V Prompt to save on window close No significant digits English 2 W Prompt to save on application close Ok Cancel FIGURE 2 29 Frequency Options window 20 ArmedXpert Menu ARMEDXPERT USER S MANUAL The fourth main section is the Quality Control section This section has two subsections Options and Ladder and Controls The Quality Control settings are used during the Quality Control Checks The Quality Control Checks are discussed in Chapter 5 The first subsection Options contains the settings that are used during certain RFU and CODIS Quality Control Checks The top section allows you to set the RFU quality control options You can set the Low scale data figure and the Off scale data settings by entering the required amount in each box The bottom section allows you to set the CODIS quality control options You can set the OSD off scale data and the PHR Imbalance settings by entering the required amounts in each box ArmedXpert Options o x General oO ptions _ Ladders and Controls Data RFU quality control options Interpretation Low scale data Juality Lontro Reporting Off scale dat
119. f the screen you can select the relationship types to include in your calculations including Unrelated Full Siblings Parents and Offsprings Half Siblings Uncles and Nephews and First Cousins Unrelated by default is checked The system will automatically calculate the frequency for each locus and for each selected relationship type by ethnicity At the bottom of the page are the calculations by ethnicity for the entire profile The calculations are shown in both exponential and alphanumeric form Examples of the Frequency Single Source Page are shown in Figures 7 43 and 7 44 on the following page J Unrelated Full Siblings Parents amp Offspring Half Siblings Uncles Nephews First Cousins FIGURE 7 43 Relationship Type Selections 94 Tab Five Interpretation ARMEDXPERT USER S MANUAL Frequency Single Source XX0167 99XX9999K1 11 Blood Vict 06 06 20 G02 XX0167 99XX9999K1 11 Blood Vict 06 06 20 G02 Frequency Half Sibs Frequency Uncles First Cousins Neph s Frequency Parents and Offspring Frequency Frequency Unrelated Full Siblings Locus Locus Profile Allele 1 Allele 2 085117 1213 12 13 0 17050922 15 1 2930 29 30 91811 0 2321 0 2906 0 2906 0 086509876 0 41641209 0 2906 0 18752418 0 13598627 0 3238 0 3238 0 107035976 0 43811161 0 3238 0 21432322 0 15958483 0 3062 0 3062 0 095882856 0 42653961 0 3062 0 19997922 0 14686883 0 16495574 0 435
120. g up a drop down list of available connection Select the appropriate connection type Connection Name Local PE Connection Type SQL Server Connection String ape erver Remoting FIGURE 1 6 Changing Connection Type Type in an appropriate Connection String The Connection String for a SQLite connection can be changed to any user defined name Just highlight the current name shown and enter the new name The current name shown in the example below is ArmedXpert The db file is created in the same folder as the Armed Xpert application Login c 5 x Login Connection Properties 4 b Connection Name Local PC z Connection Type SQLite onnection String data sourcez rnedxpert db Save this Configuration Delete this Configuration Ok Cancel Options lt lt FIGURE 1 7 Connection Properties Window 4 Introduction ARMEDXPERT USER S MANUAL ArmedXpert allows you to create multiply databases You can share a database with another computer by copying the database from your computer to the other computer s ArmedXpert application folder Lb Note When copying a database onto your computer from another s make sure you do not already have a db file with the same name If so rename one of the db files so that it is not overwritten Once finished click on the Save this Configuration button If the Save this Configuration button is
121. ghlighted will move to the right hand box As shown below in Figure 4 13 the word Vict was added to the Selection Filter box and all samples that include the word Vict are highlighted The Ignore Case option allows all forms of the filter to be highlighted regardless of lower or upper case The Also select tables option allows tables to also be highlighted In the example shown below the Also select table option is not checked so even though the table contains the word Vict it is not highlighted Datasource Commit o amp amp Select items to commit to the datasource DEMO 2 Component 4 Vict_Mix_Stains_Analyst tet Ladder Identifiler 06 06 20 F03 E Ladder Identifiler 06 06 20 403 Ladder Identifiler 06 06 20 401 240156 1 9999990 1 15 2F1 Shirt Vict 06 06 20 220156 3 9999990 1 15 2F3 Shirt Vict 06 06 20 E 240159 1 9999990 1 15 8F1 Shirt Vict 06 06 20 F 220161 1 GA003F1 06 06 20 H01 0162 1 Reag BlankF1 06 06 20 B02 0162 2 Reag BlankF2 06 06 20 C02 20164 99499990 1 2 LFS Vict 06 06 20 D02 260165 04004 QA 06 06 20 E02 lt 0166 Reag Blank 06 06 20 F02 X157 39933331 1 Blood Vict 06 06 20 G02 m m s FEE ma Mm mm m amm ii 9 V Ignore Case Also select tables nit items as FIGURE 4 13 Datasource Commit Table window with filter being used The table name and Type kit will be filled in you can change these if wanted Once finished choosing samples and or tab
122. he columns the user defined width when changing the views The column width remains the same no matter what 1s being viewed Click on the circle to the left of the desired choice Samples I User Fit FIGURE 3 12 Fit Section Alleles 2 Samples A Headings 5 J Controls O Base Pairs All 3 M Indicate clipped data E Zoom 10095 Organize C Samples _ RFUs _ User View Ft Zoom ShowlHide Windows DEMO 2 Component 4 Vict Mix Stains Analyst txt D851179 8 9 10 11 12 13 14 15 16 17 18 19 FALSE 24 25 26 27 28 28 2 29 29 2 30 30 2 31 31 2 32 32 2 33 33 2 34 34 2 35 35 2 36 37 38 6 7 8 9 10 11 12 8 9 10 11 12 13 14 15 16 17 18 19 24 24 2 25 26 27 28 28 2 29 29 2 30 30 2 31 31 2 32 32 2 33 33 2 34 34 2 35 35 2 36 37 38 6 7 8 9 10 11 12 8 9 10 11 12 13 14 15 16 17 18 19 24 24 2 25 26 27 28 28 2 29 29 2 30 30 2 31 31 2 32 32 2 33 33 2 34 34 2 35 35 2 36 37 38 6 7 8 9 10 11 12 13 28 9 10 12 13 28 29 30 9 10 12 13 28 29 30 9 10 1 12 13 28 29 30 9 10 11 12 12 13 28 29 30 9 10 12 29 31 9 12 FIGURE 3 13 Column widths are widen to show All e All 2 Alleles Samples x 2 Headings gt J Controls C_J Base Pairs J All 4 indicate clipped dat
123. hed with adding click the Plot button X OSIRIS Plot c Add OSIRIS plt files in the order that you want them to appear in the final report Double click a listed plt file to edit the name that appears on the report Plot Print Up Down Print Options Y xis Scale Axis Visibility Plot Layout Fit per channel Top most only 1 locus per page Fit per locus Every plot Asis Custom Min Max FIGURE 2 49 OSIRIS Plot Window 33 ArmedXpert Menu ARMEDXPERT USER S MANUAL Export The Export command allows you to export your Page Data Frequency analysis or Mixture interpretation if you wish to save it and resume it later You also have an option to save any page in a workbook friendly format so that you can open it in Excel or as an Image Finally you have the option to export a sample using a user created plugin When you click on Export the options below will appear They will be shown in color once you have selected a table on the screen However if you do not they will be shown gray as seen in below To save a page data click on Page Data A Save As Window will appear You can name the page anything you wish The default folder to save a page data is in the Page Data folder located in ArmedXpert Folder However you can change the folder to save it to Once you have chosen the name and folder click the Save button Page Data Save in the page data format
124. hown all Loci with Restricted RMP click on the box next to Apply Restricted Globally If you do not all the other loci will have the Modified RMP applied You can also choose to have the Homozygote Threshold HT to be restricted globally by clicking on the box to left of Restrict HT Globally Make sure the Contributor number is correct Finally click the Open Frequency Report button A mixture frequency report will then open to aide you with making your calls X RMP E RMP Method Modified RMP Modified RMP itd E Apply Restricted Globally Forced mAMP Restrict HT Globally Restricted RMF Contributors 2 v Frequency Open Report Clear Ti FIGURE 7 38 Mixture Interpretation Frequency Window 92 Tab Five Interpretation ARMEDXPERT USER S MANUAL To open an OSIRIS Plot File choose OSIRIS Plot File from the list You can change from a full e gram single plot or multiple plots by choosing each option in the drop down list once the OSIRIS Plot File is open x c 5 E EBDEBEDB V Analyzed Raw Ladder MinRFU 0 100 V Markers ILS Labels t ne ern nr i nny FIGURE 7 39 Ostis Plot File To open a Virtual Electropherogram choose Virtual Electropherogram from the list You can change from a full e gram single plot or multiple plots by choosing each option in the drop down list once the virtual Hlectropherogram is open X ca 5
