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Medical applications of haplotype-based SNP maps: learning to walk before we run

Nature Genetics volume 32, page 353 (2002)Cite this article

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Ever since Risch and Merikangas1 introduced the concept of whole-genome association using single-nucleotide polymorphisms (SNPs) in 1996, the question of how many SNPs would be required for whole-genome association studies has been extensively debated2,3. The initial prediction of one million SNPs has recently been reduced to approximately 300,000 (ref. 4). Furthermore, it is clear that chromosomally mapped and ordered SNP variants can be grouped into bins/blocks as distinct 'haplotypes'5,6. Recently, the National Human Genome Research Institute proposed the development of a map of the common haplotype patterns in at least three ethnic populations.

The scientific community is currently divided regarding the perceived need for genome-wide maps of common haplotype blocks. Most support the proposal of constructing haplotype maps to maximize information content and to minimize the number of SNPs required for whole- genome genotyping. The scope of its utility is, however, bounded. Its applicability may not extend beyond the ethnic groups chosen, and is limited by the representativeness of the few samples studied. Furthermore, rare and sometimes detrimental variants are the ones most likely to be missed entirely from the derived SNP set. Pharmacogenetics focuses on the prediction of safety and efficacy following pharmaceutical treatment and clearly stands to benefit from the increased efficiency of a complete haplotype map. A practical question is whether common haplotype maps for several ethnic populations are essential, or even necessary, for immediate pharmacogenetic applications to advance.

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  1. Genetics Research, GlaxoSmithKline, Research Triangle Park, 27709, North Carolina, USA

    Eric Lai, Clive Bowman, Aruna Bansal, Arlene Hughes, Michael Mosteller & Allen D. Roses

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  1. Eric Lai
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  2. Clive Bowman
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  3. Aruna Bansal
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  4. Arlene Hughes
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  5. Michael Mosteller
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  6. Allen D. Roses
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Correspondence to Allen D. Roses.

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Lai, E., Bowman, C., Bansal, A. et al. Medical applications of haplotype-based SNP maps: learning to walk before we run. Nat Genet 32, 353 (2002). https://doi.org/10.1038/ng1102-353

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