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<p>Tumor tissues obtained in the clinical setting typically have low purity and display treatment-associated genetic heterogeneity, contributing to variants at low variant allele fractions (VAF). We present a pan-cancer landscape and the therapeutic impact of somatic variants detected at low VAF (≤10%) from tumor tissues in 331,503 patients, across 78 tumor types, that received an FDA-approved comprehensive genomic profiling (CGP) test targeting ~324 genes during routine clinical care. 29% of patients had at least one variant detected at VAF ≤10% and 16% at VAF ≤5%. Among the frequently diagnosed tumors, several cases showed low VAF variants: pancreatic (37%), non-small cell lung cancer (35%), colorectal (29%) and prostate (24%). Treatment resistance-associated alterations had lower median VAF than driver alterations, although variants with VAF ≤5% comprised both driver and resistance alterations. This highlights the importance of CGP in detecting low VAF variants, to better inform clinical actionability and guide personalized treatment for patients with cancer.</p>

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Tissue-based genomic profiling of 300,000 tumors highlights the detection of variants with low allele fraction

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年6月17日

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  • Saumya D. Sisoudiya,
  • Hanna Tukachinsky,
  • Rachel B. Keller-Evans,
  • Alexa B. Schrock,
  • Richard S. P. Huang,
  • Ole Gjoerup,
  • Michael J. Pishvaian,
  • Rachna Shroff,
  • Ethan S. Sokol,
  • Lucas Dennis,
  • Garrett M. Frampton,
  • Smruthy Sivakumar

摘要

Tumor tissues obtained in the clinical setting typically have low purity and display treatment-associated genetic heterogeneity, contributing to variants at low variant allele fractions (VAF). We present a pan-cancer landscape and the therapeutic impact of somatic variants detected at low VAF (≤10%) from tumor tissues in 331,503 patients, across 78 tumor types, that received an FDA-approved comprehensive genomic profiling (CGP) test targeting ~324 genes during routine clinical care. 29% of patients had at least one variant detected at VAF ≤10% and 16% at VAF ≤5%. Among the frequently diagnosed tumors, several cases showed low VAF variants: pancreatic (37%), non-small cell lung cancer (35%), colorectal (29%) and prostate (24%). Treatment resistance-associated alterations had lower median VAF than driver alterations, although variants with VAF ≤5% comprised both driver and resistance alterations. This highlights the importance of CGP in detecting low VAF variants, to better inform clinical actionability and guide personalized treatment for patients with cancer.