ArticlePLoS genetics2013
Low frequency variants, collapsed based on biological knowledge, uncover complexity of population stratification in 1000 genomes project data.
Article in PLoS genetics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- Whole-exome sequencing to analyze population structure, parental inbreeding, and familial linkage.Proceedings of the National Academy of Sciences of the United States of America · 2016Trial
- Landscape of rare-allele variants in cultivated and wild soybean genomes.The plant genome · 2025Article
- Unlocking Allelic Diversity for Sustainable Development of Salinity Stress Tolerance in Rice.Current genomics · 2021Review
- Controlling for human population stratification in rare variant association studies.Scientific reports · 2021Article
- Rare and common variant discovery by whole-genome sequencing of 101 Thoroughbred racehorses.Scientific reports · 2021Article
- Determining population stratification and subgroup effects in association studies of rare genetic variants for nicotine dependence.Psychiatric genetics · 2019Article
- Functional architecture of low-frequency variants highlights strength of negative selection across coding and non-coding annotations.Nature genetics · 2018Article
- On the substructure controls in rare variant analysis: Principal components or variance components?Genetic epidemiology · 2018Article
- PLATO software provides analytic framework for investigating complexity beyond genome-wide association studies.Nature communications · 2017Article
- Extremely Rare Polymorphisms in Saccharomyces cerevisiae Allow Inference of the Mutational Spectrum.PLoS genetics · 2017Article
- Comprehensive genetic testing with ethnic-specific filtering by allele frequency in a Japanese hearing-loss population.Clinical genetics · 2016Article
- Atlas of Cryptic Genetic Relatedness Among 1000 Human Genomes.Genome biology and evolution · 2016Article
- Genomic variations and distinct evolutionary rate of rare alleles in Arabidopsis thaliana.BMC evolutionary biology · 2016Article
- Leveraging ancestry to improve causal variant identification in exome sequencing for monogenic disorders.European journal of human genetics : EJHG · 2016Article
- KNOWLEDGE DRIVEN BINNING AND PHEWAS ANALYSIS IN MARSHFIELD PERSONALIZED MEDICINE RESEARCH PROJECT USING BIOBIN.Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing · 2016Article
- The Role of Metabotropic Glutamate Receptor Genes in Schizophrenia.Current neuropharmacology · 2016Review
- A biologically informed method for detecting rare variant associations.BioData mining · 2016Article
- Cruchaga & Goate reply.Nature · 2015Article
- Inference of distant genetic relations in humans using "1000 genomes".Genome biology and evolution · 2015Article
- Dissecting ancestry genomic background in substance dependence genome-wide association studies.Pharmacogenomics · 2015Article
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Authors and funding
7 authors.
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Abstract
Analyses investigating low frequency variants have the potential for explaining additional genetic heritability of many complex human traits. However, the natural frequencies of rare variation between human populations strongly confound genetic analyses. We have applied a novel collapsing method to identify biological features with low frequency variant burden differences in thirteen populations sequenced by the 1000 Genomes Project. Our flexible collapsing tool utilizes expert biological knowledge from multiple publicly available database sources to direct feature selection. Variants were collapsed according to genetically driven features, such as evolutionary conserved regions, regulatory regions genes, and pathways. We have conducted an extensive comparison of low frequency variant burden differences (MAF<0.03) between populations from 1000 Genomes Project Phase I data. We found that on average 26.87% of gene bins, 35.47% of intergenic bins, 42.85% of pathway bins, 14.86% of ORegAnno regulatory bins, and 5.97% of evolutionary conserved regions show statistically significant differences in low frequency variant burden across populations from the 1000 Genomes Project. The proportion of bins with significant differences in low frequency burden depends on the ancestral similarity of the two populations compared and types of features tested. Even closely related populations had notable differences in low frequency burden, but fewer differences than populations from different continents. Furthermore, conserved or functionally relevant regions had fewer significant differences in low frequency burden than regions under less evolutionary constraint. This degree of low frequency variant differentiation across diverse populations and feature elements highlights the critical importance of considering population stratification in the new era of DNA sequencing and low frequency variant genomic analyses.
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