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Nat Methods. 2004 Nov;1(2):109-11.

Genotyping over 100,000 SNPs on a pair of oligonucleotide arrays.

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  • 1Affymetrix, Inc., 3380 Central Expressway, Santa Clara, California 95051, USA.


We present a genotyping method for simultaneously scoring 116,204 SNPs using oligonucleotide arrays. At call rates >99%, reproducibility is >99.97% and accuracy, as measured by inheritance in trios and concordance with the HapMap Project, is >99.7%. Average intermarker distance is 23.6 kb, and 92% of the genome is within 100 kb of a SNP marker. Average heterozygosity is 0.30, with 105,511 SNPs having minor allele frequencies >5%.

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