%0 Journal Article
%T Evaluating the performance of Affymetrix SNP Array 6.0 platform with 400 Japanese individuals
%A Nao Nishida
%A Asako Koike
%A Atsushi Tajima
%A Yuko Ogasawara
%A Yoshimi Ishibashi
%A Yasuka Uehara
%A Ituro Inoue
%A Katsushi Tokunaga
%J BMC Genomics
%D 2008
%I BioMed Central
%R 10.1186/1471-2164-9-431
%X 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.Together with technology developments on large-scale single nucleotide polymorphism (SNP) genotyping [1,2], there have been a number of genome-wide association studies (GWAS) to identify candidate susceptibility or resistance genetic factors for multifactorial diseases [3-7]. It is estimated that eleven million SNPs with a greater than 1% minor allele frequency (MAF) are located in the human genome [8]. Over six million SNPs have been uploaded on public SNP databases through the Human Genome Project and international SNP discovery projects. Among these SNPs, over 900 K SNPs across the human genome are selected with an average MAF of 19.6%, 18.2% and 20.6% in the HapMap Caucasians, Asians and Africans, respectively, and can be simultaneously genotyped using Affymetrix Genome-Wide Human SNP Array 6.0 platform [9]. Several studies have evaluated the coverage of commercial platforms using HapMap population data and genotype data of non-reference Caucasian populations [10-12]. Results from these studies indicated that in a non-reference Caucasian population, as well as the HapMap populations, commercial SNP typing plat
%U http://www.biomedcentral.com/1471-2164/9/431