ArticleNucleic acids research2016
Ultra-fast local-haplotype variant calling using paired-end DNA-sequencing data reveals somatic mosaicism in tumor and normal blood samples.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed, 18 citations in OpenAlex.
- Genetically transitional disease: conceptual understanding and applicability to rheumatic disease.Nature reviews. Rheumatology · 2024Review
- Validation of genetic variants from NGS data using deep convolutional neural networks.BMC bioinformatics · 2023Article
- Somatic and Germline Variant Calling from Next-Generation Sequencing Data.Advances in experimental medicine and biology · 2022Article
- Article
- Comprehensive Outline of Whole Exome Sequencing Data Analysis Tools Available in Clinical Oncology.Cancers · 2019Review
- Calling Variants in the Clinic: Informed Variant Calling Decisions Based on Biological, Clinical, and Laboratory Variables.Computational and structural biotechnology journal · 2019Review
- Detecting Somatic Mutations in Normal Cells.Trends in genetics : TIG · 2018Review
- A review of somatic single nucleotide variant calling algorithms for next-generation sequencing data.Computational and structural biotechnology journal · 2018Review
- Phased Genotyping-by-Sequencing Enhances Analysis of Genetic Diversity and Reveals Divergent Copy Number Variants in Maize.G3 (Bethesda, Md.) · 2017Article
Corrections and comments
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
Abstract
Somatic mosaicism refers to the existence of somatic mutations in a fraction of somatic cells in a single biological sample. Its importance has mainly been discussed in theory although experimental work has started to emerge linking somatic mosaicism to disease diagnosis. Through novel statistical modeling of paired-end DNA-sequencing data using blood-derived DNA from healthy donors as well as DNA from tumor samples, we present an ultra-fast computational pipeline, LocHap that searches for multiple single nucleotide variants (SNVs) that are scaffolded by the same reads. We refer to scaffolded SNVs as local haplotypes (LH). When an LH exhibits more than two genotypes, we call it a local haplotype variant (LHV). The presence of LHVs is considered evidence of somatic mosaicism because a genetically homogeneous cell population will not harbor LHVs. Applying LocHap to whole-genome and whole-exome sequence data in DNA from normal blood and tumor samples, we find wide-spread LHVs across the genome. Importantly, we find more LHVs in tumor samples than in normal samples, and more in older adults than in younger ones. We confirm the existence of LHVs and somatic mosaicism by validation studies in normal blood samples. LocHap is publicly available at http://www.compgenome.org/lochap.
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Registered trials
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