Appropriate data cleaning methods for genome-wide association study.
Genome-wide association studies (GWAS) using a large number of single nucleotide polymorphisms (SNPs) have successfully been applied to identify genetic variants of common diseases. However, genotyping using the new array technologies is often associated with spurious results that could unfavorably affect analyses of GWAS. Consequently, data cleaning is of paramount importance in excluding spurious genotyping results. In this study, we investigated the criteria required for the appropriate cleaning of 389 unrelated healthy Japanese samples analyzed using the GeneChip Human Mapping 500K Array Set for GWAS. The samples were randomly subdivided into two groups, and the allele frequencies in the groups were compared for individual SNPs as a quasi-case-control study. Then, observed results were filtered by four parameters (SNP call rate, confidence score obtained using the Bayesian Robust Linear Model with Mahalanobis genotype-calling algorithm, Hardy-Weinberg equilibrium, and minor allele frequency) and assessed for deviation from the null hypothesis. We found that appropriate data cleaning could be achieved using these four parameters. Our findings offer an avenue for obtaining appropriate data from GWAS.
Miyagawa
Taku
T
Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
Nishida
Nao
N
Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
Ohashi
Jun
J
Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
Kimura
Ryosuke
R
Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.|Department of Forensic Medicine, Tokai University School of Medicine, Isehara, Japan.
Fujimoto
Akihiro
A
Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
Kawashima
Minae
M
Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.|Department of Sleep Disorder Research, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
Koike
Asako
A
Hitachi Ltd, Central Research Laboratory, Kokubunji, Japan.
Sasaki
Tsukasa
T
Health Service Center, The University of Tokyo, Tokyo, Japan.
Tanii
Hisashi
H
Department of Psychiatry, Mie University Graduate School of Medicine, Tsu, Japan.
Otowa
Takeshi
T
Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
Momose
Yoshio
Y
Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.|The 21st Century COE Program, Center for Integrated Brain Medical Science, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
Nakahara
Yasuo
Y
Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
Gotoh
Jun
J
Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
Okazaki
Yuji
Y
Tokyo Metropolitan Matsuzawa Hospital, Tokyo, Japan.
Tsuji
Shoji
S
Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.|The 21st Century COE Program, Center for Integrated Brain Medical Science, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
Tokunaga
Katsushi
K
Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan. tokunaga@m.u-tokyo.ac.jp.
D044466:Asian People / Q000235:genetics; D019295:Computational Biology; D005787:Gene Frequency; D015894:Genome, Human / Q000235:genetics*; D005838:Genotype; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*