ArticleProceedings of the National Academy of Sciences of the United States of America2011
Demographic history and rare allele sharing among human populations.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 403 papers, 1 of them a synthesis that pooled it.
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Who cites it
403 citing papers in PubMed, 1 synthesis or guideline pooled it.
- An admixture mapping meta-analysis implicates genetic variation at 18q21 with asthma susceptibility in Latinos.The Journal of allergy and clinical immunology · 2019Pooled it
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- Allele Frequency Spectra as a General Tool for Modeling Genetic Diversity.Acta biotheoretica · 2026Article
- Interpreting GC content differences across populations at polymorphic sites.bioRxiv : the preprint server for biology · 2026Article
- Tractor workflow: a scalable Nextflow framework for local ancestry-aware genome-wide association studies.Bioinformatics (Oxford, England) · 2026Article
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- A spectral component approach leveraging identity-by-descent graphs to address recent population structure in genomic analysis.Genome research · 2026Article
- FRAME: fast reference-based ancestry makeup estimation tool.Bioinformatics advances · 2026Article
- Psoriasis risk allele function in activated Th1/17 cells with "memory" to antigen exposure.PloS one · 2026Article
- The Influence of Demographic History and Genetic Architecture on Complex Traits via Runs of Homozygosity.bioRxiv : the preprint server for biology · 2025Article
- Determining the driving factors shaping genetic architecture of complex traits in recently admixed populations.bioRxiv : the preprint server for biology · 2025Article
- The impact of non-neutral synonymous mutations when inferring selection on nonsynonymous mutations.Genetics · 2025Article
- Genome-wide selection inference at short tandem repeats.PLoS genetics · 2025Article
343 more citing papers are in PubMed but not listed here.
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10 authors.
Funding
Abstract
High-throughput sequencing technology enables population-level surveys of human genomic variation. Here, we examine the joint allele frequency distributions across continental human populations and present an approach for combining complementary aspects of whole-genome, low-coverage data and targeted high-coverage data. We apply this approach to data generated by the pilot phase of the Thousand Genomes Project, including whole-genome 2-4× coverage data for 179 samples from HapMap European, Asian, and African panels as well as high-coverage target sequencing of the exons of 800 genes from 697 individuals in seven populations. We use the site frequency spectra obtained from these data to infer demographic parameters for an Out-of-Africa model for populations of African, European, and Asian descent and to predict, by a jackknife-based approach, the amount of genetic diversity that will be discovered as sample sizes are increased. We predict that the number of discovered nonsynonymous coding variants will reach 100,000 in each population after ∼1,000 sequenced chromosomes per population, whereas ∼2,500 chromosomes will be needed for the same number of synonymous variants. Beyond this point, the number of segregating sites in the European and Asian panel populations is expected to overcome that of the African panel because of faster recent population growth. Overall, we find that the majority of human genomic variable sites are rare and exhibit little sharing among diverged populations. Our results emphasize that replication of disease association for specific rare genetic variants across diverged populations must overcome both reduced statistical power because of rarity and higher population divergence.
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