title: How many SNPs does a genome-wide haplotype map require?
abstract: We derive and compare several estimates of the number of SNPs that would be required to form the basis of a complete haplotype survey of the human genome. Our estimates make use of reports published by Stephens et al. [1], Patil et al. [2] and Daly et al. [3]. The estimated number of SNPs required for a genome-wide haplotype survey ranges from 180K (based on a European sample of 16 chromosomes) to 600K (based on an ethnically diverse sample of 164 chromosomes). We discuss the implications of using cohorts of different size and ethnic composition and the usefulness of public SNP databases for this effort. Finally, we estimate the experimental effort and cost required to complete a genome-wide haplotype survey.
authors.affiliation: Genaissance Pharmaceuticals, 5 Science Park, New Haven, CT 06511, USA. r.judson@genaissance.com
authors.forename: Richard
authors.initials: R
authors.lastname: Judson
authors.forename: Benjamin
authors.initials: B
authors.lastname: Salisbury
authors.forename: Julie
authors.initials: J
authors.lastname: Schneider
authors.forename: Andreas
authors.initials: A
authors.lastname: Windemuth
authors.forename: J Claiborne
authors.initials: JC
authors.lastname: Stephens
mesh_terms: D000465:Algorithms; D002874:Chromosome Mapping; D005787:Gene Frequency; D016678:Genome; D005838:Genotype; D006239:Haplotypes / Q000235:genetics*; D006801:Humans; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*