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What`s new SEQUENCE Pilot

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1. DL epo oj emet RR URREONE 5 1 Run SegMsesulliles impete aodio eek y EPETEHAERHELE PERPE E ROCHE ELEEE KURVE ainsi casi ipeo M PETUNT 6 Module TalkMastor usd pantera ecu S aveensanatieds bie pacar MEM Ap Aci MEE rp E DIM ADM DEN RR ER OE ME What s new SEQUENCE Pilot 4 2 1 1 All modules No changes were made to the algorithms mapping alignment variant calling etc in SEQUENCE Pilot version 4 2 1 compared to SEQUENCE Pilot version 4 2 0 verification versus validation 1 1 Db Utility check of all databases SEQUENCE Pilot version 4 2 0 introduced an updated version of the underlying database system Databases that have been built with the database system employed in SEQUENCE Pilot version 4 1 2 or lower and that have an invalid index file idx at the time of the update to SEQUENCE Pilot version 4 2 0 or higher might inherit one of the following problems performance issues inability to find a record very rare 1 2 Locking In case an order is checked in operation Joining check mark in column Order the patient is not locked anymore in case the user jumps to operation Sequence afterwards 2 Modules SeqPatient and SeqNext 2 1 GeneAdmin If entry USE CDS instead of USE mRNA is present in the downloaded genefile the mRNA entries for START and STOP CODON are not used The following options are available in case the mRNA entries should be used anyway lis ini file enter CheckMRNAGeneEntry yes in section SeqP
2. Homozygous Bases and Total number of bases of a result file as well as their percentage value are listed now in the dialogue Edit Bases field Info 4 Module SeqPatient 4 1 Operation Sequence Reports o Family Report the electropherogram can optionally be printed for the defined orders mutations only Therefore the following 1is ini entries are available for section SeqPilot PrintFamilyVar all this is the default setting All electropherograms are printed like in all older versions PrintFamilyVar current print all electroherograms which are set in the current order other mutations from other orders are printed like defined in the other order PrintFamilyVar currentonly print all electroherograms which are set in the current order other mutations are ignored PrintFamilyVar orders in case at least one order has the print electropherogram set for a mutation the electropherogram of this mutation is printed for all other orders as well Analysis of sequences containing a frameshift and a SNP For determining the exact base position of the SNP the following is done In case both sequencing directions are present the position of the SNP is only determined in the sequence in which the SNP is sequenced first Variants after first frameshift variant are not called if the remaining bases are covered by other sequences Frameshift analysis o Split mode view If a position is selected the corresponding position
3. What s new SEQU ENCE Pilot Version 4 2 1 04 20 2015 SEQUENCE JSI Pilot medical systems GmbH www jelmedisys com 5 gis I gi ge genet developed by JSI medical systems GmbH Tullastr 18 77975 Ettenheim GERMANY phone 49 7822 440150 0 Fax 49 7822 440150 20 email mail jsi medisys com web JSI medical systems Corp One Boston Place Suite 2600 Boston MA 02108 USA phone 1 617 933 7241 fax 1 617 933 7246 email mail us jsi medisys com www jsi medisys com for research use only Table of Contents HE sell RE T ML tp RT 1 1 Db Utility check of Erici NN UU et Pera ree iT eee epee pate M 2 Modules SegPauent and SegNexi ss asecatarkndbast ern M Kap E ai eR LA KR E EA a FR UE EROR PER MU RLR cec currere Ra c IHE 2A kutato n DADIE P 2 3 Seg encelM tation Database assanar da bad dax ra NA pr AA R ARERIA E Rial PA El aa DE A A T EE AE A EONA E IEA AE ATOT 3 Modules SeqPatient and SEQHLA cccccccceeeeeeeeeeeeeeeeeeeeeeeeeeeeaaaaaaeaesaaeeeeeeeeeeeeeeeeeeeeaeaaaaaeneneneeees 3 1 Operation Seguente escsa ea nae RE raa ARA CREER AR e RREQARENP RD EMEN ee EEE R PRA AE DPA TR seb Or Rae dix 22 Edil Bacon cxi br ben o sd cea vti Ra DEAD RERO AUD PME DLE EH I baa UL do P4 AM dU pud A Module SegP atien ssec bx oH prx Ra UU UHR Led RES HERR HER HE CE FH AR PORTA ptc UA UE F Ameen SAM EES LM 9 pie ascites osc oso ana E xS
