Clinical validation of a high-performance somatic exome sequencing assay: from target-enrichment strategy to variant calling
Clinical whole-exome sequencing (WES) has revolutionized clinical diagnostics by enabling scalable, cost-effective molecular profiling to detect somatic variants and identify novel therapeutic targets. In particular, the clinical evaluation of somatic variants relies on both high-quality sequencing data and robust variant detection with rapid turnaround times. We developed an updated WES workflow utilizing a co-developed Twist Bioscience targeting panel and the DRAGEN (Dynamic Read Analysis for GENomics) platform, benchmarked with cell line mixtures containing >40,000 simulated variants and a clinical cohort of FFPE tumor specimens. Our assay, the Broad Clinical Somatic Whole Exome Assay V6.0, demonstrated high sensitivity (96.9% for SNVs with variant allele fraction [VAF] >10% at ≥125X; 93.5% for InDels with VAF > 20% at ≥125X) and low false positive rates (0.04 and 0.01 per Mb, respectively). The assay meets clinical requirements and enables large-scale, accurate variant profiling of cancers, expanding opportunities for molecular diagnostics across diverse clinical settings.
Authors
- Chip Stewart (ORCID: https://orcid.org/0000-0003-2245-9552)
- Justin Abreu
- Micah Rickles-Young (ORCID: https://orcid.org/0009-0004-0843-883X)
- Edyta Małolepsza
- Taylor O’Connell (ORCID: https://orcid.org/0000-0003-1384-5304)
- Severine Catreux (ORCID: https://orcid.org/0009-0008-1813-1240)
- Junko Tsuji (ORCID: https://orcid.org/0000-0003-0139-3750)
- Max Jan (ORCID: https://orcid.org/0000-0002-7071-5517)
- Katie Larkin
- Kenneth J. Livak (ORCID: https://orcid.org/0000-0001-9105-5856)
- Carrie Cibulskis (ORCID: https://orcid.org/0000-0002-1996-8957)
- David A. Reardon (ORCID: https://orcid.org/0000-0001-6674-0157)
- Konrad Scheffler (ORCID: https://orcid.org/0000-0002-6041-8367)
- S. Li
- Theo Heyns
- Caroline L Petersen
- Alyssa Friedman
- Mark Fleharty
- Fanny Dao
- Niall Lennon
- J. Bryan
- Varun Jain
- Catherine J. Wu
- Patrick A. Ott
- Heidi Rehm
- Gad Getz
Institutions
- Broad Institute (US)
- The University of Texas MD Anderson Cancer Center (US)
- Harvard University (US)
- Illumina (United States) (US)
- Dana-Farber Cancer Institute (US)
- Center for Cancer Research (US)
Publication Details
- Journal
- npj Genomic Medicine
- Published
- 2026-04-10
- DOI
- https://doi.org/10.1038/s41525-026-00569-w
- Primary Topic
- Cancer Genomics and Diagnostics
- Type
- article
- Field-Weighted Citation Impact
- 0.00
Funders
- Dana-Farber Cancer Institute
- Parker Institute for Cancer Immunotherapy
- National Cancer Institute