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Genotype imputation is potentially a zero-cost method for bridging gaps in coverage and power between genotyping platforms. Here, we quantify these gains in power and coverage by using 1,376 population controls that are from the 1958 British Birth Cohort and were genotyped by the Wellcome Trust Case-Control Consortium with the Illumina HumanHap 550 and Affymetrix SNP Array 5.0 platforms. Approximately 50% of genotypes at single-nucleotide polymorphisms (SNPs) exclusively on the HumanHap 550 can be accurately imputed from direct genotypes on the SNP Array 5.0 or Illumina HumanHap 300. This roughly halves differences in coverage and power between the platforms. When the relative cost of currently available genome-wide SNP platforms is accounted for, and finances are limited but sample size is not, the highest-powered strategy in European populations is to genotype a larger number of individuals with the HumanHap 300 platform and carry out imputation. Platforms consisting of around 1 million SNPs offer poor cost efficiency for SNP association in European populations.

Original publication

DOI

10.1016/j.ajhg.2008.06.008

Type

Journal article

Journal

Am J Hum Genet

Publication Date

07/2008

Volume

83

Pages

112 - 119

Keywords

Algorithms, Alleles, Cohort Studies, Computer Simulation, Cost Control, Discriminant Analysis, Gene Frequency, Genetic Variation, Genetics, Population, Genome, Genotype, Haplotypes, Humans, Medical Laboratory Science, Oligonucleotide Array Sequence Analysis, Polymorphism, Single Nucleotide, Recombination, Genetic