title: Detailed analysis of Japanese population substructure with a focus on the southwest islands of Japan.
abstract: Uncovering population structure is important for properly conducting association studies and for examining the demographic history of a population. Here, we examined the Japanese population substructure using data from the Japan Multi-Institutional Collaborative Cohort (J-MICC), which covers all but the northern region of Japan. Using 222 autosomal loci from 4502 subjects, we investigated population substructure by estimating F(ST) among populations, testing population differentiation, and performing principal component analysis (PCA) and correspondence analysis (CA). All analyses revealed a low but significant differentiation between the Amami Islanders and the mainland Japanese population. Furthermore, we examined the genetic differentiation between the mainland population, Amami Islanders and Okinawa Islanders using six loci included in both the Pan-Asian SNP (PASNP) consortium data and the J-MICC data. This analysis revealed that the Amami and Okinawa Islanders were differentiated from the mainland population. In conclusion, we revealed a low but significant level of genetic differentiation between the mainland population and populations in or to the south of the Amami Islands, although genetic variation between both populations might be clinal. Therefore, the possibility of population stratification must be considered when enrolling the islander population of this area, such as in the J-MICC study.
authors.affiliation: Clinical Trial Management Center, Nagoya City University Hospital, Nagoya, Japan. nishiyama@minos.ocn.ne.jp
authors.forename: Takeshi
authors.initials: T
authors.lastname: Nishiyama
authors.forename: Hirohisa
authors.initials: H
authors.lastname: Kishino
authors.forename: Sadao
authors.initials: S
authors.lastname: Suzuki
authors.forename: Ryosuke
authors.initials: R
authors.lastname: Ando
authors.forename: Hideshi
authors.initials: H
authors.lastname: Niimura
authors.forename: Hirokazu
authors.initials: H
authors.lastname: Uemura
authors.forename: Mikako
authors.initials: M
authors.lastname: Horita
authors.forename: Keizo
authors.initials: K
authors.lastname: Ohnaka
authors.forename: Nagato
authors.initials: N
authors.lastname: Kuriyama
authors.forename: Haruo
authors.initials: H
authors.lastname: Mikami
authors.forename: Naoyuki
authors.initials: N
authors.lastname: Takashima
authors.forename: Keitaro
authors.initials: K
authors.lastname: Mastuo
authors.forename: Yin
authors.initials: Y
authors.lastname: Guang
authors.forename: Kenji
authors.initials: K
authors.lastname: Wakai
authors.forename: Nobuyuki
authors.initials: N
authors.lastname: Hamajima
authors.forename: Hideo
authors.initials: H
authors.lastname: Tanaka
mesh_terms: D000328:Adult; D015331:Cohort Studies; D005260:Female; D014644:Genetic Variation; D005843:Geography; D006801:Humans; D007564:Japan; D008297:Male; D008875:Middle Aged; D020641:Polymorphism, Single Nucleotide; D011157:Population Dynamics; D044382:Population Groups / Q000235:genetics*