What`s new SEQUENCE Pilot
Contents
1. EFERERIEDENM AS FECE ERR DE XS MESERM RAI KRERU a REPERTA 5 5 9 Operation Geouenceitlechropnberodram nennen nne nenne nnne senis 5 5 10 Operation Seguence CNV WIDODIM ce 5 5 11 Operation PAA edle NT i i T TETTE 5 b BIOS eege eege 5 6 1 Operation Sequence dialogue Edit Baees enean 5 T KOTE S rg E EEN 6 A HEASSEINSE OBEN LUNES E 6 B Poe REESEN Ee 6 MM irc EE 6 What s new SEQUENCE Pilot 3 5 1 2 1 All modules 1 1 License The message you get in case your program is unlicensed changed You are now asked which module you want to test Moreover the path of the 1is ini file is listed 2 Modules SeqPatient SeqNext and SeqC 2 1 Gene Admin In case an isoform is selected in Gene Admin the isoform is pre selected when the dialogue Change Gene is opened Extras change gene 2 2 Operation Mutation master file New button Organ Phenotype Here organs and phenotypes can be defined These can be added to mutations listed in the mutation database dialogue Mutation see below Dialogue Mutation The dialogue has been worked over o Effect was renamed into Mut Effect o D mut Effect Here a percent value of a mutation effect can be selected o Ethnicity It s possible to choose an ethnicity in the drop down list Only ethnicities that are added in the Orders table of this dialogue are available left click into the column order o p mut Causality Here a percent value of a mutation causality can be selected o Organ Phen2. What s new SEQUENCE Pilot Version 3 5 1 10 10 2011 SEQUENCE Pilot JSI medical systems GmbH www jsi medisys com x developed by JSI medical systems GmbH JSI medical systems Corp Friedhofstr 5 1901 Newport Blvd Suite 350 77971 Kippenheim Costa Mesa CA 92627 GERMANY USA phone 49 78 25 86 41 15 phone 1 949 999 2092 fax 49 78 25 86 49 46 fax 1 949 999 2093 email mail jsi medisys com email mail us jsi medisys com web www jsi medisys com for research use only Table of Contents UM iioc oe M E 3 TT EIER PRETIO EEN 3 2 Modules SeqPatient SeqNext and Geo 3 Ed BEIDE MUI EE 3 2 2 Operation Mutation master TII sacsaikpeeniku kn ad pn ER Rex QERSIET AED E EPA AXI Ried nau ER RP RE ERU Ed SEEN I o RR ER ndn 3 3 Modules SeqNext and S87 LANA EE 3 3 1 Operation Run Automatic start of a Dr EE 3 gu EE a a 1i EE 3 To Rea OUT DEET 4 4 Modules SegPatient and Seg BR no ttn siae tin bri Eu atn i Rao POR REN RR FR dac tt Nite uw idera as darn 4 4 1 Operation SeqPrimer master el 4 ele E 4 21 Qbsragons Possis And POOL a pdackbuee DE RERREFEE RU AEPED FIN AFREAAQSEREVERERE NER NR RERFUIIERE AE eege 4 5 2 Operation PCR Groups master fiel 4 EE EEN Eeer 4 sme p lilo ue o 1115 EE 4 S9 Oly cie ge Ses a cial miim 5 5 6 Operation Joining and operation Worklist column Eie 5 5 7 Operation Worklist Select Order D n5 Lbs Seguente TIR oer pt pEEPERHHEREE ITE AEREREEEL
3. e rosekits html Those can be added to your installation following the instructions after executing the downloaded file 8 Module Talkmaster 8 1 Export of data MLPA data SeqNext data and SeqHLA 454 data can be exported What s new SEQUENCE Pilot 3 5 1 6
4. entered into the field Barcode in the following way o barcodetf barcode2 fragments are labelled with barcode 1 or barcode 2 o barcodelt barcode 2 fragments start with barcode 1 and ends with barcode 2 New table Organ Phenotype to add an organ phenotype to be analysed Only organs phenotypes that are pre defined in the operation Mutation master file can be added 5 4 Operation Joining New item Org P to search for orders with defined organs phenotypes in the dialogue part Select Orders What s new SEQUENCE Pilot 3 5 1 4 Context menu item settings is not available any more in the Lower Table only in the Upper table Context menu item settings in the Upper Table The dialogue File settings includes the Organ Phenotype table Organs Phenotypes can be added or removed by pressing the corresponding button Only organs phenotypes that are pre defined in the operation Mutation master file can be added 5 5 Operation Orderlist File line In case several files are loaded in one Run the file names are listed in the file line separated by For one file loaded in one Run the path of the file is listed 5 6 Operation Joining and operation Worklist column File In case several files are loaded in one Run the file names are listed in this column separated by For one file loaded in one Run the path of the file is listed 5 7 Operation Worklist Select Orders New item Org P to search for orders with defined organs phen
