Join us at the upcoming American Society of Human Genetics 2019 Annual Meeting!
October 16 to 18, 2019
Stop by Booth #1331 to say hello.
Or attend one of our two poster sessions:
Whole Genome Sequencing (WGS) as a first-line diagnostic test: Its success is in the details.
Poster #2514. Presented by Alex Kaplun, PhD Wednesday 10/16 from 3-4pm.
WGS is well positioned to become the clinical diagnostic standard for rare genetic disorders due to the benefits inherent in PCR-free, genome-wide sequencing combined with its continually decreasing cost. Initial published reports are supportive of this paradigm shift, yet all WGS assays are not created equal. We’ve undertaken the challenge to develop and validate a clinical WGS pipeline that supports simultaneous analysis and interpretation of multiple variant types, resulting in a clinically available alternative to sequential testing.
Clinical grade whole genome sequencing (WGS) is conducted on an Illumina platform using the Illumina TruSeq DNA PCR-Free Library Preparation Kit. With the PCR-free protocol, significantly less average coverage is required compared to panels and exomes. Specifically, we find that 30X mean mappable coverage provides a highly uniform sequencing depth with 97.3% of nucleotides covered at ≥8X and 99.4% of HGMD and ClinVar annotated variants covered at ≥8X – a depth that is sufficient for specific and sensitive variant calling. Following alignment of reads, a combination of open source and proprietary algorithms call small sequence change variants, structural variants, mitochondrial variants and tandem repeat expansions. Variants are subjected to annotation and filtering before being presented to our clinicians for interpretation within the context of the patient’s clinical symptoms and medical history.
In 2018, we obtained full CLIA accreditation and CAP certification for all four components of our WGS pipeline: small sequence changes, structural variants, mitochondrial variants and short tandem repeats. We will present a combination of secondary and tertiary validation results which demonstrate >99% sensitivity, specificity and PPV for single nucleotide variants; >95% sensitivity and specificity for indels up to 50 nucleotides; >96% clinical sensitivity for structural variants; the ability to detect mitochondrial heteroplasmy levels down to 5%; and >99% sensitivity for tandem repeat expansions spanning >20 known pathogenic loci. We will additionally present cases representative of those processed in the first 18 months that the full Genomic Unity™ test has been available for clinical use.
Tandem whole genome analysis enables comprehensive family planning.
Poster #544. Presented by Nir Neerman Thursday 10/17 from 3-4pm.
A variety of carrier screening tests are offered with the promise of helping young couples with family planning. Available tests generally focus on a small subset of specific conditions and genes. While these tests are able to detect the most common causes of selected recessive conditions, they are unable to provide information about the large number of rare disorders that are less common. On the surface, when looked at on an individual basis, these disorders are deceptively rare. It’s only when the set of more than 5,000 diseases with a genetic basis are considered as a whole, it becomes apparent that the impact is significant. Whole genome sequencing (WGS) provides the ability to detect variants that cause these conditions, as well as the ability to identify complex variants that cause the more commonly screened conditions but go undetected with other tests. Tandem analysis of reproductive partner genomes via WGS has the potential to provide a comprehensive assessment of shared carrier risks.
To test the tandem analysis approach, we started with our clinical WGS pipeline which has been validated for detection of small sequence changes, mitochondrial variants, structural variants and more than 20 tandem repeat expansions. This is the same pipeline that is currently used for the clinical WGS tests performed in our lab, including our Genomic Inform™ test for healthy individuals – a physician-ordered clinical test that includes carrier status analysis and reporting. We then adapted the annotation filters and variant interpretation workflow to additionally process and analyze whole genomes of potential reproductive partners in tandem, evaluating more than 50 paired genomes.
Identified variants included small sequence changes in commonly (i.e. CFTR: cystic fibrosis) and uncommonly (i.e. SEPN1: multiminicore disease; congenital myopathy with fiber-type disproportion) screened genes, large structural variants as well as premutation alleles of tandem repeat genes like FMR1 which is responsible for Fragile X syndrome. The tandem analysis workflow successfully identified dual carrier genome pairings with the potential to produce offspring inheriting two copies of the same deleterious variant. It also identified dual carrier pairings that involved the potential to inherit compound heterozygous variants in the same gene, including examples of structural variants paired with small sequence changes. We will present examples for each case type.