ArticleGenome research2002
Haplotype and linkage disequilibrium architecture for human cancer-associated genes.
Article in Genome research, 2002. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed.
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- PIP-SNP: a pipeline for processing SNP data featured as linkage disequilibrium bin mapping, genotype imputing and marker synthesizing.NAR genomics and bioinformatics · 2021Article
- Association Analysis of Single Nucleotide Polymorphisms in the 5' Regulatory Region of the IL-6 Gene withGenes · 2019Article
- Genetic Diversity, Population Structure and Ancestral Origin of Australian Wheat.Frontiers in plant science · 2017Article
- Germline genetic profiling in prostate cancer: latest developments and potential clinical applications.Future science OA · 2016Review
- Cloud computing-based TagSNP selection algorithm for human genome data.International journal of molecular sciences · 2015Article
- Variation in human β-defensin genes: new insights from a multi-population study.International journal of immunogenetics · 2013Article
- Worldwide variation in human drug-metabolism enzyme genes CYP2B6 and UGT2B7: implications for HIV/AIDS treatment.Pharmacogenomics · 2012Article
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- Family-based and population-based association studies validate PTPRD as a risk factor for restless legs syndrome.Movement disorders : official journal of the Movement Disorder Society · 2011Article
- Rare BRCA1 haplotypes including 3'UTR SNPs associated with breast cancer risk.Cell cycle (Georgetown, Tex.) · 2011Article
- Linkage disequilibrium reveals different demographic history in egg laying chickens.BMC genetics · 2010Article
- Genome-wide association studies in cancer--current and future directions.Carcinogenesis · 2010Article
- Comparative description of haplotype structure and genetic diversity of MDR1 (ABCB1) in HIV-positive and HIV-negative populations.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2010Article
- Common genetic variation in TP53 and risk of human papillomavirus persistence and progression to CIN3/cancer revisited.Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology · 2009Article
- Evidence of gene conversion in the evolutionary process of the codon 41/42 (-CTTT) mutation causing beta-thalassemia in southern China.Journal of molecular evolution · 2008Article
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- Genetic variation in p53 and ATM haplotypes and risk of glioma and meningioma.Journal of neuro-oncology · 2007Article
- Mutation-positive and mutation-negative patients with Cowden and Bannayan-Riley-Ruvalcaba syndromes associated with distinct 10q haplotypes.American journal of human genetics · 2006Article
- Efficient selection of tagging single-nucleotide polymorphisms in multiple populations.Human genetics · 2006Article
Corrections and comments
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Authors and funding
5 authors.
Funding
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.
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