TY - JOUR
T1 - One in seven pathogenic variants can be challenging to detect by NGS
T2 - an analysis of 450,000 patients with implications for clinical sensitivity and genetic test implementation
AU - Lincoln, Stephen E.
AU - Hambuch, Tina
AU - Zook, Justin M.
AU - Bristow, Sara L.
AU - Hatchell, Kathryn
AU - Truty, Rebecca
AU - Kennemer, Michael
AU - Shirts, Brian H.
AU - Fellowes, Andrew
AU - Chowdhury, Shimul
AU - Klee, Eric W.
AU - Mahamdallie, Shazia
AU - Cleveland, Megan H.
AU - Vallone, Peter M.
AU - Ding, Yan
AU - Seal, Sheila
AU - DeSilva, Wasanthi
AU - Tomson, Farol L.
AU - Huang, Catherine
AU - Garlick, Russell K.
AU - Rahman, Nazneen
AU - Salit, Marc
AU - Kingsmore, Stephen F.
AU - Ferber, Matthew J.
AU - Aradhya, Swaroop
AU - Nussbaum, Robert L.
N1 - Publisher Copyright:
© 2021, The Author(s).
PY - 2021/9
Y1 - 2021/9
N2 - Purpose: To evaluate the impact of technically challenging variants on the implementation, validation, and diagnostic yield of commonly used clinical genetic tests. Such variants include large indels, small copy-number variants (CNVs), complex alterations, and variants in low-complexity or segmentally duplicated regions. Methods: An interlaboratory pilot study used synthetic specimens to assess detection of challenging variant types by various next-generation sequencing (NGS)–based workflows. One well-performing workflow was further validated and used in clinician-ordered testing of more than 450,000 patients. Results: In the interlaboratory study, only 2 of 13 challenging variants were detected by all 10 workflows, and just 3 workflows detected all 13. Limitations were also observed among 11 less-challenging indels. In clinical testing, 21.6% of patients carried one or more pathogenic variants, of which 13.8% (17,561) were classified as technically challenging. These variants were of diverse types, affecting 556 of 1,217 genes across hereditary cancer, cardiovascular, neurological, pediatric, reproductive carrier screening, and other indicated tests. Conclusion: The analytic and clinical sensitivity of NGS workflows can vary considerably, particularly for prevalent, technically challenging variants. This can have important implications for the design and validation of tests (by laboratories) and the selection of tests (by clinicians) for a wide range of clinical indications.
AB - Purpose: To evaluate the impact of technically challenging variants on the implementation, validation, and diagnostic yield of commonly used clinical genetic tests. Such variants include large indels, small copy-number variants (CNVs), complex alterations, and variants in low-complexity or segmentally duplicated regions. Methods: An interlaboratory pilot study used synthetic specimens to assess detection of challenging variant types by various next-generation sequencing (NGS)–based workflows. One well-performing workflow was further validated and used in clinician-ordered testing of more than 450,000 patients. Results: In the interlaboratory study, only 2 of 13 challenging variants were detected by all 10 workflows, and just 3 workflows detected all 13. Limitations were also observed among 11 less-challenging indels. In clinical testing, 21.6% of patients carried one or more pathogenic variants, of which 13.8% (17,561) were classified as technically challenging. These variants were of diverse types, affecting 556 of 1,217 genes across hereditary cancer, cardiovascular, neurological, pediatric, reproductive carrier screening, and other indicated tests. Conclusion: The analytic and clinical sensitivity of NGS workflows can vary considerably, particularly for prevalent, technically challenging variants. This can have important implications for the design and validation of tests (by laboratories) and the selection of tests (by clinicians) for a wide range of clinical indications.
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U2 - 10.1038/s41436-021-01187-w
DO - 10.1038/s41436-021-01187-w
M3 - Article
C2 - 34007000
AN - SCOPUS:85106232838
SN - 1098-3600
VL - 23
SP - 1673
EP - 1680
JO - Genetics in Medicine
JF - Genetics in Medicine
IS - 9
ER -