Global survey of haplotype frequencies and linkage disequilibrium at the RET locus

Pratima Chattopadhyay, Andrew J. Pakstis, Namita Mukherjee, Sudha Iyengar, Adekunle Odunsi, Friday Okonofua, Batsheva Bonne-Tamir, William Speed, Judith R. Kidd, Kenneth K. Kidd*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

14 Scopus citations


We have constructed haplotypes based on normal variation at six polymorphic sites-five single nucleotide polymorphisms (SNPs) and one short tandem repeat polymorphism (STRP)-at the RET locus for samples of normal individuals from 32 populations distributed across the major continental regions of the world. The haplotyped system spans 41.6 kilobases and encompasses most of the coding region of the gene. All of the markers are polymorphic in all regions of the world and in most individual populations. Expected heterozygosities for the six-site haplotypes range from 82 to 94% for all populations studied except for two Amerindian groups from the Amazon basin at 61 and 76%. Individual populations had from four to eight haplotypes with frequencies exceeding 5%. In general, African, southwest Asian and European groups have the highest numbers of total and of commonly occurring haplotypes; the lowest numbers are observed in Amerindian populations. Overall linkage disequilibrium (LD) for the five SNP sites was very significant (P≤0.001) for all the non-African populations, but significant at that level for only one of the seven African populations. In general, the permutation-based ξ coefficient that quantifies overall LD tends to increase the farther the population is from Africa, but variability of this measure of LD is often large within geographic regions. Pairwise LD measures among the SNPs also show considerable variation among populations. Association of STRP alleles with the SNP-defined background haplotypes is generally higher outside of Africa than in Africa, but is highly variable.

Original languageEnglish
Pages (from-to)760-769
Number of pages10
JournalEuropean Journal of Human Genetics
Issue number10
StatePublished - Oct 2003


FundersFunder number
National Institutes of HealthMH62495
National Institute of General Medical SciencesP01GM057672


    • Haplotypes
    • Linkage disequilibrium
    • Polymorphisms
    • Population genetics


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