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Article

Integrated approach to generate artificial samples with low tumor fraction for somatic variant calling benchmarking.

BMC bioinformatics - 8 May 2024

Sergi Aldo, Beltrame Luca, Marchini Sergio, Masseroli Marco

Abstract excerpt

BACKGROUND: High-throughput sequencing (HTS) has become the gold standard approach for variant analysis in cancer research. However, somatic variants may occur at low fractions due to contamination from normal cells or tumor heterogeneity; this poses a significant challenge for standard HTS analysis pipelines. The problem is exacerbated in scenarios with minimal tumor DNA, such as circulating tumor DNA in plasma....

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PMID: 38720249
DOI: 10.1186/s12859-024-05793-8
PMCID: PMC11077792

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