High-throughput variation detection and genotyping using microarrays

The genetic dissection of complex traits may ultimately require a large num ber of SNPs to be a genotyped in multiple individuals who exhibit phenotypi c variation in a trait of interest. Microarray technology can enable rapid genotyping of variation specific to study samples. To facilitate their use, we have developed an automated statistical method (ABACUS) to analyze micr oarray hybridization data and applied this method to Affymetrix Variation D etection Arrays (VDAS). ABACUS provides a quality score to individual genot ypes, allowing investigators to focus their attention on sites that give ac curate information. We have applied ABACUS to an experiment encompassing 32 autosomal and eight X-linked genomic regions, each consisting of similar t o 50 kb of unique sequence spanning a 100-kb region, in 40 humans. At suffi ciently high-quality scores, we are able to read similar to 80% of all site s. To assess the accuracy of SNP detection, 108 of 108 SNPs have been exper imentally confirmed; an additional 371 SNPs have been confirmed electronica lly. To access the accuracy of diploid genotypes at segregating autosomal s ites, we confirmed 1515 of 1515 homozygous calls, and 420 of 423 (99.29%) h eterozygotes. In replicate experiments, consisting of independent amplifica tion of identical samples followed by hybridization to distinct microarrays of the same design, genotyping is highly repeatable. In an autosomal repli cate experiment, 813,295 of 813,295 genotypes are called identically (inclu ding 351 heterozygotes); at an X-linked focus in males (haploid), 841,236 o f 841,236 sites are called identically.