4. ilot respective genefile in the GeneFiles directory FT CheckMRNAGeneEntry yes 2 2 Mutation Database When a new mutation is added to the mutation database all old orders also archived ones are checked to set the Frequency Depending on the amount of archived orders this can take very long To switch off this function please enter the following line in section SeqPilot for SeqPatient and or SeqNext for SeqNext CheckNewMutationTotalOrders no of your lis ini SeqPilot bin Please note By default this function is switched on for the module SeqPatient and switched What s new SEQUENCE Pilot 4 2 1 3 off for module SeqNext 2 3 Sequence Mutation Database If a variation mutation in the Variation Mutation table is shown with the hint not detected during the archiving process it will be not be added to the Frequency in the mutation database Mutation master file any more Accordingly the box in column mut DB is not checked by default 2 4 SNP DBs New SNP databases are available on our homepage for download In case you already have SNP databases in your installation the old entries have to be removed first Please contact our support team for help For the new SNP database package the following additional information is available o COSMIC IDs are now listed in the Variation Mutation table The corresponding SNP can also be jumped to in the internet by using WebRef show o For database ClinVar additional inf
5. is marked in the 2nd allele sequence as well This helps determining the correct IUB in the split mode view n case a SNP as well as a frameshift are present in a sequence there are two positions marked in the electropherogram when the SNP is selected in the Variation Mutation table The first position is the position of the mutation as listed in the Variation Mutation table the 2 position is the position of the mutation in the second allele regarding the frameshift This helps in validating base calling and to do edits in case of false positives base changes 5 Module SeqNext 5 1 Run SeqNResultfilesimporter In case there are many ROls with Analysis mode only mapping defined more ROls with Analysis state only mapping than other ROIs for the Run the reads are pre filtered The pre filtering makes analysis faster What s new SEQUENCE Pilot 4 2 1 5 5 2 Operation Sequence Genes in section Genes Chromosomes can only be ignored context menu ignore toggle when no ROI Group is select in section RO Groups first entry Unused Reads In case very big panels e g TruSightOne are analysed the File including all Unsused Reads can become very big Therefore we recommend to set the following 1is ini entry in the section SeqPilot SaveUnusedReads NO If switched to NO reads from ROls set to mapping only will not be saved in this file 6 Module TalkMaster Pending jobs can be shown up now via the bu
6. ormation is present ClinVar offers a second description file which was implemented as database ClinVarVCF Special Filter Modes were added to ensure that AND as well as OR combinations of several filter steps are possible The Basic filter corresponds to the setting that was used in the previous version The new Expert Filter Modes AND and OR are present With those the filter steps can now be linked either with operator OR or operator AND For detailed information please have a look at the User Manual SeqNext or contact our support team 3 Modules SeqPatient and SeqHLA 3 1 Operation Sequence Technical and medical validation TV or MV can be set for orders with the State ignore or incomplete even without the presence of files The automatic TalkMaster export can then be started for these orders Moreover ignored genes can be validated now Therefore the following entry has to be made in the 1is ini file located in the bin directory of your SeqPilot installation section SeqPilot ValidateCheckIgnore NO Please note If set to No an order will only get validated if all genes also ignored ones are validated With the default setting YES ignored genes do not have to be validated On tab Protocol all changed bases for a selected gene are listed now in the version 4 2 0 all changed bases for all genes were listed What s new SEQUENCE Pilot 4 2 1 4 3 2 Edit Bases The number of
7. tton Export Pending Jobs of the Joining or Worklist In case of our module SeqNext all information from the Summary can be exported What s new SEQUENCE Pilot 4 2 1 6

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