ArticleHuman mutation2022
de novo variant calling identifies cancer mutation signatures in the 1000 Genomes Project.
Article in Human mutation, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 17 citations in OpenAlex.
- Chromatin-associated intronic RNAs from long genes form introsomes that shape nuclear architecture in neuronal cells.bioRxiv : the preprint server for biology · 2026Article
- Sex-aware genome-wide assessment of de novo variants in autism across coding and noncoding regions.Human genomics · 2026Article
- Whole-genome sequencing reveals individual and cohort level insights into chromosome 9p syndromes.Genome medicine · 2025Article
- Whole-genome sequencing reveals rare and structural variants contributing to psoriasis and identifies CERCAM as a risk gene.Cell genomics · 2025Article
- Prematurity and genetic liability for autism spectrum disorder.Genome medicine · 2025Article
- CNPI: Rapid Analyses of Human Copy Number Data.Journal of molecular biology · 2025Article
- Prematurity and Genetic Liability for Autism Spectrum Disorder.medRxiv : the preprint server for health sciences · 2025Article
- Efficient identification of de novo mutations in family trios: a consensus-based informatic approach.Life science alliance · 2025Article
- Contribution ofmedRxiv : the preprint server for health sciences · 2024Article
- Automated Identification of GermlinebioRxiv : the preprint server for biology · 2024Article
- HAT: de novo variant calling for highly accurate short-read and long-read sequencing data.Bioinformatics (Oxford, England) · 2024Article
- Mosaic chromosomal alterations in peripheral blood leukocytes of children in sub-Saharan Africa.Nature communications · 2023Article
- Rare variants found in clinical gene panels illuminate the genetic and allelic architecture of orofacial clefting.Genetics in medicine : official journal of the American College of Medical Genetics · 2023Article
- Acorn: an R package for de novo variant analysis.BMC bioinformatics · 2023Article
- The landscape of somatic mutations in lymphoblastoid cell lines.Cell genomics · 2023Article
- de novo variant calling identifies cancer mutation signatures in the 1000 Genomes Project.Human mutation · 2022Article
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Corrections and comments
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Authors and funding
17 authors at 3 institutions in 1 country.
Funding
Abstract
Detection of de novo variants (DNVs) is critical for studies of disease-related variation and mutation rates. To accelerate DNV calling, we developed a graphics processing units-based workflow. We applied our workflow to whole-genome sequencing data from three parent-child sequenced cohorts including the Simons Simplex Collection (SSC), Simons Foundation Powering Autism Research (SPARK), and the 1000 Genomes Project (1000G) that were sequenced using DNA from blood, saliva, and lymphoblastoid cell lines (LCLs), respectively. The SSC and SPARK DNV callsets were within expectations for number of DNVs, percent at CpG sites, phasing to the paternal chromosome of origin, and average allele balance. However, the 1000G DNV callset was not within expectations and contained excessive DNVs that are likely cell line artifacts. Mutation signature analysis revealed 30% of 1000G DNV signatures matched B-cell lymphoma. Furthermore, we found variants in DNA repair genes and at Clinvar pathogenic or likely-pathogenic sites and significant excess of protein-coding DNVs in IGLL5; a gene known to be involved in B-cell lymphomas. Our study provides a new rapid DNV caller for the field and elucidates important implications of using sequencing data from LCLs for reference building and disease-related projects.
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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.