125. hown in Figure 7 24 below You can click on the box under the allele you would like to select for each Profile A check mark will show on all selected alleles By reclicking on a box that contains a checkmark it will be removed If you would like to call an Any or an Obligate right click on the box under the appropriate allele and across from the right profile a drop down list will appear as seen in Figure 7 25 below You can then click on the appropriate choice You can also delete an allele using the drop down list Once chosen you can move to a different locus using the lt or gt arrows next to the locus to move forward ot backward or click on the V arrow on the locus box to move to a specific locus You can close this window by clicking on the X in the upper right hand corner 85 Tab Five Interpretation ARMEDXPERT USER S MANUAL cep mPH SU lt HT 125 mP ock locus Binet call repor cai Add Comment A Mixture Interpretation of XX0156 1 99XX999901 15 2F1 D851179 2 e Reset 12 13 1580 2345 Profile 1 J J 4 Profile 2 FIGURE 7 24 Calls made from Popout Calls Window D851179 2 bel a Reset 12 13 1580 2345 Profile 1 Profile 2 A Obligate T5 N Remove Allele FIGURE 7 25 Choosing Any in the Popout Calls Window Note Once you make a call with any of the methods it will be recorded in all the methods Therefore you can change meth
126. hted yellow Ladder Identifiler 06 06 20 F03 EEA AC AETI CITA AEE EE E ER RE SECRET Cee een ee Ladder Identifiler 06 06 20 A03 8 9 10 24 24 2 6 7 8 6 7 8 9 12 13 4 5 8 9 10 5 89 15 1617 9 10 11 12 11 12 13 67 7 9 10 X Y 78 9 17 18 19 20 Ladder Identifiler 06 06 20 A01 9 10 Sn sns onse 1 5 n5 n 10 ses 15361 esos ass ez n310 Xv 2 29 s tea XX0156 1 99XX9999Q1 15 2F1 Shirt Vict 06 06 20 D01 xs peso 9 10 in 121 15 16 eai 8 11 1219 12 13129 20 2625 8 2 15 17 18 19 8 11 14 15 17 XY 9 12 22 222 2F3 Shirt Vict_06 06 20 01 o mu RISE 11 12 9 12 13 19 20 24 25 13 14 14 2 a9 6 11 14 15 37 Ba 2 eas faas o sao po ase esate fonz wlohe wahe m lenante 22 2 24 XX0161 1QA003F1 06 06 20 H01 28 211 asa 10 Tasis 6 amp 9 113 ma 1314 1417 amp n 12 22 26 XX0162 1 Reag BlankF1 06 06 20 B02 eee Ca pepe E er E XX0162 2 Reag BlankF2 06 06 20 CO2 Ee ae ee E a Ce eae ee ae ee E ES ne XX0164 99XX9999Q1 2 LFS Vict 06 06 20 D02 28 29 EES 10 11 12 15 16 69 3 8 11 12 9 12 13 19 20 24 25 13 14 14 2 18 2 15 17 18 19 8 11 14 15 17 X Y 9 12 22 22 2 24 25 XX0165 QA004 QA 06 06 20 E02 12 res zie sn mo Be smi 1618 xv an aem 10 14 7 peces eniin es eed sees scarce ud ee 15 16 6 93 812 1213
127. ill be shown If no check mark is shown headings and or clipped data will be hidden Headings Indicate clipped data Show Hide FIGURE 3 17 Show Hide Section TET Views l Data QCChecks Match amp Compo Interpretatio Reporting 5 Alleles Jg Samples R v i D Controls Base Pairs All a ES ES We Zoom 10099 Organize Samples RFUs O User View Fit Zoom Show Windows DEMO 2 Component 4 Vict Mix Stains Analyst txt MENO IEEE O LB Se ae PM N ol fF 2 Ladder Identifier 06 06 20 A01 8 9 10 FALSE 24 6 7 8 6 7 8 9 12 13 4 5 8 9 10 5 8 9 15 16 17 9 10 11 12 11 12 13 67 7 9 10 X Y 4 Ladder Identifiler 06 06 20 F03 8 9 10 24 242 67 8 6 7 8 9 12 13 4 5 89 10 5 8 9 15 16 17 9 10 11 12 11 12 13 6 7 7 9 10 XY 7 8 5 XX0153 99XX9999Q1 15 12F1 Shirt Vict 06 06 20 H02 13 28 9 10 1011 15 693 1 12 9 12 1925 14182 1518 11 1417 XY 91 FIGURE 3 18 Headings Shown EENEN Views Data QC Checks Match amp Con Allele e s S Samples 59 Controls _ Base Pairs All oe ao a Zoom 10 i C Samples C RFUs User View Zoom DEMO_I_2 Compone nt_4_Vict_Mix_Stains_Analyst txt Ladder Identifiler 06 06 20 A01 E 8 9
128. indow will appear All committed tables and individual samples will show up in the left hand side box based on whether a check mark is in the boxes left of Search Tables or Search Profiles The individual profiles are shown highlighted green below in Figure 4 17 and the tables are highlighted orange Click on the next to the Sample Table if you wish to select a specific sample from the sample table Click on the sample or the whole sample table you wish to commit click the gt button and your selection will be move to the Selected samples amp sources box on the right Once finished with your selection click the Load button The Data will load and open on its own table Datasource Load ca E EE les amp sources _ Selected samples amp sources LADDERSA amp NDCONTROLSCHECK TABLE C Documents and SettingsK PICS SpermFinder My Doct LaddersandLontra sCheck Y 28Mar1 2 xls xlsx SD041 o lt J Ignore Case Also select tables Search J Search Tables Search Profiles Delete Load FIGURE 4 17 Datasource Load Window If you would like to delete a sample table or a specific sample from a committed Datasource you do it from this window Move the table or sample you want to delete to the right side of the window as described above To have the individual profiles to show like the Staff Profile click on the box next to Search Profiles 57 Tab Two
129. ine tables quickly with advanced sorting Control Checks Allele Ordering Max Stutter Low Scale and Off Scale RFUs Allele formatting Allele count Check X Off Scale Data Peak Height Ratio Find Where Reference is Included Find Included to the Comparisons Reference Find Foreign to Reference Find Where Reference Mixture Interpretation Includes Foreign List Foreign Alleles Combine References and compare tables instantly Displays all possible combinations for 2 or 3 contributor scenarios Flags possible stochastic effects Allows for peak height ratio thresholds minimum RF Us minimum proportions and max stutter per locus Audit trail real time proportion charting and sort for possible DNA degradation Random Match Probability RMP Modified Restricted amp Unrestricted Likelihood Ratios Restricted and Unrestricted Statist CPE CPI RMNB and Single Source with relatedness All stats tatistics can be generated automatically saved and opened without manual typing There is no limit on number of population frequencies that can be stored Automated Sample vs Database results Total Data and CODIS Reports Disposition Forms Checks Samples and Statistics fit single page format CODIS n Common Message Format CMF v 1 0 v3 0 v3 1 and v3 2 Introduction ARMEDXPERT USER S MANUAL Signing into ArmedXpert When you start Armed Xpert the Login window will open Enter you
130. is made up of two sections The top section contains different Mixture Interpretation Window settings and defaults ArmedXpert Options o s Mixture Interpretation Quality Control Frequencies Frequency ptions Mixture interpretation settings nter aretati or Quality Control Default peak height ratio List proportions as dilutions Reporting Default minimum peak height mPH Admin Console Default homozygote threshold HT 125 Warm when specified contributors different than mixture Default minimum proporition mF 4 Prompt to save on window close Default stutter 100 a Prompt to save on application Sort loci by allele count close FIGURE 2 11 Mixture Interpretation settings You can set default values for the Peak Height ratio PHR minimum Peak Height mPH Homozygote Threshold HT and the minimum Proportion mP You can also set the default stutter percentage that 1s used To do this add the appropriate default values into the box right of each type Once set the mixture interpretation window will only show allele possibilities equal or greater than the value set For example if the minimum peak height mPH is set at 50 as shown below the Mixture Interpretation Window will only include allele possibilities equal to or greater than 50 mPH Note The mixture interpretations settings can be changed in the Mixture Interpretation Window for a specific sample or locus This does not
131. isconnect 58 Show Hide 45 single Source 94 Sort 59 Sort Sample 60 Stutter 82 Template Report 118 Total Data 108 View 7 36 39 View Call Report 88 Virtual Electropherogram 93 Zoom 44
132. ist below will appear Select the appropriate type of file you wish to import Once in Armed Xpert you can export the sample tables as Page Data You can then import it back into Armed Xpert using the Page Data option The method is designed to give users the ability to return to the original files or Tab delimited table files such as GMIDIdentifiler GMIDPowerplex 16 Profiler Plus and others It also allows you to load other table types such as previously exported page data Osiris Analysis Report and CODIS Index file Finally you can load other files such as Plugins previously exported frequency analysis calculations previously exported mixture interpretations and open working copies stored in the Page Data format F Export view b Print gt 0000000 Tab delimited table files GMIDIdentiFiler GMIDPowerplex16 GMIDProfilerCOfiler Profiler Plus GMIDSizeStd GMID filer GTProfilerCOfiler Other Other table types E g A Page Data Import samples that were previously exported as page data Osiris Analysis Report Import report generated by the Open Source Indep Review Interp System CODIS Index Import a CODIS Index file Other Files a Plugins Use a plugin to import samples Frequency Analysis Load a previously exported frequency analysis sheet to resume interpretation Mixture Interpretation Resume an exported mixture interpre
