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Detailed Analysis of Japanese Population Substructure with a Focus on the Southwest Islands of Japan

Author

Listed:
  • Takeshi Nishiyama
  • Hirohisa Kishino
  • Sadao Suzuki
  • Ryosuke Ando
  • Hideshi Niimura
  • Hirokazu Uemura
  • Mikako Horita
  • Keizo Ohnaka
  • Nagato Kuriyama
  • Haruo Mikami
  • Naoyuki Takashima
  • Keitaro Mastuo
  • Yin Guang
  • Kenji Wakai
  • Nobuyuki Hamajima
  • Hideo Tanaka
  • for the J-MICC Study Group

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 FST 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.

Suggested Citation

  • Takeshi Nishiyama & Hirohisa Kishino & Sadao Suzuki & Ryosuke Ando & Hideshi Niimura & Hirokazu Uemura & Mikako Horita & Keizo Ohnaka & Nagato Kuriyama & Haruo Mikami & Naoyuki Takashima & Keitaro Mas, 2012. "Detailed Analysis of Japanese Population Substructure with a Focus on the Southwest Islands of Japan," PLOS ONE, Public Library of Science, vol. 7(4), pages 1-7, April.
    • Handle: RePEc:plo:pone00:0035000
    DOI: 10.1371/journal.pone.0035000
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    References listed on IDEAS

    as
    1. B. Devlin & Kathryn Roeder, 1999. "Genomic Control for Association Studies," Biometrics, The International Biometric Society, vol. 55(4), pages 997-1004, December.
    2. Chao Tian & Roman Kosoy & Annette Lee & Michael Ransom & John W Belmont & Peter K Gregersen & Michael F Seldin, 2008. "Analysis of East Asia Genetic Substructure Using Genome-Wide SNP Arrays," PLOS ONE, Public Library of Science, vol. 3(12), pages 1-10, December.
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