5. file is saved in your SEQUENCE Pilot installation which shows that an order was archived Therefore for all archived orders the file archive txt is present in the corresponding folder in the directory SeqNResults of your installation 4 Modules SeqPatient and SeqHLA 4 1 Operation SeqPrimer master file The automatic naming of forward and reverse direction in the SegPrimer Name by default F forward and R reverse can be changed in the 1is ini file located in the bin directory of your installation Therefore enter the desired character in the 1is ini section SeqPilot behind the following entries SeqPrimerForwardDescription SeqPrimerReverseDescription e g for lower case f for forward primer and lower case r for reverse primer enter SeqPrimerForwardDescription f SeqPrimerReverseDescription r 5 Module SeqNext 5 1 Operations Poollist and Pool Patient pools can be analysed using the operations Poollist and Pool See User Manual SeqNext chapter 10 Patient Pool analysis for detailed information 5 2 Operation PCR Groups master file New field Control is available This is only relevant for CNV analysis Here the controls that should be used for an analysis date or default can be selected 5 3 Operation Run The sequencing platform used has to be selected in the dialogue Settings The following platforms are available 454 lon Torrent MiSeq Solexa SOLID Two barcodes to identify fragments of one patient can be
6. otype table Defined organs phenotypes can be added to or removed from mutations listed in the mutation database New table column Zygosity in the Orders table Entry is homo for a homozygous mutation and het for a heterozygous mutation 3 Modules SeqNext and SeqHLA454 3 1 Operation Run Automatic start of a run A run can be started automatically after files are analysed on your sequencer Therefore all parameters needed for the operation Run have to be defined in a txt file The txt file has to be saved in the directory bin Autorun SeqNext for SeqNext or bin Autorun SeqNextHLA for SeqHLA454 of your SEQUENCE Pilot installation For further information about the txt file see User Manual SeqNext chapter 8 3 4 5 Automatic start of a Run or contact our support team 3 2 Operation Joining Result files can be joined to medical validated or archived orders Therefore enter JoinRFValidatedOrder YES in the section SeqNext or SeqNextHLA respectively Archived orders are then reactivated automatically in case further data is imported for this patient The new result file is joined to the order and the state MV is removed If you want to create a new patient order in case the order is medically validated enter additionally CreateOrderByRun YES Or CreateOrderByProject YES in case you use projects in the section SeqNext or SeqNextHLA respectively What s new SEQUENCE Pilot 3 5 1 3 3 3 Operation Archiving During archiving an empty
7. otypes 5 8 Operation Sequence Files Several files loaded in one Run are listed in one line The number of files 7 file or 2 files is shown in the column File Moreover in case only one file is loaded the file name is listed The context menu item show gt info has been worked over The information shows the path of all files loaded in one Run New context menu item show gt organ phenotype to show a list of organs phenotypes added to the file 5 9 Operation Sequence Electropherogram New context menu item copy in the gene sequence and the result file sequences e seq part copies the sequence shown on the screen seq complete copies the sequence of the complete Gene Chromosome 5 10 Operation Sequence CNV window In the control settings button control settings tab Selections archived controls are not available any longer 5 11 Operation Archiving Select Orders New item Org P to search for orders with defined organs phenotypes 6 Module SeqPatient 6 1 Operation Sequence dialogue Edit Bases Context menu for a selected position in the gene line What s new SEQUENCE Pilot 3 5 1 5 2 allele Delete bases and 2 allele Insert bases The maximum number of bases that can be inserted deleted is 1000 7 Module SeqHLA 7 1 HLA SBT kits from R O S E For HLA SBT Kits from R O S E pre defined amplification modules and sequencing primers are available to download on our homepage hitp www jsi medisys d
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