133. l for the unreferenced profiles Note The Auto call Reference feature is only auto populating the profile with the chosen reference It is not taking into account any calculations ot making any kind of interpretation The List Foreign w auto call option will list all alleles that are foreign to the reference on the View Call Report Click on this to enable it before you click on Auto call references button n amp Views Data QC Checks Match Comparison Interpretation Reporting a v V Highlight i 4 amp 3 amp wy Begin Mixture Singe Lkeihood Probab ky RMP Interpretation Source Ratio of Inclusion Mixture Interpretation Frequency Calculations Mixture Interpretation DDA Interpretation Setup Pick vi mouse 2400155 3 999999111 5 2F 3 Shirt Viet 06 06 20 EOT Operations i Locus D851173 2 r Profle 08 12 13 P Avg 0 46 r Mehestto Profle09 n a P Avg 0 54 Alleles 12 13 alleles l RFUs 602 1632 below mPH OR beco1e7 s3 lt 9999K1 1 1 Blooe Remove Reference Dp 8 1 1442 i pe Look bo e f Ps n s Select a reference to apply Apply Reference Apply Fieference c z 1 Select a reference to apply Age d AppiyStute Add Profle s Select a reference to apply Apply Reference Select areterence to apply Apply Reference Aulo call references k iy Ust foreign wel suto call
134. les and all info is filled in correctly click the Commit button When finished with the window click the Done button to close the window Commit items as Table Individual Profiles 4 Table Name DEMO_ _2 Component_4_Vict_Mix_Stains_Analyst txt Type kit Identifiler 5 Commit Done FIGURE 4 14 Datasource Commit Table bottom portion of window 55 Tab Two Data ARMEDXPERT USER S MANUAL You can commit individual profiles such as staff profiles as shown in Figure 4 15 below QA profiles and SRM profiles Click on the appropriate sample table so it is open and active on the screen Then click the Commit Sample to Data Source button All the individual samples will show on the right side of the window our staff profile example is shown as alphanumeric as opposed to names Click on the sample you would like to commit and click the gt button to move it to the left side of the window or click the gt gt button and all the samples will move to the left side of the window X AImetdAr Views Data QCChecks Match amp Comparison Interpretation Reporting 2an 9 amp 882 New Edit Change Combine Commit Samples Load Samples Connect Disconnect Sort Sample Sample Kit Sources to Data Source From Data Source Server Server Samples Data Source Sort C Program Files NicheVision Inc Arme dX pert dat
135. licking on the Pick via mouse button and selecting the appropriate sample with your mouse or clicking the W arrow and selecting the appropriate sample from the drop down list of all available samples Setup vi mouse y FIGURE 7 3 Select Pick via mouse section 76 Tab Five Interpretation ARMEDXPERT USER S MANUAL Note Once you select a sample it cannot be changed If you select the incorrect sample close the mixture interpretation window and open a new one Once the sample is selected the information will fill into the Mixture Interpretation Window The selected sample and current locus will be highlighted on the sample table page If you prefer for the selected sample to not be highlighted uncheck the box next to Highlight in Mixture Interpretation Section as shown below in figure 7 4 Interpretation Mixture Interpretation DDA Interpretation Setup Pick via mouse 1 990 lt 999901 15 2F1 Shirt Vict 06 06 20 D01 Y Locus D851179 2 gt Major 19 13 P Avg 0 69 2 2 green 5 Minor n a P Avg 0 31 1 0 mPH 75 aeui BIS ij Ignore Alleles RFUs 1580 2345 Below mPH BPs 140 144 Lock locus mP 0 00 nes AAS 12 13 phr 0 64 p 0 98 12 p 0 02 49 0 1 12 13 phr 1 00 p 0 81 13 p 0 19 4 3 1 OT TYDES A amp DD 111 Jer p 0 40 Fi or c IDI itor 2 allele mixture of ty oes AB amp AB 1 1 cc 12 13 phr 0
136. llows you to assign allele exclusions to what is imported into ArmedXpert from your sample data Any artifact that is listed and has a check mark will not be imported into ArmedXpert There are a few default items already assigned in Armed Xpett You can add new exclusions by clicking the Add Exclusion button This will allow you fill in an exclusion title first and then an artifact name n ArmedX pert Options c General Sample source import options Allele exclusions Select All Exclusion Title Artifact Interpretation Quality Control Pull up pu Minus ma Spike sp Stutter st C inc inc C False FALSE Reporting Admin Console Ok Cancel FIGURE 2 9 Data options You can turn off an exclusion listed by clicking on the box next to each title and removing the check mark Allele exclusions can be deleted from the list by clicking on the exclusion so it is highlighted then clicking on the Delete Exclusion button A confirmation message will appear to confirm that you would like to delete it Click Yes to complete the deletion Are you sure you want to delete this filter mr No FIGURE 2 10 Delete Confirmation Window 11 ArmedXpert Menu ARMEDXPERT USER S MANUAL The third main section is Interpretation This section has four subsections Mixture Interpretation Quality Control Frequencies and Frequency Options The first subsection Mixture Interpretation
137. low scale 30 243 is below scale Done FIGURE 5 17 Example of QC Review Window different Check 68 Tab Three QC Checks ARMEDXPERT USER S MANUAL Tab Four Match amp Comparison he Match amp Compatison tab is used to perform a match of a reference sample to other samples on your sample table or to compare one table to another table There are two sections Samples and Sources The sample section allows you to match and compare one or more samples against a sample table It also allows you to match and compate a sample against a profile The source section allows you to compare one table against another E ArmedXpert v3 0 7 91 Views Data QC Checks Match amp Comparison Interpretation Reporting wo T 3 0 e Table Reference A m Set Find Where Find Included in Find Foreign Find Where Reference Match amp Clear B Table Reference B gt Compare Reference Reference is Included the Reference toReference Includes Foreign Compare Profiles Match Tables Samples Sources FIGURE 6 1 March amp Comparison Tab Samples The Samples section is used to compare reference sample s to other samples on any opened sample table To start matching you must first set a reference or multiple references You can set any sample or samples as teference s Click on the Set Reference button The select pick via mouse window will appear as seen below in
138. matches are highlighted in a different color based on type of match There is a key on the bottom of the page In addition shown highlighted in blue on the bottom of the page is the selected reference unless the List match amp compare reference at top is selected as an option If selected the reference s is displayed at the top of the page instead of the bottom To the right of the samples are total columns These columns give a total number of each type of matches You can also do automatic sorts for these columns by enabling the correct default sort These options are selected by going to the ArmedXpert options menu as explained in Chapter 2 DEMO 2 Component 4 Vict Mix Stains Analyst txt brsezo CSFIPO DISTISB THOL D15317 p168539 251338 vwa 018551 Amel DSSIB FGA fed 910 10 11 15 693 1102 022 1925 14182 1518 HM 1417 XY 9 1 2225 0168 99499992 Blood Susp 06 06 20 H02 11 Re XX0153 99XX9999Q1 15 12F1 Shirt Vict 06 06 20 02 XX0156 1 99XX9999Q1 15 2F1 Shirt Vict 06 06 20 D01 FIGURE 6 4 Reference displayed at the top of the page option Note There are two additional quick ways to choose your reference You can also click on the appropriate sample that you want to set as a reference and hit the F1 key This will automatically highlight the sample you are on and start the Find Where Reference is Included comparison You can also just select with your mouse the
139. medXpert Menu Any character except new line Xn aorb Group 4 Passive Group Range a or b or c Not a or b orc Letter between a and Upper case letter between A and Q Digit between O and 7 nth group subpattern Note Ranges are inclusive Pattern Modifiers Global match Case insensitive Multiple lines Treat string as single line Allow comments and white space in pattern Evaluate replacement Ungreedy pattern Metacharacters must be escaped L Available free from AddcedBytes com ARMEDXPERT USER S MANUAL The bottom section allows you to change the table to use when checking controls If you would like to change the default table first change the type of table you are uploading from the drop down list to the left of the select table box Then click on the Select Table button UN 41i Select the table to use when checking controls Identifiler Select Table FIGURE 2 33 Bottom of the Ladder and controls option Window Click on the appropriate table on the left and click on the gt button The table will move to the box on the right Click on the Load button to load the table Note The table has to be committed to the database to appear in this window If you have not committed the table you would like to use go to the instruction in chapter 4 of this manual for instructions on how to Commit Samples to Data Source Datasource Load oS
