ArticlePloS one2013
Comprehensive characterization of human genome variation by high coverage whole-genome sequencing of forty four Caucasians.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers, 3 of them syntheses that pooled it.
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Who cites it
37 citing papers in PubMed, 3 syntheses or guidelines pooled it, 80 citations in OpenAlex.
- Association of Cognition-Related Genetic Polymorphisms with Elite Athlete Status: A Meta-Analysis.Genes · 2026Pooled it
- Integrative genomic analysis predicts novel functional enhancer-SNPs for bone mineral density.Human genetics · 2019Pooled it
- Predicting Functional Effects of Synonymous Variants: A Systematic Review and Perspectives.Frontiers in genetics · 2019Pooled it
- Identification of high-risk SNPs in SLC22A transporter genes: their potential role in PCOS and metformin uptake.BMC genomic data · 2026Article
- Functional Enrichment Analysis Identifying Regulatory Information Associated with Human Fracture.Calcified tissue international · 2023Article
- Distinct mutational processes shape selection of MHC class I and class II mutations across primary and metastatic tumors.Cell reports · 2023Article
- Multi-omic stratification of the missense variant cysteinome.bioRxiv : the preprint server for biology · 2023Article
- A Novel Synonymous Variant of PHEX in a Patient with X-Linked Hypophosphatemia.Calcified tissue international · 2022Article
- Genome interpretation using in silico predictors of variant impact.Human genetics · 2022Review
- Synonymous ADAMTS13 variants impact molecular characteristics and contribute to variability in active protein abundance.Blood advances · 2022Article
- shRNAs Targeting a CommonInternational journal of molecular sciences · 2022Article
- Review
- Decoding the effects of synonymous variants.Nucleic acids research · 2021Article
- DNA copy number variation: Main characteristics, evolutionary significance, and pathological aspects.Biomedical journal · 2021Review
- Review
- Identification of novel functional CpG-SNPs associated with Type 2 diabetes and birth weight.Aging · 2021Article
- Mutational Landscape of the Proglucagon-Derived Peptides.Frontiers in endocrinology · 2021Article
- Low Diversity of Human Variation Despite Mostly Mild Functional Impact of De Novo Variants.Frontiers in molecular biosciences · 2021Article
- Article
- Identification of novel functional CpG-SNPs associated with type 2 diabetes and coronary artery disease.Molecular genetics and genomics : MGG · 2020Article
Corrections and comments
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Authors and funding
13 authors at 3 institutions in 2 countries.
Funding
Abstract
Whole genome sequencing studies are essential to obtain a comprehensive understanding of the vast pattern of human genomic variations. Here we report the results of a high-coverage whole genome sequencing study for 44 unrelated healthy Caucasian adults, each sequenced to over 50-fold coverage (averaging 65.8×). We identified approximately 11 million single nucleotide polymorphisms (SNPs), 2.8 million short insertions and deletions, and over 500,000 block substitutions. We showed that, although previous studies, including the 1000 Genomes Project Phase 1 study, have catalogued the vast majority of common SNPs, many of the low-frequency and rare variants remain undiscovered. For instance, approximately 1.4 million SNPs and 1.3 million short indels that we found were novel to both the dbSNP and the 1000 Genomes Project Phase 1 data sets, and the majority of which (∼96%) have a minor allele frequency less than 5%. On average, each individual genome carried ∼3.3 million SNPs and ∼492,000 indels/block substitutions, including approximately 179 variants that were predicted to cause loss of function of the gene products. Moreover, each individual genome carried an average of 44 such loss-of-function variants in a homozygous state, which would completely "knock out" the corresponding genes. Across all the 44 genomes, a total of 182 genes were "knocked-out" in at least one individual genome, among which 46 genes were "knocked out" in over 30% of our samples, suggesting that a number of genes are commonly "knocked-out" in general populations. Gene ontology analysis suggested that these commonly "knocked-out" genes are enriched in biological process related to antigen processing and immune response. Our results contribute towards a comprehensive characterization of human genomic variation, especially for less-common and rare variants, and provide an invaluable resource for future genetic studies of human variation and diseases.
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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.