A population-based LD map of the human chromosome 6p |
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Authors: | Hong Xiang Yu Jer-Ming Chia Guillaume Bourque Marie Vivien Wong Soh Ha Chan Ee Chee Ren |
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Institution: | (1) W.H.O Collaborating Center for Immunology, Faculty of Medicine, National University of Singapore, MD4 5th Floor, 5 Science Drive 2, Singapore, 117597, Singapore;(2) Department of Microbiology, Faculty of Medicine, National University of Singapore, MD4 5th Floor, 5 Science Drive 2, Singapore, 117597, Singapore;(3) Genome Institute of Singapore, Genome #02-01, 60 Biopolis Street, Singapore, 138672, Singapore |
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Abstract: | The recent publication of the complete sequence of human chromosome 6 provides a platform from which to investigate genomic
sequence variation. We report here a detailed linkage disequilibrium (LD) pattern map across the entire human chromosome 6p
by using a set of 1152 single nucleotide polymorphisms (SNPs) in a population of 198 Singaporean Chinese, with 326 SNPs focused
in the major histocompatibility complex (MHC) region. Our analysis shows some unexpectedly high segments of strong LD in a
10-Mb region that includes the extremely polymorphic and gene-rich MHC loci and many non-MHC genes. These include the telomeric
peri-MHC region that harbors olfactory receptors, histones and zinc finger clusters, and the centromeric peri-MHC region that
contains several unknown open reading frames. The data also help refine a human–mouse synteny break in the region between
28.6 and 29.4 Mb. The population-based LD map presented here will provide an essential resource for understanding the genomic
sequence variation of chromosome 6p and LD mapping of disease genes of complex genetic traits.
Electronic supplementary material Electronic supplementary material is available for this article at and accessible for authorised users.
H. Yu and J.-M. Chia should be regarded as joint first authors. |
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Keywords: | Major histocompatibility complex (MHC) Linkage disequilibrium Chromosome 6p Human genome Single nucleotide polymorphisms (SNPs) |
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