ArticleGenome biology2021
Comprehensive identification of somatic nucleotide variants in human brain tissue.
Article in Genome biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed, 48 citations in OpenAlex.
- High-throughput evaluation of in vitro CRISPR activities enables optimized large-scale multiplex enrichment of rare variants.Nature biomedical engineering · 2026Article
- A recurrent sequencing artifact on Illumina sequencers with two-color fluorescent dye chemistry and its impact on somatic variant detection.Genome biology · 2026Article
- Disease insights from brain somatic mosaicism.Experimental & molecular medicine · 2026Review
- Genomic landscape and molecular subtypes of primary central nervous system lymphoma.Blood cancer journal · 2025Article
- A personalized multi-platform assessment of somatic mosaicism in the human frontal cortex.bioRxiv : the preprint server for biology · 2025Article
- Comprehensive benchmarking of somatic mutation detection by the SMaHT Network.bioRxiv : the preprint server for biology · 2025Article
- A recurrent sequencing artifact on Illumina sequencers with two-color fluorescent dye chemistry and its impact on somatic variant detection.bioRxiv : the preprint server for biology · 2025Article
- Establishment and molecular characterisation of patient-derived organoids for primary central nervous system lymphoma.Leukemia · 2025Article
- Direct measurement of the male germline mutation rate in individuals using sequential sperm samples.Nature communications · 2025Article
- Cerebellum mitochondrial DNA copy number is increased in Parkinson's disease.Brain communications · 2025Article
- Backtracking Cell Phylogenies in the Human Brain with Somatic Mosaic Variants.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Somatic mutations in autoinflammatory and autoimmune disease.Nature reviews. Rheumatology · 2024Review
- Somatic mosaicism in schizophrenia brains reveals prenatal mutational processes.Science (New York, N.Y.) · 2024Article
- Somatic nuclear mitochondrial DNA insertions are prevalent in the human brain and accumulate over time in fibroblasts.PLoS biology · 2024Article
- Genomic Mosaicism of the Brain: Origin, Impact, and Utility.Neuroscience bulletin · 2024Review
- Review
- Mapping recurrent mosaic copy number variation in human neurons.Nature communications · 2024Article
- Bioinformatics of germline variant discovery for rare disease diagnostics: current approaches and remaining challenges.Briefings in bioinformatics · 2024Review
- Comprehensive benchmarking and guidelines of mosaic variant calling strategies.Nature methods · 2023Article
- Genomic data resources of the Brain Somatic Mosaicism Network for neuropsychiatric diseases.Scientific data · 2023Article
Corrections and comments
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Authors and funding
51 authors at 15 institutions in 2 countries.
Funding
Abstract
backgroundPost-zygotic mutations incurred during DNA replication, DNA repair, and other cellular processes lead to somatic mosaicism. Somatic mosaicism is an established cause of various diseases, including cancers. However, detecting mosaic variants in DNA from non-cancerous somatic tissues poses significant challenges, particularly if the variants only are present in a small fraction of cells.
resultsHere, the Brain Somatic Mosaicism Network conducts a coordinated, multi-institutional study to examine the ability of existing methods to detect simulated somatic single-nucleotide variants (SNVs) in DNA mixing experiments, generate multiple replicates of whole-genome sequencing data from the dorsolateral prefrontal cortex, other brain regions, dura mater, and dural fibroblasts of a single neurotypical individual, devise strategies to discover somatic SNVs, and apply various approaches to validate somatic SNVs. These efforts lead to the identification of 43 bona fide somatic SNVs that range in variant allele fractions from ~ 0.005 to ~ 0.28. Guided by these results, we devise best practices for calling mosaic SNVs from 250× whole-genome sequencing data in the accessible portion of the human genome that achieve 90% specificity and sensitivity. Finally, we demonstrate that analysis of multiple bulk DNA samples from a single individual allows the reconstruction of early developmental cell lineage trees.
conclusionsThis study provides a unified set of best practices to detect somatic SNVs in non-cancerous tissues. The data and methods are freely available to the scientific community and should serve as a guide to assess the contributions of somatic SNVs to neuropsychiatric diseases.
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