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Genetic variation at the chromosome 16 chemokine gene cluster: Development of a strategy for association studies in complex disease

Lookup NU author(s): Dr John Mansfield

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Abstract

The chemokine gene cluster [CCL22, CX3CL1, CCL17] (previously known as [SCYA22, SCYD1, SCYA17]) is a candidate locus for one of the susceptibility genes for inflammatory bowel disease that are located in the pericentromeric region of chromosome 16. Screening for sequence variation at this locus led to the detection of 14 single nucleotide polymorphisms (SNPs). An efficient experimental and computational approach was developed to estimate allele frequencies and pairwise linkage disequilibrium relationships between SNPs at this locus, and to test them for association with inflammatory bowel disease. The 12 common SNPs were assigned to 5 distinct linkage disequilibrium groups. Genotyping of one SNP from each linkage disequilibrium group in a large cohort of families with inflammatory bowel disease did not provide convincing evidence of association with either Crohn's disease or ulcerative colitis. We describe an efficient experimental design from SNP screening to association testing. This strategy can be used to test candidate genes for involvement in susceptibility to complex disease.

Publication metadata

Author(s): Fisher SA, Moody A, Mirza MM, Cuthbert AP, Hampe J, Macpherson A, Sanderson J, Forbes A, Mansfield J, Schreiber S, Lewis CM, Mathew CG

Publication type: Article

Publication status: Published

Journal: Annals of Human Genetics

Year: 2003

Volume: 67

Issue: 5

Pages: 377-390

ISSN (print): 0003-4800

ISSN (electronic): 1469-1809

Publisher: Wiley-Blackwell

URL: http://dx.doi.org/10.1046/j.1469-1809.2003.00040.x

DOI: 10.1046/j.1469-1809.2003.00040.x

PubMed id: 12940913

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