title: Appropriate data cleaning methods for genome-wide association study.
abstract: 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.
authors.affiliation: Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
authors.forename: Taku
authors.initials: T
authors.lastname: Miyagawa
authors.affiliation: Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
authors.forename: Nao
authors.initials: N
authors.lastname: Nishida
authors.affiliation: Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
authors.forename: Jun
authors.initials: J
authors.lastname: Ohashi
authors.affiliation: 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.
authors.forename: Ryosuke
authors.initials: R
authors.lastname: Kimura
authors.affiliation: Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
authors.forename: Akihiro
authors.initials: A
authors.lastname: Fujimoto
authors.affiliation: 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.
authors.forename: Minae
authors.initials: M
authors.lastname: Kawashima
authors.affiliation: Hitachi Ltd, Central Research Laboratory, Kokubunji, Japan.
authors.forename: Asako
authors.initials: A
authors.lastname: Koike
authors.affiliation: Health Service Center, The University of Tokyo, Tokyo, Japan.
authors.forename: Tsukasa
authors.initials: T
authors.lastname: Sasaki
authors.affiliation: Department of Psychiatry, Mie University Graduate School of Medicine, Tsu, Japan.
authors.forename: Hisashi
authors.initials: H
authors.lastname: Tanii
authors.affiliation: Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
authors.forename: Takeshi
authors.initials: T
authors.lastname: Otowa
authors.affiliation: 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.
authors.forename: Yoshio
authors.initials: Y
authors.lastname: Momose
authors.affiliation: Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
authors.forename: Yasuo
authors.initials: Y
authors.lastname: Nakahara
authors.affiliation: Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
authors.forename: Jun
authors.initials: J
authors.lastname: Gotoh
authors.affiliation: Tokyo Metropolitan Matsuzawa Hospital, Tokyo, Japan.
authors.forename: Yuji
authors.initials: Y
authors.lastname: Okazaki
authors.affiliation: 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.
authors.forename: Shoji
authors.initials: S
authors.lastname: Tsuji
authors.affiliation: 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.
authors.forename: Katsushi
authors.initials: K
authors.lastname: Tokunaga
mesh_terms: 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*