ArticleBMC medical genomics2010
Disease-associated alleles in genome-wide association studies are enriched for derived low frequency alleles relative to HapMap and neutral expectations.
Article in BMC medical genomics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 41 citations in OpenAlex.
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- MethHaplo: combining allele-specific DNA methylation and SNPs for haplotype region identification.BMC bioinformatics · 2020Article
- Population Levels Assessment of the Distribution of Disease-Associated Variants With Emphasis on Armenians - A Machine Learning Approach.Frontiers in genetics · 2019Article
- Genetic disease risks can be misestimated across global populations.Genome biology · 2018Article
- Genetic Hitchhiking and Population Bottlenecks Contribute to Prostate Cancer Disparities in Men of African Descent.Cancer research · 2018Article
- Challenges imposed by minor reference alleles on the identification and reporting of clinical variants from exome data.BMC genomics · 2018Article
- Empirical Bayes Estimation of Semi-parametric Hierarchical Mixture Models for Unbiased Characterization of Polygenic Disease Architectures.Frontiers in genetics · 2018Article
- Inferences of African evolutionary history from genomic data.Current opinion in genetics & development · 2016Review
- Biased gene conversion skews allele frequencies in human populations, increasing the disease burden of recessive alleles.American journal of human genetics · 2014Article
- Inherited polymorphisms in hyaluronan synthase 1 predict risk of systemic B-cell malignancies but not of breast cancer.PloS one · 2014Article
- Population Genomics of Human Adaptation.Annual review of ecology, evolution, and systematics · 2013Article
- SNP ascertainment bias in population genetic analyses: why it is important, and how to correct it.BioEssays : news and reviews in molecular, cellular and developmental biology · 2013Review
- Analysis of the genetic basis of disease in the context of worldwide human relationships and migration.PLoS genetics · 2013Article
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Abstract
backgroundGenome-wide association studies give insight into the genetic basis of common diseases. An open question is whether the allele frequency distributions and ancestral vs. derived states of disease-associated alleles differ from the rest of the genome. Characteristics of disease-associated alleles can be used to increase the yield of future studies.
methodsThe set of all common disease-associated alleles found in genome-wide association studies prior to January 2010 was analyzed and compared with HapMap and theoretical null expectations. In addition, allele frequency distributions of different disease classes were assessed. Ages of HapMap and disease-associated alleles were also estimated.
resultsThe allele frequency distribution of HapMap alleles was qualitatively similar to neutral expectations. However, disease-associated alleles were more likely to be low frequency derived alleles relative to null expectations. 43.7% of disease-associated alleles were ancestral alleles. The mean frequency of disease-associated alleles was less than randomly chosen CEU HapMap alleles (0.394 vs. 0.610, after accounting for probability of detection). Similar patterns were observed for the subset of disease-associated alleles that have been verified in multiple studies. SNPs implicated in genome-wide association studies were enriched for young SNPs compared to randomly selected HapMap loci. Odds ratios of disease-associated alleles tended to be less than 1.5 and varied by frequency, confirming previous studies.
conclusionsAlleles associated with genetic disease differ from randomly selected HapMap alleles and neutral expectations. The evolutionary history of alleles (frequency and ancestral vs. derived state) influences whether they are implicated in genome-wide association studies.
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