ArticleGenome research2009
Genome-wide comparisons of variation in linkage disequilibrium.
Article in Genome research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers, 6 of them syntheses that pooled it.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
39 citing papers in PubMed, 6 syntheses or guidelines pooled it.
- Meta-Analysis of Genetic Variants Associated With HBV Infection Susceptibility and Hepatocellular Carcinoma Risk.Journal of viral hepatitis · 2026Pooled it
- A meta-analysis of genome-wide association studies of asthma in Puerto Ricans.The European respiratory journal · 2017Pooled it
- A Meta-Assembly of Selection Signatures in Cattle.PloS one · 2016Pooled it
- A genome-wide association study of atopic dermatitis identifies loci with overlapping effects on asthma and psoriasis.Human molecular genetics · 2013Pooled it
- Efficiency of trans-ethnic genome-wide meta-analysis and fine-mapping.European journal of human genetics : EJHG · 2012Pooled it
- Transferability of type 2 diabetes implicated loci in multi-ethnic cohorts from Southeast Asia.PLoS genetics · 2011Pooled it
- A study of sex-specific genetic effects underlying risk of orofacial clefts also highlights the potential impact of sequencing errors due to short read mis-mapping.medRxiv : the preprint server for health sciences · 2026Article
- A reference panel for linkage disequilibrium and genotype imputation using whole-genome sequencing data from 2,680 participants across India.HGG advances · 2026Article
- Allele frequency impacts the cross-ancestry portability of gene expression prediction in lymphoblastoid cell lines.American journal of human genetics · 2024Article
- Clarifying the causes of consistent and inconsistent findings in genetics.Genetic epidemiology · 2022Review
- Genomic divergence landscape in recurrently hybridizingEvolution letters · 2021Article
- Uncovering Sub-Structure and Genomic Profiles in Across-Countries Subpopulations of Angus Cattle.Scientific reports · 2020Article
- Heterogeneity in the distribution of 159 drug-response related SNPs in world populations and their genetic relatedness.PloS one · 2020Article
- Convergent evolution in Arabidopsis halleri and Arabidopsis arenosa on calamine metalliferous soils.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2019Article
- Genome-wide scan reveals population stratification and footprints of recent selection in Nelore cattle.Genetics, selection, evolution : GSE · 2018Article
- Regional evaluation of childhood acute lymphoblastic leukemia genetic susceptibility loci among Japanese.Scientific reports · 2018Article
- Risk estimation model for nonalcoholic fatty liver disease in the Japanese using multiple genetic markers.PloS one · 2018Article
- Testing Domestication Scenarios of Lima Bean (Frontiers in plant science · 2017Article
- On the performance of tests for the detection of signatures of selection: a case study with the Spanish autochthonous beef cattle populations.Genetics, selection, evolution : GSE · 2016Article
- A Combined Linkage and Exome Sequencing Analysis for Electrocardiogram Parameters in the Erasmus Rucphen Family Study.Frontiers in genetics · 2016Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Current genome-wide surveys of common diseases and complex traits fundamentally aim to detect indirect associations where the single nucleotide polymorphisms (SNPs) carrying the association signals are not biologically active but are in linkage disequilibrium (LD) with some unknown functional polymorphisms. Reproducing any novel discoveries from these genome-wide scans in independent studies is now a prerequisite for the putative findings to be accepted. Significant differences in patterns of LD between populations can affect the portability of phenotypic associations when the replication effort or meta-analyses are attempted in populations that are distinct from the original population in which the genome-wide study is performed. Here, we introduce a novel method for genome-wide analyses of LD variations between populations that allow the identification of candidate regions with different patterns of LD. The evidence of LD variation provided by the introduced method correlated with the degree of differences in the frequencies of the most common haplotype across the populations. Identified regions also resulted in greater variation in the success of replication attempts compared with random regions in the genome. A separate permutation strategy introduced for assessing LD variation in the absence of genome-wide data also correctly identified the expected variation in LD patterns in two well-established regions undergoing strong population-specific evolutionary pressure. Importantly, this method addresses whether a failure to reproduce a disease association in a disparate population is due to underlying differences in LD structure with an unknown functional polymorphism, which is vital in the current climate of replicating and fine-mapping established findings from genome-wide association studies.
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