Bioscientia genomic sequencing
The Bioscientia laboratory in Ingelheim, Germany, is part of the international operations of Sonic Healthcare Limited. It provides a comprehensive medical genetic testing service which is accredited for medical testing by both the German regulatory authorities and the College of American Pathologists.
Bioscentia’s multigene panels use customised sequence capture libraries and multiplexed sequencing.
Exons and flanking intronic sequences (35 bp) are targeted and enriched from the patient’s DNA sample using the NimbleGen SeqCap EZ Choice sequence capture approach.
- DNA samples are then pooled and sequenced in a multiplexing procedure using Illumina MiSeq or HiSeq sequencing-by-synthesis technology. For gene panels, the average coverage is >200-fold, with typical coverage being 400- to 500-fold.
- Mapping and coverage statistics are generated from the mapping output files using GATK. The high level and reproducibility of coverage enables CNV analysis.
- The interpretation of the analytical data is managed by Bioscientia’s in-house bioinformatics team using a stepwise filtering process that has been developed and validated by Bioscientia, and published in the peer-reviewed literature.
- Sequence variants of interest are verified by Sanger sequencing. CNVs are validated by commercial MLPA kit (if available) or by RT-qPCR. If other family members are available, sequence of sequence variants with the disease state will be assessed.
For whole exome sequencing,
- Exons and flanking intronic sequences (35 bp) are targeted and enriched from the patient’s DNA sample using the NimbleGen SeqCap EZ Choice sequence capture approach.
- DNA samples are then pooled and sequenced in a multiplexing procedure using Illumina MiSeq or HiSeq and paired-end sequencing (2 x 100 bp) to achieve an average coverage of 100-fold.
- As with gene panels,
- statistics are generated using GATK
- interpretation of variants is managed with Bioscientia’s own bioinformatic pipeline
- variants of interest are verified by Sanger sequencing, MLPA, or RT-qPCR, and by segregation studies (if possible).