Next generation sequencing for clinical diagnostics: Five year experience of an academic laboratory

Paige Hartman, Kenny B Beckman, Kevin A Silverstein, Sophia L Yohe, Matthew Schomaker, Christine Henzler, Getiria Onsongo, Ham Ching Lam, Sarah A Munro, Jerry Daniel, Bradley Billstein, Archana Deshpande, Adam Hauge, Pawel A Mroz, Whiwon Lee, Jennifer Holle, Katie Wiens, Kylene Karnuth, Teresa Kemmer, Michaela LearyStephen Michel, Laurie Pohlman, Venugopal Thayanithy, Andrew C Nelson, Matthew Bower, Bharat Thyagarajan

Research output: Contribution to journalArticle

3 Scopus citations

Abstract

Clinical laboratories have adopted next generation sequencing (NGS) as a gold standard for the diagnosis of hereditary disorders because of its analytic accuracy, high throughput, and potential for cost-effectiveness. We describe the implementation of a single broad-based NGS sequencing assay to meet the genetic testing needs at the University of Minnesota. A single hybrid capture library preparation was used for each test ordered, data was informatically blinded to clinically-ordered genes, and identified variants were reviewed and classified by genetic counselors and molecular pathologists. We performed 2509 sequencing tests from August 2012 till December 2017. The diagnostic yield has remained steady at 25%, but the number of variants of uncertain significance (VUS) included in a patient report decreased over time with 50% of the patient reports including at least one VUS in 2012 and only 22% of the patient reports reporting a VUS in 2017 (p =.002). Among the various clinical specialties, the diagnostic yield was highest in dermatology (60% diagnostic yield) and ophthalmology (42% diagnostic yield) while the diagnostic yield was lowest in gastrointestinal diseases and pulmonary diseases (10% detection yield in both specialties). Deletion/duplication analysis was also implemented in a subset of panels ordered, with 9% of samples having a diagnostic finding using the deletion/duplication analysis. We have demonstrated the feasibility of this broad-based NGS platform to meet the needs of our academic institution by aggregating a sufficient sample volume from many individually rare tests and providing a flexible ordering for custom, patient-specific panels.

Original languageEnglish (US)
Article number100464
JournalMolecular Genetics and Metabolism Reports
Volume19
DOIs
StatePublished - Jun 2019

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Keywords

  • Copy number variation
  • Diagnostic yield
  • Molecular diagnostics
  • Next generation sequencing
  • Panel testing
  • Variants of uncertain significance

PubMed: MeSH publication types

  • Journal Article

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