ArticleNature methods2023
Comprehensive benchmarking and guidelines of mosaic variant calling strategies.
Article in Nature methods, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
23 citing papers in PubMed, 20 citations in OpenAlex.
- Advancing risk gene discovery across the allele frequency spectrum.HGG advances · 2026Review
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- Genomic Surveillance of Endemic Human Coronaviruses in Côte d'Ivoire Using Targeted Hybrid-Capture Sequencing.Viruses · 2026Article
- Characterization of subclonal variants in HG002 Genome in a Bottle reference material as a resource for benchmarking variant callers.Cell genomics · 2026Article
- Disease insights from brain somatic mosaicism.Experimental & molecular medicine · 2026Review
- Review
- Scalable and comprehensive mosaic variant calling using DRAGEN.medRxiv : the preprint server for health sciences · 2026Article
- Bi-allelic TPP1 variants in neuronal ceroid lipofuscinosis 2: clinical findings from an Iranian cohort of 20 patients, founder effect, and in silico analyses.Human genetics · 2026Article
- Synth4bench: generating synthetic data for benchmarking tumor-only somatic variant calling algorithms.Frontiers in bioinformatics · 2026Article
- MosaicSim: A Novel Mosaic Variant Simulator Reveals Diminishing Returns of Ultra-High Coverage for Mosaic Variant Detection.bioRxiv : the preprint server for biology · 2025Article
- Expanding the Genome in a Bottle Truth Set: Detection and Validation of Novel Low-frequency Variants Using High-accuracy NanoSeq.bioRxiv : the preprint server for biology · 2025Article
- Article
- Advances in single-cell DNA sequencing enable insights into human somatic mosaicism.Nature reviews. Genetics · 2025Review
- Comprehensive benchmarking of somatic single-nucleotide variant and indel detection at ultra-low allele fractions using short- and long-read data.bioRxiv : the preprint server for biology · 2025Article
- Comprehensive benchmarking of somatic mutation detection by the SMaHT Network.bioRxiv : the preprint server for biology · 2025Article
- UNISOM: Unified Somatic Calling and Machine Learning-based Classification Enhance the Discovery of CHIP.Genomics, proteomics & bioinformatics · 2025Article
- Identifying genetic errors of immunity due to mosaicism.The Journal of experimental medicine · 2025Review
- Direct measurement of the male germline mutation rate in individuals using sequential sperm samples.Nature communications · 2025Article
- A robust benchmark for detecting low-frequency variants in the HG002 Genome In A Bottle NIST reference material.bioRxiv : the preprint server for biology · 2024Article
- Precise identification of somatic and germline variants in the absence of matched normal samples.Briefings in bioinformatics · 2024Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
Rapid advances in sequencing and analysis technologies have enabled the accurate detection of diverse forms of genomic variants represented as heterozygous, homozygous and mosaic mutations. However, the best practices for mosaic variant calling remain disorganized owing to the technical and conceptual difficulties faced in evaluation. Here we present our benchmark of 11 feasible mosaic variant detection approaches based on a systematically designed whole-exome-level reference standard that mimics mosaic samples, supported by 354,258 control positive mosaic single-nucleotide variants and insertion-deletion mutations and 33,111,725 control negatives. We identified not only the best practice for mosaic variant detection but also the condition-dependent strengths and weaknesses of the current methods. Furthermore, feature-level evaluation and their combinatorial usage across multiple algorithms direct the way for immediate to prolonged improvements in mosaic variant detection. Our results will guide researchers in selecting suitable calling algorithms and suggest future strategies for developers.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.