140. mixture information area will only show combinations that are equal to or greater than the settings and include the reference profiles if applied 1 For a 2 contributor 2 allele mixture of types AA amp AB 2 2 combination s 12 13 phr 0 60 p 0 96 Ref 1 12 12 p 0 04 12 13 phr 1 00 p 0 81 Ref 1 13 13 p 0 19 2 For a 2 contributor 2 allele mixture of types AB amp AB 1 1 combination s 12 13 phr 0 67 Ref 1 12 13 phr 0 67 Ref 1 FIGURE 7 13 Mixture Information Section FIGURE 7 14 Mixture Information Section 81 Tab Five Interpretation ARMEDXPERT USER S MANUAL Apply Stutter The Mixture Interpretation tool also includes features to apply stutter You can either apply stutter to an individual locus or apply it globally to all loci To apply stutter to just the individual locus click on the Apply Stutter button If you wish to apply stutter to all loci click on the box next to Apply Globally As shown in Figures 7 15 and 7 16 the RFU amount under locus 12 was refigured from 1580 to 1392 once stutter was considered and the amount is now highlighted in green to indicate stutter was applied This also changed the calculations in the Mixture Information section If the Apply Globally option is checked it will apply stutter to all applicable alleles at each locus 12 13 1580 2345 Appl Globally Apply Stutter Add Frofile 0 08 All combinations ha
141. mp 9 15 1617 9 191 12 1 1213 67 7 9 1 8 9 10 24 24 2 6 7 8 6 7 8 9 12 13 4 5 8 9 10 5 8 9 15 16 17 9 10 11 12 11 12 13 6 7 7 9 1 0 H02 13 13 28 28 9 10 10 11 15 15 6 93 11 12 9 12 1925 14182 15 18 11 12 141 1 12 13 28 29 30 9 10 10 11 12 15 16 6 9 3 8 11 12 9 12 13 19 20 24 25 13 14 14 2 18215 17 18 19 8 11 14 15 1 12 13 28 29 30 9 10 110 11 12 15 16 6 9 3 8 11 12 9 12 13 19 20 24 25 13 14 14 2 18215 17 18 19 8 11 14 15 F01 12 13 28 29 30 9 10 10 11 12 15 16 6 9 3 8 11 12 9 12 13 19 20 24 25 13 14 14 2 182 15 17 18 19 8 11 14 15 13 14 28 311 11 12 10 10 14 18 66 89 11 13 1724 1314 1417 181 121 eur ee SS SS 12 13 28 29 30 9 10 10 11 12 15 16 6 9 3 8 11 12 9 12 13 19 20 24 25 13 14 14 2 18 2 15 17 18 19 8 11 14 15 12 12 29 31 9 12 9 10 1414 7 931 1214 9 12 1720 1315 1416 811 161 rubus E 1223 29 90 1 10 401 10 2 15 46 16 83 8 12 12 13 20 28 1142 amis eu 14 1 28 28 9 10 10 11 15 15 6 93 11 12 9 12 1925 14182 15 18 11 11 141 11 12 11 11 14 16 93 12 13 12 13 182 1215 1518 8 8 13 1 EUCH ERES ENG 30 30 10 111 10 12 14 15 8 9 3 11 11 11 12
142. mples To Data Source 54 Data Allele Exclusions 1 1 Edit Sample 51 Export 7 34 Frequency Analysis 35 Mixture Interpretation 35 Page Data 34 Fit 43 Frequencies Options 17 20 Add Frequencies 18 Highest To Lowest 13 87 Import 7 31 Frequency Analysis 32 Mixture Interpretation 32 OSIRIS Plot File 33 Page Data 31 Tab Delimited Table Files 31 Likelihood Ratio 96 Load Samples From Data Source 57 Delete 57 Login 3 Match amp Compare 9 72 73 Match And Comparison Find Foreign To Reference 71 Find Included In The Reference 71 Find Where Reference Includes Foreign 72 Find Where Reference Is Included 71 Profiles 72 Settings 9 Sources 74 Mixture Interpretation Save Options 13 Sort Loci By Allele Count 13 Mixture Interpretation Window 75 76 Apply Reference S 78 Making Calls 84 Navigation 87 123 Select Number Of Contributors 78 Settings 80 Shortcut 75 New Sample 50 Organize 46 PHR Report 113 Plug Ins 10 Popout Calls 85 Print 7 37 Probability Of Inclusion 99 Profile Naming 14 Proportion Average 88 QC Checks Allele Count 65 Check Allele Ordering 63 Check Controls 62 Check Multi 67 Check X 66 CODIS Alleles 65 CODIS Quality Control Checks 64 OSD 66 PHR 67 QC Review 68 Rfus 63 Standard Quality Control Checks 61 Stutter 63 Quality Control Ladder And Controls 22 Options 15 21 Reporting Option 25 RMP 92 101 Samples Comparison 109 Server Connect Or D
143. n The Mixture Interpretation Window will appear as shown in Figure 7 2 below Shortcut You can also open the Mixture Interpretation window by holding down the alt button and clicking on any of the loci or the sample name for the sample you wish to interpret The Mixture Interpretation window for that select sample at that locus will open If you are on the sample name the first locus 1s displayed This enables you to skip the select sample step below 75 Tab Five Interpretation ARMEDXPERT USER S MANUAL Note Do not close out of the Mixture Interpretation unless you have exported saved or printed the reports you require to document your interpretation If not once you close out of the Mixture Interpretation tool all information will be lost Mixture Interpretation DDA Interpretation c3 E Setup UE a Contributor 2 Y Pick via mouse M Operations References Locus gen os Highestto PH 0 50 lowest Allel mPH 75 HT 300 eles Ignore alleles 000 PFLIs below mPH Ils BPs Lock locus Papou View call report on report calls 1 Add Comment Apply ENR Globally stutte No sample selected 0 0 Mixture Information ie S FIGURE 7 2 Mixture Interpretation Window Select Sample To perform mixture interpretations you must first select the sample you would like to interpret Select your sample by either c
144. nation that is below the homozygote threshold HT will be highlighted pink in the Mixture Information portion of the window Locus 0195433 4 O01 a na Highestto PHi O50 Sox b n ja lowest 8 mPH 75 Alleles 13 14 14 2 18 2 c5 Ignore alleles mP 0 00 RFUs 787 410 886 292 below mPH E BPs 117 36 121 33 123 24 139 47 e on report calls Add Comment Hh di no 160 78 410 886 292 Appl E Globally Apply Stutter Add Profile 0 13 Mixture Information 1274 All combinations have PHr gt 0 5 MPh gt 75 mP gt 0 or a 2 contributor 4 allele mixture of types AC amp BD 1 3 combination s 13 14 2 phr 0 89 p 0 70 14 18 2 phr2 0 71 p 0 30 2 3 1 FIGURE 7 18 Below HT highlight Feature 83 Tab Five Interpretation ARMEDXPERT USER S MANUAL Making Calls The Mixture Interpretation Window has three different ways to make profile calls Mixture Interpretation DDA Interpretation c3 E 23 Setup Pick via mouse XX0156 1 390 999901 15 2F1 Shirt Vict 06 06 20 D01 Operations 7 References Locus 085117312 lt gt Major 12 13 P Avg 0 69 2 2 ges Minor n a P Avg 0 31 1 0 mPH 75 HT 150 gt Alleles 12 13 7 Ignore Alleles RFUs 1580 2345 Below mPH BPs 140 144 Lock locus e o 100 4 Ea 5539 Appl M Globally Apply Stutter Add Profile 0 08 s are included 12 Ne
145. not clicked the connection configurations will be not used the next time you open the program It will use the last saved configuration Finally click the Ok button to connect to the server Save this Configuration Delete this Configuration FIGURE 1 8 Connection Properties Window Using the Demo Database in ArmedXpert ArmedXpert contains a demo database This database contains various Sample Tables that can be loaded to try out the various tools and features in ArmedXpert It also contains a Staff and QA Profile There are default settings controls and frequencies set up as well The demo database can be used just as you would any other database To access to the Demo Database follow the instructions above about changing the Database Under the Connection Name drop down list choose Sqlite Demo All the other required information for the Type and String will automatically be filled in Login c3 s 2s E Login Connection Properties 4 b Connection Name 5glite Demo Connection Type SQLite Connection String Data Source C Documents and Settings All Users Application Data NicheVision Forensics Armed lt pert data 4armedpertD emo db Save this Configuration Delete this Configuration Ok Cancel Options lt lt FIGURE 1 9 Connection Properties Window for Demo Database 5 Introduction ARMEDXPERT USER S MANUAL To access the Sample Table amp Pr
146. ns of the View tab View Fit Zoom ArmedX pert M Headi All e Alleles e Samples R E Leashes Controls _ Base Pairs All M Indicate clipped data pii Zoom 100 Organize Samples 5 ser View Fk Zoom ShowlHide Windows FIGURE 3 1 views Tab View The View section gives you the option of what type of data 1s displayed The left side of the view section allows you to choose between viewing Controls Samples or All Controls and Samples The right side allows you to choose whether Alleles Base Pairs or RFU s are shown Click on the circle to the left of the desired choice Examples of all different view combinations ate shown below e Alleles Controls _ Base Pairs C Samples RFUs View FIGURE 3 2 View Section 39 Tab One Views ARMEDXPERT USER S MANUAL all Alleles Samples X E r Controls Base Pairs O All A Vir Es Es Zoom 100 2 Samples C RFUs C2 User View JL Fe zem Headings 5 Indicate clipped data Organize Show Hide Windows DEMO 2 Component 4 Vict Mix Stains Analyst txt D135317 D165539 0251338 8 9 10 5 8 9 15 16 17 8 9 10 5 8 9 15 16 17 589 D851179 021511 D75820 CSF1PO 0351358 8 9 10 FALSE 24 6 7 8 6 7 amp 9 12 13 8 9 10 24 242 67 8 6 7 8
147. ocus that you do not want to add Click the Ok button to add the Loci 16 ArmedXpert Menu ARMEDXPERT USER S MANUAL DYS456 vV DYS383l DYS390 4 DYS389ll DYS458 518 4 DYS385 DYS333 Z DYS391 DYS439 4 DYS635 X4 DYS392 YGATAH4 DYS43 DYS438 4 DYS448 Select All a The Quality Control tab opens back up with all the new Loci that have been added Add the necessary amounts for each Locus and when finished click the Ok button FIGURE 2 21 Loci Window The Delete Selected button is used to delete the item selected The third subsection is Frequencies options The top half of the screen allows you to choose which frequency tables are enabled for frequency calculations A check indicates that table is enabled for the frequency reports Click on the box next to each option to add or remove a check in the box The Theta amount can be changed here by clicking in cell next to each race in the Theta column and typing a new Theta value The bottom half of the screen allows you to choose the source of frequency ratios the system will use ArmedXpert Options G 5 x General Mixture Interpretation Quality Control Frequencies Frequency Options Data un Frequency options Interpretation i nable Quality Control E ab d Caucasian Black Admin Console Hispanic Reporting Description Enabled Delete Races Delete Sources Add Frequencies Review Frequencies
