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Published online before print October 15, 2001, 10.1101/gr.197201
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Vol. 11, Issue 11, 1913-1925, November 2001

METHODS
High-Throughput Variation Detection and Genotyping Using Microarrays

David J. Cutler,1,4 Michael E. Zwick,1 Minerva M. Carrasquillo,3 Christopher T. Yohn,1 Katherine P. Tobin,1 Carl Kashuk,1 Debra J. Mathews,3 Nila A. Shah,2 Evan E. Eichler,3 Janet A. Warrington,2 and Aravinda Chakravarti1

1 McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA; 2 Affymetrix Inc., Santa Clara, California 95051, USA; 3 Department of Genetics, Case Western Reserve University, Cleveland, Ohio 44106, USA

The genetic dissection of complex traits may ultimately require a large number of SNPs to be genotyped in multiple individuals who exhibit phenotypic 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 microarray hybridization data and applied this method to Affymetrix Variation Detection Arrays (VDAs). ABACUS provides a quality score to individual genotypes, allowing investigators to focus their attention on sites that give accurate information. We have applied ABACUS to an experiment encompassing 32 autosomal and eight X-linked genomic regions, each consisting of ~50 kb of unique sequence spanning a 100-kb region, in 40 humans. At sufficiently high-quality scores, we are able to read ~80% of all sites. To assess the accuracy of SNP detection, 108 of 108 SNPs have been experimentally confirmed; an additional 371 SNPs have been confirmed electronically. To access the accuracy of diploid genotypes at segregating autosomal sites, we confirmed 1515 of 1515 homozygous calls, and 420 of 423 (99.29%) heterozygotes. In replicate experiments, consisting of independent amplification of identical samples followed by hybridization to distinct microarrays of the same design, genotyping is highly repeatable. In an autosomal replicate experiment, 813,295 of 813,295 genotypes are called identically (including 351 heterozygotes); at an X-linked locus in males (haploid), 841,236 of 841,236 sites are called identically.

4 Corresponding author.

11:1913-1925 ©2001 by Cold Spring Harbor Laboratory Press  ISSN 1088-9051/01 $5.00
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