Haplotype and linkage disequilibrium architecture for human cancer-associated genes.

TitleHaplotype and linkage disequilibrium architecture for human cancer-associated genes.
Publication TypeJournal Article
Year of Publication2002
AuthorsBonnen, PE, Wang, PJ, Kimmel, M, Chakraborty, R, Nelson, DL
JournalGenome Res
Volume12
Issue12
Pagination1846-53
Date Published2002 Dec
ISSN1088-9051
KeywordsAlleles, Cell Line, Transformed, Chromosome Mapping, Gene Frequency, Genes, Neoplasm, Genetic Markers, Genetic Predisposition to Disease, Genome, Human, Haplotypes, Humans, Linkage Disequilibrium, Polymorphism, Single Nucleotide, Recombination, Genetic
Abstract

To facilitate association-based linkage studies we have studied the linkage disequilibrium (LD) and haplotype architecture around five genes of interest for cancer risk: ATM, BRCA1, BRCA2, RAD51, and TP53. Single nucleotide polymorphisms (SNPs) were identified and used to construct haplotypes that span 93-200 kb per locus with an average SNP density of 12 kb. These markers were genotyped in four ethnically defined populations that contained 48 each of African Americans, Asian Americans, Hispanic Americans, and European Americans. Haplotypes were inferred using an expectation maximization (EM) algorithm, and the data were analyzed using D', R(2), Fisher's exact P-values, and the four-gamete test for recombination. LD levels varied widely between loci from continuously high LD across 200 kb to a virtual absence of LD across a similar length of genome. LD structure also varied at each gene and between populations studied. This variation indicates that the success of linkage-based studies will require a precise description of LD at each locus and in each population to be studied. One striking consistency between genes was that at each locus a modest number of haplotypes present in each population accounted for a high fraction of the total number of chromosomes. We conclude that each locus has its own genomic profile with regard to LD, and despite this there is the widespread trend of relatively low haplotype diversity. As a result, a low marker density should be adequate to identify haplotypes that represent the common variation at a locus, thereby decreasing costs and increasing efficacy of association studies.

DOI10.1101/gr.483802
Alternate JournalGenome Res.
PubMed ID12466288
PubMed Central IDPMC187564
Grant ListR01 CA075432 / CA / NCI NIH HHS / United States
CA75432 / CA / NCI NIH HHS / United States