148. ods throughout the mixture interpretation without losing any calls already made using one of the other methods For example once 12 13 were called for Profile 1 it was highlighted blue in Method One and check marks were recorded marking alleles 12 13 in Methods 2 and 3 86 Tab Five Interpretation ARMEDXPERT USER S MANUAL Navigation There are a few different ways to navigate to different locus in the Mixture Interpretation Window You can use the method explained above in the Popout calls Window You can click on the V arrow next to Locus Box for a drop down list of all loci and then individually select the locus Finally you can click the lt or gt arrows to move either forward or backward to a different locus Mixture Interpretation DDA Interpretation c3 s 23 Setup Pick via mouse 0156 1 39333330 1 15 2F1 Shirt Vict 06 06 20 D01 Operations 7 Contributor 2 i References Locus D195433 4 7 lt Major 13 14 2 P Avg 0 69 2 2 7 ee PH 0 60 3 Minor 1418 2 P Avg 0 31 1 0 idi mPH 7 HT 150 3 alleles ins Mu Ignore Alleles 0 00 RFUs 787 410 886 292 oc SUL BPs 117 121 123 139 Lock locus Popout Vie call report b Add Comment iz cC TN 100 15 pez 410 186 232 L LIII LL i FIGURE 7 26 Moving to a different locus Additional Features There are four additional features to help you make calls with the Mixture Interpretation Window
149. ofiles click the Load Samples from Data Source button on the Data tab There are complete instructions on how to use this feature starting on page 55 of this manual You can also view the profiles see page 35 for instructions 2 New Sample Views Data sf Edit Change Sample Kit Samples X Datasource Load it Samples amp sources Bg ison Interpretation Reporting 339 oad Samples Connect Disconnect Sort Sort bm Data Source Server Server Samples Data Source Sort Selected samples amp sources LADDERSANDCONTROLSCHECK TABLE LaddersandControlsCheck_Yfiler Old Profi YFier Mixture1_Partial_Profile_Case Mixture2_1 blood on jeans case Mixture2_2 vag swab case Miner ek co Misture2 3 bomb case combined s Mixture2_3 bomb case combined Mixture2_3 bomb case combined Mixture2_4 underwear case Mixture3_1 who did it case Mixture3 1 who did it case Suspect2 Misture3 2 ladies mar Misture3 3 hickey case Mixture3 4 hardest mixture N _ _2 Component_Mixture_Review NV 2 Component Misture Analyst j v AA arananar Search Delete L2 J gt gt Ls hs Ignore Case Also select tables vV Search Tables Search Profiles Load FIGURE 1 1 0 Sample Tables in the Demo Database Several of the Sample Tables are from the PowerPoint Presentati
150. om Portion of Mixture Window 103 Tab Five Interpretation E ARMEDXPERT USER S MANUAL RMP XX72 2 99XX5678 Q1 2 F2 Vag Swab 06 07 14 D02 c3 e 5 XX72 2 99XX5678 Q1 2 F2 Vag Swab 06 07 14 D02 amp 11 12 13 0 2611 0 3556 0 2444 0 4212 0 2906 0 0961 20 21 z 23 0 0714 01305 01773 0 1404 Caucasian lin 1 0912E 18 1 09 Quintillion Black lin 6 918E 20 691 Quintillion Hispanic lin 1 4551E 18 1 45 Quintillion Theta 0 01 Contributors 3 Sources Ea jiii Frequencies Calculations lt ji gt Pick via mouse Contributors 3 FIGURE 7 61 Example of a 3 Person Mixture with a Sample added automatically As with all of the pages the calculation for the each ethnicity for the entire profile is located at the bottom of the page The calculations are shown in both exponential and alphanumeric form 104 Tab Five Interpretation ARMEDXPERT USER S MANUAL Tab Six Reporting he Reporting tab is used to run the available reports It has seven selections C D Form Total Data Sample Comparison CMF PHR Report Template Report and User Defined This chapter explains each report and displays sample views of each Reporting C D Total PHR User Form Data Comparison Report Report Defined Reports FIGURE 8 1 Reporting Tab C D Form The C D Form report is the CODIS Disposition Form for CODIS Administrator
151. ons on the ArmedXpert com website The PowerPoint Presentations are under the Mixture Workshop 2012 Section of the Armed Xpert com website QUESTION DNA GRAND ROUNDS CONTACT MIXTURE WORKSHOP 2012 POWERPOINT SLIDES VIDEO FROM THE 2012 MIXTURE WORKSHOP AT American Academy of Forensic Sciences Z FIGURE 1 11 ArmedXpert Website 6 Introduction ARMEDXPERT USER S MANUAL ArmedXpert Menu rmedXpert has a main command menu Click on the ArmedXpert icon on upper left hand corner of ArmedXpert to open the main menu The left portion of the menu lists the following commands Import Export View and Print On the bottom right hand corner is the ArmedXpert Options and Exit ArmedXpert buttons ArmedXpert Icon p gt ArmedXpett Basic Commands ArmedXpert E Options and Exit Armedxpert Options Exit Armedxpert ArmedXpert Buttons FIGURE 2 1 ArmedXpert Menu 7 ArmedXpert Menu ARMEDXPERT USER S MANUAL ArmedXpert Options Click on the ArmedXpert Options button to open the options or defaults for the program There are six main sections General Data Interpretation Quality Control Reporting and Admin Console On Administrator copies only They are listed on the left side of the ArmedXpert Option Window The options for each section are shown on the right hand side of the window The section highlighted indicates which section s
152. options are being shown For example in Figure 2 2 below General is highlighted on the left hand side so the General view options are shown on the right hand side of the window Once the options are set they will change for all current or subsequently opened files in Armed Xpert You can go back into option window and the options can be changed as necessary Click Ok to save the options you have selected Click Cancel to close the Option window without changing the settings To obtain the software version information click on the About ArmedXpert button on the bottom right hand corner of the window The About ArmedXpert window will open and display the version number Click Ok to close the window When a check appears next to each option that option is active Click on the box next to each option to remove a check that is shown or add a check to an empty box ArmedXpert Options c3 5 General view options Data Double homozygotes Sort Alleles By Name Interpretation Remember window sizes and locations Quality Control Wuality Lon Match amp Compare Reporting List match amp compare references at top Admin Console Do not sort automatically Sort by total matches exact included Sort by exact matches Sort by included matches Pluains Run post import plugins Open Plugins Refresh Directory Plugins About Armedpert Ok Cancel FIGURE 2 2 General view option
153. ou would like to see on the PHR report Once finished click the X on the upper right hand of the window to close the Combine Sources Window Note Remove the selected samples from the right hand side using the lt button before creating each new sample table 113 Tab Six Reporting ARMEDXPERT USER S MANUAL To tun the PHR Report Click on the PHR Report button and the PHR Report Window will open Click on Add a table button PHR Report of Description Table Double click an item to change Add a table its description Ok Cancel FIGURE 8 14 PHR Report Window The Select a table Window will open You can either select an entire table or expand the table and select individual sample s Click the gt button to move the selected table or sample to the right side of the window a iow iow yi Select a table c3 e Samples amp sources Selected samples amp sources DilutionS eries xls 1 5 Dilution 1 5 Dilution 1 0 dilution 25 Dilution 25 Dilution 1 0 dilution gt gt j ES L amp J Ignore Case Also select tables Ok Cancel FIGURE 8 15 Select a table Window Once all tables or samples have been selected and moved to the right side click on the Ok button 114 Tab Six Reporting ARMEDXPERT USER S MANUAL The PHR Report window will open back up Your chosen selections will appear Q P
154. ples USER S MANUAL The Sort option allows you to sort by any of the columns in your sample table Click on the Sort button and the Sort Window opens as shown in Figure 4 21 below Select the key s to sort by Then click on the gt button to bring over one key keys columns on the spreadsheet The gt gt button is used if selecting all the keys The keys selected will then appear in the box to the right You can change to Sort Order from Descending to Ascending by clicking on the Sort Order box and choosing from the drop down list the applicable choice You can also sort as normal or text as numbers by choosing under the drop down list in the Sort As column Once finished click the Ok button Sort Key amp 0 B 1 D 3 E 4 F 5 G 5 H 1 8 J 3 K 10 L 11 M 12 N 131 is Sort Order Descending Descending Descending Descending Descending Descending Descending Descending Descending Descending Descending Descending Descendina lll Sort As Normal Normal Normal Normal Normal Normal Normal Normal Normal Normal Normal Normal Normal 5 Sort Sort Samples Sort FIGURE 4 20 Sort Section Select the keys to sort by Sort will occur in the order that the keys appear in the second box Sort Used Range Sort Selected Range l 1 Key C 2 Sort Order Descending Ok FIGURE 4 21 sort Window 59 Tab Two Data Sort A
