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<p>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 &gt;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] &gt;10% at ≥125X; 93.5% for InDels with VAF &gt; 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.</p>

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Clinical validation of a high-performance somatic exome sequencing assay: from target-enrichment strategy to variant calling

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2026年4月10日

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  • Junko Tsuji,
  • Micah Rickles-Young,
  • Justin Abreu,
  • Alyssa Friedman,
  • Caroline Petersen,
  • J. Bryan,
  • Konrad Scheffler,
  • Taylor O’Connell,
  • Theo Heyns,
  • Edyta Malolepsza,
  • Mark Fleharty,
  • Katie Larkin,
  • Kenneth J. Livak,
  • Shuqiang Li,
  • David A. Reardon,
  • Catherine J. Wu,
  • Patrick A. Ott,
  • Fanny Dao,
  • Heidi Rehm,
  • Max Jan,
  • Chip Stewart,
  • Gad Getz,
  • Varun Jain,
  • Severine Catreux,
  • Carrie Cibulskis,
  • Niall Lennon

摘要

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.