Article

Comprehensive benchmarking of methods for mutation calling in circulating tumor DNA

2025-02-20

Abstract excerpt

Detection of somatic mutations in cell-free DNA (cfDNA) is challenging due to low variant allele frequencies and pronounced DNA degradation. Here, we present a novel approach and resource for benchmarking of somatic variant calling algorithms in cfDNA samples from cancer patients. Using longitudinally collected cfDNA samples from colorectal and breast cancer patients, we identify patient-matched samples with high...

Topics

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

Identifiers and source

Literature Corpus work: 341ea690-cf45-5931-964f-6ece1f4b3c0e
DOI: 10.1101/2025.02.16.638482

Open publication

Related research

Semantic proximity does not establish scientific evidence.

Click a neighbor to travelStep 1 · 12 closest

Comprehensive benchmarking of methods for mutation calling in circulating tumor DNADOI 10.1101/2025.02.16.638482Read

Comprehensive benchmarking of methods for mutation calling in circulating tumor DNA.Semantic proximity Read

Evaluating Bioinformatics Processing of Somatic Variant Detection in cfDNA Using Targeted Sequencing with UMIs.Semantic proximity Read

Benchmarking of duplex sequencing approaches to reveal somatic mutation landscapesSemantic proximity Read

Tumor-naïve ctDNA detection with deep learning-enhanced error suppression for sensitive mutation calling.Semantic proximity Read

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

Error-corrected flow-based sequencing at whole-genome scale and its application to circulating cell-free DNA profiling.Semantic proximity Read

Genome-wide mutational signatures in low-coverage whole genome sequencing of cell-free DNA.Semantic proximity Read

ABEMUS: platform-specific and data-informed detection of somatic SNVs in cfDNA.Semantic proximity Read

Combining mutation detection with fragmentomics features leads to improved tumor-informed ctDNA detectionSemantic proximity Read

Sensitive detection of tumor mutations from blood and its application to immunotherapy prognosisSemantic proximity Read

Benchmarking UMI-aware and standard variant callers for low frequency ctDNA variant detection.Semantic proximity Read

Enhanced specificity of high sensitivity somatic variant profiling in cell-free DNA via paired normal sequencing: design, validation, and clinical experience of the MSK-ACCESS liquid biopsy assaySemantic proximity Read