155. r User name and password Default user name is admin with no password Click the Ok button Note When you initially start ArmedXpert the first time and until you register the Registration Dialog window will open before the Login window To clear your login in history click on the Clear login history button Login e 55 User Name Password Clear login history FIGURE 1 3 Login Window Changing the Database in ArmedXpert To change the database that ArmedXpert is connected to click on the Options gt gt button The Connection Properties tab opens Change from the available databases by clicking on the W next to Connection name box to choose between the available Connection Names Login c3 E ES Login Connection Properties 4 b Connection Name SQLite Connection Type SQLite Connection String data sourcesArmedXpert db Save this Configuration Delete this Configuration Ok Cancel Options lt lt FIGURE 1 4 Connection Properties 3 Introduction ARMEDXPERT USER S MANUAL Or add a new connection name by clicking on the box next to Connection Name The box will appear in white and you can type in a new user defined name Login c 5 3 Login Connection Properties 45 Connection Name Local PC FIGURE 1 5 New Connection Name Change the connection type by clicking on the arrow next to the Connection Type box This will brin
156. repeat the steps above to apply reference If you would like to remove a reference click on the Remove Reference button Once a referenced has been removed the Remove Reference button turns back to the Apply Reference button If you would like to add a reference that has been removed click on the Apply Reference button and it will be added back as a reference References Select a reference to apply Apply Reference Select a reference to apply Apply Reference Select areference to apply Apply Reference Select a reference to apply Apply Reference Select a reference to apply Apply Reference Select a reference to apply Apply Reference Auto call references 7 List foreign wi auto call FIGURE 7 7 Reference Selection Box All selected references will be highlighted blue on the sample table The reference s will also be indicated as such i e Ref 1 Ref 2 in the Mixture Interpretation area of the Mixture Interpretation Window Note Only combinations including the references will be shown in the Mixture information area 78 Tab Five Interpretation ARMEDXPERT USER S MANUAL References Auto call references z m list foreign auto call FIGURE 7 8 Reference Selection Box Click on the Auto call references button to automatically fill in the Reference 1 as Profile 1 and Reference 2 as Profile 2 This feature will allow you to only have to select a cal
157. rmedXpert Once your table is imported click on Combine Sources under the Data tab The Combine Sources window will open Type in the selection filter box the dilution you would like to create a table for Click the gt button to move all highlighted samples to the right hand box Type in the title of the table you are creating Click on the Combine button Your new combined sample table will open Combine Sources c3 5 Select items to combine Samples amp sources Selected samples amp sources DilutionSeries xls ID B 1 1 0ng 5 0 ID Ladder 1 401 1 ID B 2 1 0ng 4 B02 ID 2 1 5ng 2 402 ID B 3 1 0ng 1 403 ID B 3 1 0ng 1 403 TE ID 1 1 5n 3 B01 m ID B 2 1 0ng 4 B02 D ID Ladder 3 B03 gt gt ID_B 1_1 0ng 5 CO1 ID_C 2_0 5ng 5 C02 ID_C 3_0 5ng 5 CO3 ID_C 1_0 5ng 7 D01 ID D 2 25ng 5 02 ID D 3 0 25ng D03 ID D 1 0 25ng 9 E01 ID F 2 1ng 0 E02 ID F 3 1ng 9 E03 ID F 1 1ng 1 F01 ID amp 3 1 5ng 5 H02 ID Ladder 5 3 wv E cJ 1 Ignore Case Also select tables Title 1 0 dilutior Combine FIGURE 8 13 Combine Sources Window In the example above 1 0ng was entered in the selection filter box All samples containing 1 0ng was highlighted in the box on the left hand side They were then moved to the right hand box using the gt button 1 0 dilution was added as the Title Repeat the steps above to create the different dilution tables for each dilution amount y
158. rp FIGURE 7 35 Added Comment Example to Calls page Mixture Interpretation Details for XX0156 1 99XX9999Q1 15 2F1 Shirt Vict 06 06 20 Dp1 Comment E Example of comment to Mixture interp we Only combinations including the following reference profiles are included 12 13 13 All combinations have PHr gt 0 MPh gt 0 mP gt 0 9851179 12 1580 13 2345 For a 2 contributor 2 allele mixture of types AB amp BB 1 2 combination s 12 13 phr 1 00 p 0 81 13 p 0 19 Comment added to D81179 call example FIGURE 7 36 Added Comment Example to Mix Interp page 91 Tab Five Interpretation ARMEDXPERT USER S MANUAL There is an Operations button to the right of the selected sample This opens a RMP report for this sample ot allows you to open an OSIRIS Plot File or Virtual Electropherogram Click on the Operations button and a drop down list will open 99599998 1 15 2F 1 Shirt Vict 06 06 20 D01 Operations Electropherogram Open OSIRIS Plot File FIGURE 7 37 Operations Button te al Elamckr S iT virtual Electropherogram Contributor H T Jperatons 7 RMP 18 iV Use Full e gram Use single plot Use multiple plots To open the RMP report choose RMP from the drop down list The locus you currently are on will be shown You can choose between Modified RMP Forced mRMP and Restricted RMP If you would like to have the report s
159. s 8 ArmedXpert Menu ARMEDXPERT USER S MANUAL The first main section General provides flexibility for how you can view your data The first option allows double homozygotes to be displayed The second option allows ArmedXpert to remember window sizes and locations when reopening When checked all windows that are reopened will open in the location and size that it was when closed previously The third option allows you to sort alleles in the sample table by None Name Base Pair or RFU General view options Double homozygotes Sort Alleles By Name Remember window sizes and locations Match amp Compare Base Pair RFU List match amp compare references at top FIGURE 2 3 General View Options first three options The fourth option lets you choose how the Match amp Compare feature is viewed To move the references used during the match and compare feature from the bottom of the page to the top of the page as shown in Figures 2 5 2 6 below click on the List match compare references at top box The four choices listed on the bottom of the Match amp Compate section allow you to choose sorting options for your Match amp Compare data Click on the circle next to the option of your choice Match amp Compare List match amp compare references at top Do not sort automatically Sort by total matches exact included C Sort by exact matches Sort by included matches FIGURE 2
160. s Normal E B Normal Cancel Sort As Normal Text Numbers Sort Order Descending Ascendinc Descending ARMEDXPERT USER S MANUAL The Sort Sample option allows you to sort by the samples on your sample table Click on Sort Samples and the Sort Sample window will open You can either perform an auto sort or manually sort the samples To Auto Sort the samples click on Sample Name or Allele Count manual sort the samples click on any of the sample names with your mouse Drag the sample name to the place you would like the sample to appear Do this until your samples are in the order you would like them to appear Once finished click on the Ok button X Sort Samples c e es Auto sort by DEMO 2 Component 4 Vict Mix Stains Analysttxt 19 entries Sample Name Ladder Identifiler 06 06 20 F03 Allele Count Ladder Identifiler 06 06 20 403 Ladder Identifiler 06 06 20 401 QADO3F1 06 06 20 H01 ee 9640168 SSX lt 9999K2 Blood Susp 06 06 20 H02 9040156 3 99499990 1 15 2F3 Shirt Vict 06 06 20 E01 bes0156 1 99 lt 999901 15 2F1 Shirt Vict 06 06 20 D0 ee 900165 04004 04 06 06 20 E02 0167 99669999K1 11 Blood Vict 06 06 20 G02 0153 9999990 1 15 12F1 Shirt Vict 06 06 20 H02 ee 9060164 994999901 2 LFS Vict 06 06 20 D02 XND153 1 99999901 15 8F1 Shirt Vict 06 06 20 F01 9060169 04026 QA 06 06 20 B03 90
161. sample s that you would like to set as the reference then click one of the compare buttons These two only wotk if the reference is on the same sample table as the one that you want to match and compate to 70 Tab Four Match amp Comparison ARMEDXPERT USER S MANUAL Find Where Reference is Included is used to find loci that include the reference All loci that contain an exact match to the reference are highlighted orange All loci that contain the reference and additional allele s are highlighted yellow PEMU ZComponent 4 VKT MIX Stats Analyst txt O uw D75820 CSF1PO D351358 THO1 D135317 D165539 0251338 0195433 vWA TPOX D18S51 Amel D5S amp 18 Ladder Identifiler 06 06 20 A01 9 10 11 12 17 18 19 20 14 1 13 0 Ladder Identifiler 06 06 20 A03 17 18 19 20 14 1 13 0 Ladder Identifiler 06 06 20 F03 14 1 13 0 XX0153 99Xx99991 15 12F1 Shirt Vict 06 06 20 H02 16 16 0 0 XX0156 1 99XX9999Q1 15 2F1 Shirt Vict 06 06 20 D01 16 4 12 0 XX0156 3 99XX9999Q1 15 2F3 Shirt Vict 06 06 20 E01 16 4 12 0 XX0159 1 99XX9999Q1 15 8F1 Shirt Vict 06 06 20 F01 16 4 12 0 XX0161 1 QAO03F1 06 06 20 H01 4 1 3 0 XX0162 1 Reag BlankF1 06 06 20 802 XX0162 2 Reag BlankF2 06 06 20 C02 XX0164 99XX9999Q1 2 LFS Vict 06 06 20 D02 16 4 12 0 XX0165 QA004 QA 06 06 20 E02 7 9 3 12 14 A 3 2 1 0 XX0166 Reag Blank 06 06 20 F02 Eme Emm eed 10 12 a 1 3 0 16 16 0 0 XX0169 QA026 QA 06 06 20 803 11 12 11 14 16
