SNP profile within the human major histocompatibility complex reveals an extreme and interrupted level of nucleotide diversity

Silvana Gaudieri, Roger L. Dawkins, Kaori Habara, Jerzy K. Kulski, Takashi Gojobori*

*Corresponding author for this work

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86 Scopus citations


The human major histocompatibility complex (MHC) is characterized by polymorphic multicopy gene families, such as HLA and MIC (PERB11); duplications; insertions and deletions (indels); and uneven rates of recombination. Polymorphisms at the antigen recognition sites of the HLA class I and II genes and at associated neutral sites have been attributed to balancing selection and a hitchhiking effect, respectively. We, and others, have previously shown that nucleotide diversity between MHC haplotypes at non-HLA sites is unusually high (>10%) and up to several times greater than elsewhere in the genome (0.08%-0.2%). We report here the most extensive analysis of nucleotide diversity within a continuous sequence in the genome. We constructed a single nucleotide polymorphism (SNP) profile that reveals a pattern of extreme but interrupted levels of nucleotide diversity by comparing a continuous sequence within haplotypes in three genomic subregions of the MHC. A comparison of several haplotypes within one of the genomic subregions containing the HLA-B and -C loci suggests that positive selection is operating over the whole subgenomic region, including HLA and non-HLA genes.

Original languageEnglish (US)
Pages (from-to)1579-1586
Number of pages8
JournalGenome Research
Issue number10
StatePublished - Nov 8 2000

ASJC Scopus subject areas

  • Genetics

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