Tissue-based genomic profiling of 300,000 tumors highlights the detection of variants with low allele fraction
Abstract 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 V...
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| Main Authors: | , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2025-06-01
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| Series: | npj Precision Oncology |
| Online Access: | https://doi.org/10.1038/s41698-025-00991-w |
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| Summary: | Abstract 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. |
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| ISSN: | 2397-768X |