162. select an item to activate the cell Error Cell Book1 SheetlIES Book1 Sheetl F5 Book1 Sheetl EB Book1 Sheetl F5 Booki SheetlIE7 Book1 Sheet F Book1 Sheetl E8 Book1 Sheetl F8 Book1 Sheetl ES Book1 Sheet F3 Book1 Sheetl E10 Book1 Sheetl F10 lt Error Text User did not specify a value for variable User did not specify a value for variable User did not specify a value for variable User did not specify a value for variable User did not specify a value for variable User did not specify a value for variable User did not specify a value for variable User did not specify a value for variable User did not specify a value for variable User did not specify a value for variable User did not specify a value for variable User did not specify a value for variable Reevaluz Item4 Name Item Name Itern4 tem5 Item4 temb Item4 Item tem4 Item5 Item tem5 FI GURE 8 25 Template Report Window with errors Tab Six Reporting 119 ARMEDXPERT USER S MANUAL Minimize the Template Report Window and view the User defined report that 15 automatically generated in ArmedXpert This report may be edited the Case Number Date and Comments may be entered directly on the sheet AX mixtures txt 01 Identifiler Kit Standard 10 10 04 01_ 02 PCR Negative Control 10 10 04 02 ID Allelic Ladder 10 10 04 2 1D ID Allelic Ladder 10 10 04 ID Mix
163. ser and delete a user Enter a New User click on the New User command The New User box will open Type in the appropriate information Only the User Name and Role are required to be filled in There is a drop down list for the Role options Click on the arrow and select the appropriate role Click on Ok once finished 28 ArmedXpert Menu ARMEDXPERT USER S MANUAL New User User Name First N ame Last Name Password Confirm Password Role User M Ok Cancel FIGURE 2 41 New User window To Edit a User click on the user name you would like to edit Then click on the Edit User command The user information will be filled in Change or add any information that 1s appropriate for that user To change a password enter the current login password and click on Reset password Type in New Password and confirm it in the next box Click on Ok Edit User c E User Name FistName Last Name Password Reset password New Password Confirm password Role DefaultAdmin M Review Settings Ok Cancel FIGURE 2 42 Edit User window To delete a user click on the user name you would like to delete Then click on the Delete User command The User name will be deleted 29 ArmedXpert Menu ARMEDXPERT USER S MANUAL The second tab is Database There are two available feature Run SQL Updater and Reset QA The Run SQL Updater
164. t button The Edit Source window will open Click on the arrow next to the Kit name Change to the approptiate kit from the drop down list Note If the kit that you wanted is not showing please contact NicheVision Q Edi Source c3 s Kit Identifiler lad Loci 1 D851179 2 D21511 xD75820 4 CSFIPO 5D351358 amp THO 7 D135317 amp D165538 9 D251338 10 D195433 1t wA 12 TPOX 13 D18551 4 Amel 15D55818 16 FGA Dk Cancel FIGURE 4 7 Edit Source Window 51 Tab Two Data ARMEDXPERT USER S MANUAL To combine sample table s or sample s into one new combined sample table click on the Combine Source button This will open the Combine Sources window Note Each of the sample tables must be open to use this feature Combine Sources c3 E Select items to combine Samples amp sources Selected samples amp sources DEMO_ _2 Component_4_Vict_Mix_Stains_Analpst tet A DEMO 2 Component 4 Vict Mix Stains Review t t Ladder Identifiler 06 06 20 F03 Ladder Identifiler 06 06 20 403 mE Ladder Identifiler 06 06 20 401 gt 0155 1 99 lt 999901 15 2F1 Shirt Vict 06 06 20 AS 220156 3 9999990 1 15 2F3 Shirt Vict 06 06 20 E 2040159 1 99499990 1 15 8F1 Shirt Vict 06 06 20 F xc 0151 1 QAO03F1 06 06 20 H01 0152 1 Reag BlankF1 06 06 20 B02 0162 2 Reag BlankF2 06 06 20 C02 m 240164 33 24338301 2 LFS Vict 06 06 20 D02 280165 gADO4 QA 06 06 20 E02 lt lt 0166 Re
165. t Import window will open Click the Ok button All the frequency data will appear in the Add Frequencies window Once finished you are ready to commit the frequencies Add Frequencies Deserphoe Detenst Comes Pase iroot kom fe FIGURE 2 27 Add Frequency Window 19 ArmedXpert Menu ARMEDXPERT USER S MANUAL Click on the Review Frequencies button to review Frequencies You can also make changes to the Frequencies from the review Frequencies window Just type the appropriate change in the cell Once you have made your changes click on the Commit button Frequency Review 021511 D21511 b21511 D21511 D21511 021511 D21511 021511 021511 D21511 D21511 D21511 D21511 021511 021511 FIGURE 2 28 Frequency Review Window with frequencies The fourth subsection is additional Frequency Options The top section allows you to set the single source frequency calculation database size and gives you a choice to either use Theta or not The middle section allows you the option to use Theta or not for the RMP calculation It also gives you an option to include Locus Detail in the RMP calculation report The bottom section allows you set the number of significant digits displayed in the frequency calculations It also gives you a choice of prompting to save on the window or application close for a frequency calculation page ArmedXpert Options c3 General Mixture Interpretation Quality Control Fr
166. tailed information of all the highlighted results shown during each of the checks It explains why the locus was highlighted After performing a check click on the Begin Review command This must be done before you click on the Clear Checks command move to the next or previous highlighted sample s locus there are three different ways You can click on the Prev or Next buttons you can type a number directly in the number box to go directly to a certain number or click the up and down arrow buttons next to the number box X QC Review Prev Next 1 5 722 FIGURE 5 16 QC Review Moving Tools Move to each highlighted result to obtain information about it Each highlighted result is at a specific sample s locus which will be outlined on the sample table when reviewing the result Some of results have fixes that can be done such as remove an allele during the stutter check review as shown below Click on any fix that you would like to have done Once you are finished with QC review window click on the Done button X QC Review o x X QC Review ca a Prev Next 1 lt 2 718 Pev Next 3 gt 18 The peak height ratio of 16 308 to 15 1309 is 0 24 which is less than 0 5 30 2 58 is 8 298 of 31 2 699 30 2 could be stutter Remove allele Remove allele ALL Done _ Done X QC Review E Prev Next 4 5 22 D21511 Alleles RFUs 28 1025 23 278 30 243 29 278 is be
167. tation OSIRIS Plot File Load a plot file generated by OSIRIS FIGURE 2 45 Import Menu 31 ArmedXpert Menu ARMEDXPERT USER S MANUAL Once you select the type of data you are importing the open window appears Select from the list the file you wish to import Then click the Open button If the file is located in another folder change the folder by clicking on the arrow next to the Look in box The table files will then open in ArmedXpert as shown in Figure 2 46 below The file name will appear on the upper left hand corner of the page Look in Identifiler 9 DEMO I 2 Component 4 ict Mix Stains Review Ext My Recent DEMO I 2 Component Vict and 5 Susps D3 Extra Allele txt Documents DEMO I 3 Component Mo Controls V S1 S2 E txt a File name Iv My Network Files of type Iv FIGURE 2 46 Open Window o oga D21511 D7S820 CSFIPO D351358 THO1 D135317 D165539 D251338 D195433 vwa TPOX Amel 055818 FGA mmm PE 9 10 24 25 6 7 8 6 7 8 9 Ladder Identifiler 06 06 20 A03 Ladder Identifiler 06 06 20 F03 XX0153 99XX9999Q1 15 12F1 Shirt Vict 06 06 20 H02 1 11 14 17 XX0156 1 99XX9999Q1 15 2F1 Shirt Vict 06 06 20 D01 14 15 17 XX0156 3 99XX9999Q1 15 2F3 Shirt Vict 06 06 20 E01 XX0159 1 99XX9999Q1 15 8F1 Shirt Vict 06 06 20 FO1 9 12 XX0161 1QA003F1 06 06 20 H01 13 14 28 31 1 11 12 10 10 1418 66 9 1 13 15 24 1314 1417 8 11 1212 X
168. te 39 H 45 ara 44 I SNR TRE RRERM 45 e uv 46 BE RT qu m 49 BN ON ae 49 TVA SONIC scat de spa 54 v 59 puppi rere errr tr eter 61 CMe Gl era lt lt rep rn rrr rte 61 OB tak ee eee 64 m 68 TAB FOUR MATCH amp COMPARISON 69 SATAN T 69 74 TAB FIVE INTERPRE TATION iisssssccascscsustesseoertnrsesiessncsuwentverannatancs iis Nisar Vettes pre AO olemrmec EE reer ar rer ren EE cherries fis MUR 94 Db Gs PORLUN G 105 S0 tC eT rT errr re rr rc tee 105 NDA E 105 Sy hoa elles Wiles aay 67 Cree rer rrr acer tem etter etu E renter 109 d I 111 slo i 113 AW Saal ol hiked We red M 118 IB cg ds 120 Append As EROLISOVS e adi terit tux etenim 121 Appendix B Contact Information eere 122 ARMEDXPERT USER S MANUAL Introduction ArmedXperf Developed by analysts for analysts rm
