Article

Comprehensive benchmarking of somatic single-nucleotide variant and indel detection at ultra-low allele fractions using short- and long-read data

2025-10-14

Abstract excerpt

Mosaic mutations in normal tissues occur at low variant allele fractions (VAFs), complicating detection. To benchmark strategies, the SMaHT Network created a cell-line mixture (1:49) and produced ultra-deep whole-genome sequencing using short and long reads (five centers, 180–500× each). We assembled a reference of 44,008 mosaic SNVs and 2,059 Indels, cross-validation between platforms to expose limits of short-re...

Topics

Open a Topic to create a Post that cites this publication.

Identifiers and source

Literature Corpus work: 94a5b8c9-dbb5-53ab-8716-29ad9b771951
DOI: 10.1101/2025.10.13.681545

Open publication

Related research

Semantic proximity does not establish scientific evidence.

Click a neighbor to travelStep 1 · 12 closest

Comprehensive benchmarking of somatic single-nucleotide variant and indel detection at ultra-low allele fractions using short- and long-read dataDOI 10.1101/2025.10.13.681545Read

Comprehensive benchmarking of somatic mutation detection by the SMaHT NetworkSemantic proximity Read

Comprehensive benchmarking of somatic structural variant detection at ultra-low allele fractionsSemantic proximity Read

Assessing and Optimizing Low-Frequency Somatic Mutation Detection: A Multi-Platform High-Throughput Sequencing PerspectiveSemantic proximity Read

Prevalence and detection of low-allele-fraction variants in clinical cancer samples.Semantic proximity Read

Comprehensive benchmarking of SNV callers for highly admixed tumor data.Semantic proximity Read

Detection of somatic structural variants from short-read next-generation sequencing data.Semantic proximity Read

Establishment of reference standards for multifaceted mosaic variant analysis.Semantic proximity Read

Detection of somatic structural variants from short-read next-generation sequencing dataSemantic proximity Read

DeepSomatic: Accurate somatic small variant discovery for multiple sequencing technologiesSemantic proximity Read

Performance of common analysis methods for detecting low-frequency single nucleotide variants in targeted next-generation sequence data.Semantic proximity Read

De novo detection of somatic variants in high-quality long-read single-cell RNA sequencing dataSemantic proximity Read

De novo detection of somatic variants in high-quality long-read single-cell RNA sequencing data.Semantic proximity Read