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Haplotype structure and linkage disequilibrium in chemokine and chemokine receptor genes.
Hum Genomics. 2004 May; 1(4):255-73.HG

Abstract

To dissect the haplotype structure of candidate genes for disease association studies, it is important to understand the nature of genetic variation at these loci in different populations. We present a survey of haplotype structure and linkage disequilibrium of chemokine and chemokine receptor genes in 11 geographically-distinct population samples (n=728). Chemokine proteins are involved in intercellular signalling and the immune response. These molecules are important modulators of human immunodeficiency virus (HIV)-1 infection and the progression of the acquired immune deficiency syndrome, tumour development and the metastatic process of cancer. To study the extent of genetic variation in this gene family, single nucleotide polymorphisms (SNPs) from 13 chemokine and chemokine receptor genes were genotyped using the 5' nuclease assay (TaqMan). SNP haplotypes, estimated from unphased genotypes using the Expectation-Maximization-algorithm, are described in a cluster of four CC-chemokine receptor genes (CCR3, CCR2, CCR5 and CCRL2) on chromosome 3p21, and a cluster of three CC-chemokine genes [MPIF-1 (CCL23), PARC (CCL18) and MIP-1alpha (CCL3)] on chromosome 17q11-12. The 32 base pair (bp) deletion in exon 4 of CCR5 was also included in the haplotype analysis of 3p21. A total of 87.5 per cent of the variation of 14 biallelic loci scattered over 150 kilobases of 3p21 is explained by 11 haplotypes which have a frequency of at least 1 per cent in the total sample. An analysis of haplotype blocks in this region indicates recombination between CCR2 and CCR5, although long-range pairwise linkage disequilibrium across the region appears to remain intact on two common haplotypes. A reduced-median network demonstrates a clear relationship between 3p21 haplotypes, rooted by the putative ancestral haplotype determined by direct sequencing of four primate species. Analysis of six SNPs on 17q11-12 indicates that 97.5 per cent of the variation is explained by 15 haplotypes, representing at least 1 per cent of the total sample. Additionally, a possible signature of selection at a non-synonymous coding SNP (M106V) in the MPIF-1 (CCL23) gene warrants further study. We anticipate that the results of this study of chemokine and chemokine receptor variation will be applicable to more extensive surveys of long-range haplotype structure in these gene regions and to association studies of HIV-1 disease and cancer.

Authors+Show Affiliations

Laboratory of Genomic Diversity, Human Genetics Section, National Cancer Institute, Frederick, MD 21702, USA. vclark@genetics.bsd.uchicago.eduNo affiliation info available

Pub Type(s)

Journal Article

Language

eng

PubMed ID

15588486

Citation

Clark, Vanessa J., and Michael Dean. "Haplotype Structure and Linkage Disequilibrium in Chemokine and Chemokine Receptor Genes." Human Genomics, vol. 1, no. 4, 2004, pp. 255-73.
Clark VJ, Dean M. Haplotype structure and linkage disequilibrium in chemokine and chemokine receptor genes. Hum Genomics. 2004;1(4):255-73.
Clark, V. J., & Dean, M. (2004). Haplotype structure and linkage disequilibrium in chemokine and chemokine receptor genes. Human Genomics, 1(4), 255-73.
Clark VJ, Dean M. Haplotype Structure and Linkage Disequilibrium in Chemokine and Chemokine Receptor Genes. Hum Genomics. 2004;1(4):255-73. PubMed PMID: 15588486.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Haplotype structure and linkage disequilibrium in chemokine and chemokine receptor genes. AU - Clark,Vanessa J, AU - Dean,Michael, PY - 2004/12/14/pubmed PY - 2005/3/30/medline PY - 2004/12/14/entrez SP - 255 EP - 73 JF - Human genomics JO - Hum. Genomics VL - 1 IS - 4 N2 - To dissect the haplotype structure of candidate genes for disease association studies, it is important to understand the nature of genetic variation at these loci in different populations. We present a survey of haplotype structure and linkage disequilibrium of chemokine and chemokine receptor genes in 11 geographically-distinct population samples (n=728). Chemokine proteins are involved in intercellular signalling and the immune response. These molecules are important modulators of human immunodeficiency virus (HIV)-1 infection and the progression of the acquired immune deficiency syndrome, tumour development and the metastatic process of cancer. To study the extent of genetic variation in this gene family, single nucleotide polymorphisms (SNPs) from 13 chemokine and chemokine receptor genes were genotyped using the 5' nuclease assay (TaqMan). SNP haplotypes, estimated from unphased genotypes using the Expectation-Maximization-algorithm, are described in a cluster of four CC-chemokine receptor genes (CCR3, CCR2, CCR5 and CCRL2) on chromosome 3p21, and a cluster of three CC-chemokine genes [MPIF-1 (CCL23), PARC (CCL18) and MIP-1alpha (CCL3)] on chromosome 17q11-12. The 32 base pair (bp) deletion in exon 4 of CCR5 was also included in the haplotype analysis of 3p21. A total of 87.5 per cent of the variation of 14 biallelic loci scattered over 150 kilobases of 3p21 is explained by 11 haplotypes which have a frequency of at least 1 per cent in the total sample. An analysis of haplotype blocks in this region indicates recombination between CCR2 and CCR5, although long-range pairwise linkage disequilibrium across the region appears to remain intact on two common haplotypes. A reduced-median network demonstrates a clear relationship between 3p21 haplotypes, rooted by the putative ancestral haplotype determined by direct sequencing of four primate species. Analysis of six SNPs on 17q11-12 indicates that 97.5 per cent of the variation is explained by 15 haplotypes, representing at least 1 per cent of the total sample. Additionally, a possible signature of selection at a non-synonymous coding SNP (M106V) in the MPIF-1 (CCL23) gene warrants further study. We anticipate that the results of this study of chemokine and chemokine receptor variation will be applicable to more extensive surveys of long-range haplotype structure in these gene regions and to association studies of HIV-1 disease and cancer. SN - 1473-9542 UR - https://www.unboundmedicine.com/medline/citation/15588486/Haplotype_structure_and_linkage_disequilibrium_in_chemokine_and_chemokine_receptor_genes_ L2 - https://humgenomics.biomedcentral.com/articles/10.1186/1479-7364-1-4-255 DB - PRIME DP - Unbound Medicine ER -