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Can the SOPHiA solutions be used with any sequencer type or platform?

To confirm, please contact support ([email protected]) to find out if an application already exists for your sequencer.

– 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)?

To create a sample sheet for a MiSeqTM, we recommend using the “”Illumina experiment manager”” software (see details below). The list of index sequences can be found in the annex part of the Bundle Solution by SOPHiA GENETICS protocol.

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?

When stored in low bind tubes, DNA being very stable, libraries may stay at –20°C for months/years prior to usage.

After a long-term storage, it is preferable to repeat quantification by a fluorometric quantitation (e.g. Qubit®, Thermo Fisher Scientific) before usage.