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Evaluating the performance of Affymetrix SNP Array 6.0 platform with 400 Japanese individuals

Nao Nishida1*, Asako Koike2, Atsushi Tajima3, Yuko Ogasawara1, Yoshimi Ishibashi1, Yasuka Uehara1, Ituro Inoue3 and Katsushi Tokunaga1

Author Affiliations

1 Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan

2 Central Research Laboratory, Hitachi Ltd, Tokyo, Japan

3 Division of Molecular Life Science, School of Medicine, Tokai University, Isehara, Japan

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BMC Genomics 2008, 9:431  doi:10.1186/1471-2164-9-431

Published: 22 September 2008



With improvements in genotyping technologies, genome-wide association studies with hundreds of thousands of SNPs allow the identification of candidate genetic loci for multifactorial diseases in different populations. However, genotyping errors caused by genotyping platforms or genotype calling algorithms may lead to inflation of false associations between markers and phenotypes. In addition, the number of SNPs available for genome-wide association studies in the Japanese population has been investigated using only 45 samples in the HapMap project, which could lead to an inaccurate estimation of the number of SNPs with low minor allele frequencies. We genotyped 400 Japanese samples in order to estimate the number of SNPs available for genome-wide association studies in the Japanese population and to examine the performance of the current SNP Array 6.0 platform and the genotype calling algorithm "Birdseed".


About 20% of the 909,622 SNP markers on the array were revealed to be monomorphic in the Japanese population. Consequently, 661,599 SNPs were available for genome-wide association studies in the Japanese population, after excluding the poorly behaving SNPs. The Birdseed algorithm accurately determined the genotype calls of each sample with a high overall call rate of over 99.5% and a high concordance rate of over 99.8% using more than 48 samples after removing low-quality samples by adjusting QC criteria.


Our results confirmed that the SNP Array 6.0 platform reached the level reported by the manufacturer, and thus genome-wide association studies using the SNP Array 6.0 platform have considerable potential to identify candidate susceptibility or resistance genetic factors for multifactorial diseases in the Japanese population, as well as in other populations.