Genetically indistinguishable SNPs and their influence on inferring the location of disease-associated variants

Robert Lawrence, David M. Evans, Andrew P. Morris, Xiayi Ke, Sarah Hunt, Marta Paolucci, Jiannis Ragoussis, Panos Deloukas, David Bentley, Lon R. Cardon

    Research output: Contribution to journalArticlepeer-review


    As part of a recent high-density linkage disequilibrium (LD) study of chromosome 20, we obtained genotypes for ∼30,000 SNPs at a density of 1 SNP/2 kb on four different population samples (47 CEPH founders; 91 UK unrelateds [unrelated white individuals of western European ancestry]; 97 African Americans; 42 East Asians). We observed that ∼50% of SNPs had at least one genetically indistinguishable partner; i.e., for every individual considered, their genotype at the first locus was identical to their genotype at the second locus, or in LD terms, the SNPs were in "perfect" LD (r2 = 1.0). These "genetically indistinguishable SNPs" (giSNPs) formed into clusters of varying size. The larger the cluster, the greater the tendency to be located within genes and to overlap with giSNP clusters in other population samples. As might be expected for this map density, many giSNPs were located close to one another, thus reflecting local regions of undetected recombination or haplotype blocks. However, ∼1/3 of giSNP clusters had intermingled, non-indistinguishable SNPs with incomplete LD (D′ and r2
    Original languageEnglish
    Pages (from-to)1503-1510
    Number of pages7
    JournalGenome research
    Issue number11
    Publication statusPublished - Nov 2005


    • genetics: African Americans
    • genetics: Asian Continental Ancestry Group
    • methods: Chromosome Mapping
    • genetics: Chromosomes, Human, Pair 20
    • Computer Simulation
    • genetics: European Continental Ancestry Group
    • Evolution, Molecular
    • Gene Components
    • methods: Genetic Screening
    • methods: Genomics
    • Genotype
    • Great Britain
    • Humans
    • Linkage Disequilibrium
    • genetics: Polymorphism, Single Nucleotide
    • Sample Size


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