Technology

Genomed’s mission is to bring high-quality genetic testing into mainstream medical practice. Our commitment to quality includes:

– Quality testing backed by peer-reviewed studies showing 100% analytic sensitivity and specificity compared to historical hereditary cancer genetic testing laboratories.

– Ongoing contributions to both ClinVar and patient registries.

– Meeting and exceeding standards for accreditation at national and state levels, including College of American Pathologists (CAP) accreditation and Clinical Laboratory Improvement Amendments (CLIA) certification.

Variant classification

Our partner’s laboratory variant classifications are based on a rigorous, logical, and reproducible assessment of available evidence. The method of variant interpretation enables a comprehensive review of the available literature and evidence, transparent in logic and conclusions, and clear explanations.

Our partner’s laboratory systematic process adheres closely to the recommendations from the American College of Medical Genetics (ACMG) and was published in Genetics in Medicine, the official journal of ACMG. It represents the industry standard among clinical genetic testing laboratories.

In addition, Our partner’s laboratory state-of-the-art Functional Modeling Platform (FMP) provides clarity for patients with variants of uncertain significance (VUS). By pulling in many lines of evidence from both lab experiments and computational analyses, FMP can accurately predict how some VUS will affect gene function. For 1 in 40 (or 2.5%) of, that means we can provide a more definitive variant classification (benign, likely benign, likely pathogenic, or pathogenic), rather than a VUS.

Variant confirmation

Our partner’s laboratory confirms clinically significant findings that do not meet stringent NGS quality metrics, using orthogonal technologies including Sanger sequencing, PacBio long read sequencing, aCGH (array comparative genome hybridization), and MLPA (multiplex ligation-dependent probe amplification). To guard against false negative results, Our partner’s laboratory runs multiple overlapping assays to redundantly target each variant.

Additionally, Our partner’s laboratory confirms CNV events by performing aCGH with a custom designed exon-focused microarray. This is the industry standard technique for these events.

Sensitivity and coverage

Diagnostic genetic testing requires a carefully constructed assay to thoroughly interrogate genes of medical importance. Our partner’s laboratory assays comprehensively report sequence changes and deletion/duplication events in coding exons, splice sites, and other regions known to harbor pathogenic mutations.

Del/dup events account for a significant proportion of pathogenic changes in hereditary disorders. Other commercially available gene panels and standard exome sequencing approaches do not always include del/dup testing or may have significant limitations, which can result in missing an important genetic change. 

Data sharing

Our partner’s laboratory submits all clinically reported variants, their classifications (i.e., pathogenic, benign, VUS, etc.) and the underlying evidence for and against pathogenicity to ClinVar. The sharing of data through ClinVar is unique in that it allows ongoing:

– inter-laboratory quality control

– detailed peer review of variant classifications

– consensus classification by the global community of experts

No other mechanism, including published scientific papers, solves these important problems. We encourage you to ask other testing providers if they share all variants, classifications, and evidence to public databases.