Haplotype mapping

Judson R, Salisbury B, Schneider J, Windemuth A, Stephens JC (2002) How many SNPs does a genome-wide haplotype map require Pharmacogenomics 3 379-391 Kim DK, him SW, Lee S, et al (2000) Serotonin transporter gene polymorphism and antidepressant response. Neuroreport 11 215-219... 

The International HapMap Consortium. A haplotype map of the human genome. Nature 2005 437 1299-1320. 

In the foreseeable future, extensive SNP patterns or haplotype maps of the complete human genome may reveal multiple and complex genetic variants that function individually to modulate induction or that interact to influence induction of DMEs. 

Selection is expected to produce LD non-randomly across the genome, whereas all the other factors should act randomly over the genome. Some regions, such as HLA, show strong evidence of selection and significant LD which spans 3 cM or more. The LD and haplotype structure of the genome is currently being studied by the National Institutes of Health Haplotype Map project (Sec. 4.5). 

International HapMap Project. URL http //www.hapmap.org/. Partnership of scientists and funding agencies from Canada, China, Japan, Nigeria, the United Kingdom, and the United States to develop a public haplotype map that will help researchers find genes associated with human disease and response to pharmaceuticals. 

In other words, it is believed that a set of haplotype blocks exist, where SNPs within such block boundaries change together, that is, knowing one would reveal the identity of the others. The existence of such boundaries has been the subject of much debate. The haplotype blocks in older populations (e.g., Africans) range from less than 1 Kb to 100 Kb, and in younger populations (e.g., Finns) from more than 50 Kb to more than 1 Mb [7]. The International Haplotype Map project (HapMap) was funded a few years ago and is moving quickly toward completion. The hope is that with the aid of haplotype blocks, one may be able to scale down from analysis of 3 million SNPs to approximately 300,000 SNPs. 

International HapMap Consortium (2007). A second generation human haplotype map of over 3.1 million SNPs. Nature, 449 851 861. 

Holford, T.R. Multivariate Methods in Epidemiology. New York Oxford University Press, 2002. International Haplotype Map Consortium. Nature 2003 426 789-796. 

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