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Can the SOPHiA solutions be used with any sequencer type or platform?
– If the application already exists, it could be activated for immediate use.
– If it does not exist, more time will be needed to develop the application (via our Set-Up Programs).
All SOPHiA GENETICS applications are optimized using real clinical data for a specific combination of sequencer, sample type, gene panel and amplification technology (capture, amplicon, others).
How are Illumina MiSeq™ Sample Sheets created (for use with Bundle Solutions by SOPHiA GENETICS)?
Follow these instructions in the “”Illumina experiment manager”” software:
– Open the software and click on “Create Sample Sheet”
– Choose “MiSeq”, then “Other”, followed by “FASTQ Only”
– Enter the Reagent Cartridge Barcode (for example MS5903244-300V2 found on the front of the cartridge)
– For the Library Prep Kit, select “TruSeq HT” (Note: if TruSeqHT indices do not appear (new version of Illumina software) select “TruSeq DNA PCR-Free” as the Library Prep Workflow. Followed by “TruSeq DNA CD Indexes” (96 indexes) as the Index Adapters.)
– For Index reads select “2”
– Enter the experiment name
– Enter the investigator name
– Enter a brief description of the experiment
– The date should be automatically entered as the current date; if not, enter the date in the MM/DD/YYYY format.
– Select “Paired End” for read type
– For “Cycles Read 1” choose the number of cycles (for example 151 for a V2 300 cartridge or 301 for a V3 600 cartridge)
– For “Cycles Read 2” choose the same number of cycles as above
– Select “Use Adapter Trimming” and “Use Adapter Trimming Read 2”
– Click on “Next”
– Click on “Add Blank Row” as many times as correlates to the number of samples you have.
– Enter the “Sample ID”, “Index 1 (I7)” and “Index 2 (i5)”” for all your samples according to the table found in the Annex of the Bundle Solution by SOPHiA GENETICS protocol
– Select “Finish” and save the file in “csv” format
How long can individual libraries and captured libraries be stored at -20°C before sequencing?
After a long-term storage, it is preferable to repeat quantification by a fluorometric quantitation (e.g. Qubit®, Thermo Fisher Scientific) before usage.