169. terpretation was exported will appear along with the settings used and references applied You can now continue using the Mixture Interpretation tool xu Vews Dats QCCheds Match amp Comperison Irterpretaban Reporting Y gt x 1 J 3 J LI Y Begn Mitre Se Ubethood Probab ty Mixture Interpretation Sarte Raio Incduson Interpretation Frequency Calodations DDA Interpretation f 900156 1 99639999 1015 2F1 Shit Viet 06 06 20 00 xi Highest to L2 Lew DESTITS pn rent Me 1213 H Profle n a Abees 12 13 RFU 1560 2145 BPs 13955 144 26 1 For a 2 contnbutor 2 allele mixture of types AA amp AB 2 2 combination s 12 13 phr 0 61 p 0 86 Ret 1 12 p 7 0 04 12 13 phr 1 00 p 081 Ref 1 13 0 19 2 For a 2 contnbutor 2 allele mixture of types AB amp AB 1 1 combination s Ref 1 12 13X phr 67 FIGURE 2 48 Mixture Interpretation Imported Click on OSIRIS Plot file to import in an OSIRIS plot file When you select this option the OSIRIS Plot window will open as shown below Click the Add button to add the OSIRIS plt files Add them in the otder you want them to appear in the final report Double click on a listed plt file to edit the name Click on any of the OSIRIS plt files listed and click the Remove button to remove them from the list On the bottom of the window are the available options Select the options that are preferred Once finis
170. the proportions of your calls in a graphical format by clicking on the View call report button The call report will open The mixture is shown on the top of the page and the profiles are shown below that Below the profiles will be the alleles that are foreign to the reference if you selected this option when selecting your reference A graph showing the proportion of each profile by loci is generated below the profiles Below the graph are the proportions that relate to the graph As you make your calls the alleles will auto populate the report You can customize how the report appears by clicking the arrow next to View call report button It will bring up a drop down list as shown below b Note The graph only shows the proportions for the locus that have completed combinations called Helerences FHr03 ve Alleles mpu MPH 175 HT 100 0 00 View call report T gt View call report 5 Chart Sort loci to show degredation 20 FIGURE 7 29 view call report button V Column Clustered FT Column Stacked Column Stacked 100 29 Calls 28 m Sort loci in default order 32 Sort loci by allele count USER 16 Sort loci to show degredation 88 Tab Five Interpretation ARMEDXPERT USER S MANUAL ArmedXpert v3 0 7 942 ox views Data QC Checks Match amp Comparison Interpretation Reporting o V Highlight EI Imi d 5 3 By
171. ttributes will be reordered by the change You can also add attributes by clicking on the Add Attribute button and entering in the appropriate attribute on the next available line You can also delete any attribute by clicking on it and then clicking on the Delete Attribute button You can edit any of the attributes by double clicking on it and then typing in the edit Note Any attribute with a in front of it cannot be deleted or edited It is a required attribute Reporting Options CODIS CMF Attributes gt Common Messaging Format CMF Attributes 17 attributes Order Attribute SPECIMENID CMFPACKETTYPE BATCH PACKETVERSION DNATECH SPECIMENNLIMBER SAMPLEID SPECIMENCATEGORY TISSUETYPE Rs ll eo c1 9 cto ro Double click an item to edit Items beginning with an Add Attribute Delete Attribute asterisk can only have their order changed FIGURE 2 39 CMF Attributes Section 27 ArmedXpert Menu ARMEDXPERT USER S MANUAL The final section is Admin Console This section will only be available if you have administration capabilities It has two tabs Users and Database ArmedXpert Administration X Users Database e New Edit Delete User User User User Administration User Name First Name Last Name DateCreated admin 10 22 2010 1 38 PM FIGURE 2 40 ArmedXpert Administration User Window The first tab Users allows you to enter a new user edit a u
172. ture M F Neat 10 10 04 Mix Mixture MEC IST 10 0 0X MIK Lab Case No CN001 Date 2 13 12 Mixture M F 1 10 10 10 04 2 Mix Table 1 Results of Short Tandem Repeat Loci for Identifiler Analysis Mixture M F 1 100 10 10 04 2 Mix Mixture M F 1 4 10 10 04 Mix Mine M303 DOT Dae Mixture 100 1 10 10 04 2 Mix D8S1179 10 11 14 10 14 o T past ao ma fF Mixture M F Neat O 10 10 04 Mix D75820 12 i NR denotes No Result URG denotes Unresolved Genotype Denotes Inconclusive Results FIGURE 8 26 Template Report L NOTE Ensure that the original excel spreadsheet has wide enough columns to prevent any numbers from being cut off when viewing the User defined report The cell widths cannot be edited in ArmedXpert If you right click on the User defined report a variety of editing options are available User Defined The User Defined feature allows you to run plug in reports that you have added to ArmedXpert Click on the User Defined button and the available plug in will show Select the appropriate plug in 7 Data QC Checks Match amp rere meer pretation Reporting ne CD Total Samples PHR Templ te User Form Data Comparison Report Repoft Defined Reports FIGURE 8 27 User Defined Button 120 Tab Six Reporting ARMEDXPERT USER S MANUAL Appendix A Hot Keys
173. ucasian D851179 12 0 125 FIGURE 2 24 Manually add frequency window 18 ArmedXpert Menu ARMEDXPERT USER S MANUAL Method Two To paste in the frequencies first open the data into excel It should be in the same order Race Locus Allele and Frequency Highlight all the data you want to paste into ArmedXpert Click the Copy button in Excel r fx Home Insert Page Layout Formulas Data Review View Calibri u a E em l a E Wrap Tet General F e z uio A E m E E Mergea Centers o tb 328 Conaitic Formattii fa Font la Alignment Tu Number fa Copy Ctrl Copy the selection and put it on E G the Clipboard 0 01 FBI 29 Caucasian D8S1179 0 01 FBI 30 Caucasian 851179 0 01 31 Caucasian D8S1179 0 01 FBI 32 Caucasian D8S1179 0 01 FBI 33 Caucasian D8S1179 0 01 FBI 34 Caucasian 851179 0 01 FIGURE 2 25 Copy Frequencies from Excel Go back to ArmedXpert and click on the Paste button All the data will show up in the Text Import Window Click the OK button All the data will show up in the Add Frequency window Once finished you are ready to commit the frequencies Comma Serer ers ere ENS Terese GEEEETRESS SER EERE RERaeeS FIGURE 2 26 Text Import Window Method Three To import a txt or csv file containing your frequencies click on the Import from file button Select the appropriate txt or csv file from the Open window The Tex
174. ve PHr gt 0 5 MPh gt 75 mP 0 For a 2 contributor 2 allele mixture of types AA AB 2 2 combination s 12 13 phr 0 64 p 0 98 12 p 002 49 0 1 12 13 phr 1 00 p 0 81 13 p 7 0 19 4 3 1 For a 2 contributor 2 allele mixture of types AA amp BB 1 1 combination s 13 p 0 60 12 p 0 40 1 5 1 For 8 2 contributor 2 allele mixture of types AB amp AB 1 1 combination s 12 13fphr 0 67 12 13fphr 0 67 FIGURE 7 15 Mixture Information before stutter applied As shown below once Stutter has been applied the Apply Stutter button changes to Remove Stutter In addition in the Mixture Information portion of the window a note has been made to indicate that the RFU s have been recalculated for stutter remove Stutter on a specific locus click the Remove Stutter button If you want to turn the Apply Globally feature off click the box left of it and the check mark will be removed All Stutter applied to all loci will be removed J Globally For a 2 contributor 2 allele mixture of types AA AB 2 2 combination s 12 13 phr 0 56 p 0 98 12 p 0 02 49 1 12 13 phr 1 00 p 0 75 13 p 0 25 3 1 For a 2 contributor 2 allele mixture of types AA amp BB 1 1 combination s 13 p 0 63 12 p 0 37 1 7 1 For a 2 contributor 2 allele mixture of types AB amp AB 1 1 combination s FIGURE 7 16 Mixture Information after stutter applie
175. you want the Evidence to appear first make sure you add the evidence first to the report and so on EJ gt Evidence Victim Define er Alleles for Pick via mouse 3 Duplicate Suspect Elim Evidence FIGURE 8 4 Bottom of the CODIS Disposition Form Window There is also a define alleles for evidence option This adds a column of alleles next to the evidence columns that you want to send to codis So add your evidence first and then click on the circle next to Define Alleles for Evidence Choose the sample you want to add from the Mixture Interpretation Call View Report you created when using the Mixture Interpretation Window It will be added in a column next to the evidence information as shown in Figure 8 5 106 Tab Six Reporting ARMEDXPERT USER S MANUAL Define Alleles for Evidence Column iz Correct results were obtained for all controls f Bue itis XX0156 1 99XX9999Q1 15 2F1 Shirt Vict XX0167 99XX9999K1 11 Blood Vict 06 06 20 G02 06 06 20 D01 851179 ie 13 3915 4443 D851179 12 13 1580 2345 D21511 28 29 30 916 1144 994 D21511 29 30 3448 3618 D75820 D7S820 9 10 594 2480 CSF1PO 10 11 12 2001 609 1157 CSF1PO 10 12 2698 2497 D351358 15 16 2333 2426 D351358 15 16 1548 747 THO1 6 9 3 1337 1465 THO1 2489 2309 D135317 2299 2202 D135317 8 11 12 677 444 978 D16S539 9 12 13 409 1355 944 D165539 14 13 2328 2316 D2513

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