ArticleAmerican journal of human genetics2006
Biases and reconciliation in estimates of linkage disequilibrium in the human genome.
Article in American journal of human genetics, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
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- So many Nigerians: why is Nigeria overrepresented as the ancestral genetic homeland of Legacy African North Americans?American journal of human genetics · 2021Article
- LD-annot: A Bioinformatics Tool to Automatically Provide Candidate SNPs With Annotations for Genetically Linked Genes.Frontiers in genetics · 2019Article
- Confounding of linkage disequilibrium patterns in large scale DNA based gene-gene interaction studies.BioData mining · 2019Article
- Genomic basis of the differences between cider and dessert apple varieties.Evolutionary applications · 2015Article
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- Diversity, differentiation, and linkage disequilibrium: prospects for association mapping in the malaria vector Anopheles arabiensis.G3 (Bethesda, Md.) · 2014Article
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- Genomewide association studies: history, rationale, and prospects for psychiatric disorders.The American journal of psychiatry · 2009Review
- Gene expression levels are a target of recent natural selection in the human genome.Molecular biology and evolution · 2009Article
- Power consequences of linkage disequilibrium variation between populations.Genetic epidemiology · 2009Article
- Linkage disequilibrium between STRPs and SNPs across the human genome.American journal of human genetics · 2008Article
- Association analysis of the chromosome 4p15-p16 candidate region for bipolar disorder and schizophrenia.Molecular psychiatry · 2007Article
- Information capture using SNPs from HapMap and whole-genome chips differs in a sample of inflammatory and cardiovascular gene-centric regions from genome-wide estimates.Genome research · 2007Article
- A periodic pattern of SNPs in the human genome.Genome research · 2007Article
- Linkage disequilibrium in wild mice.PLoS genetics · 2007Article
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- Recent human effective population size estimated from linkage disequilibrium.Genome research · 2007Article
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6 authors.
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Abstract
Genetic association studies of common disease often rely on linkage disequilibrium (LD) along the human genome and in the population under study. Although understanding the characteristics of this correlation has been the focus of many large-scale surveys (culminating in genomewide haplotype maps), the results of different studies have yielded wide-ranging estimates. Since understanding these differences (and whether they can be reconciled) has important implications for whole-genome association studies, in this article we dissect biases in these estimations that are due to known aspects of study design and analytic methodology. In particular, we document in the empirical data that the long-known complicating effects of allele frequency, marker density, and sample size largely reconcile all large-scale surveys. Two exceptions are an underappraisal of redundancy among single-nucleotide polymorphisms (SNPs) when evaluation is limited to short regions (as in candidate-gene resequencing studies) and an inflation in the extent of LD in HapMap phase I, which is likely due to oversampling of specific haplotypes in the creation of the public SNP map. Understanding these factors can guide the understanding of empirical LD surveys and has implications for genetic association studies.
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