TY - JOUR
T1 - Analysis of mainland Japanese and Okinawan Japanese populations using the precision ID Ancestry Panel
AU - Nakanishi, Hiroaki
AU - Pereira, Vania
AU - Børsting, Claus
AU - Yamamoto, Toshimichi
AU - Tvedebrink, Torben
AU - Hara, Masaaki
AU - Takada, Aya
AU - Saito, Kazuyuki
AU - Morling, Niels
N1 - Copyright © 2017 Elsevier B.V. All rights reserved.
PY - 2018
Y1 - 2018
N2 - We typed 165 AIMs in 49 mainland Japanese and 47 Okinawa Japanese using the Precision ID Ancestry Panel (Thermo Fisher Scientific). None of the 165 SNPs showed significant deviation from Hardy-Weinberg equilibrium in the mainland Japanese. One SNP (rs3943253) showed significant deviation from Hardy-Weinberg equilibrium in Okinawa Japanese. Fisher's exact tests showed that the genotype frequencies of 14 loci were significantly different (p<0.05) between the two populations before correction for multiple testing. After Bonferroni correction, only rs671 remained statistically significant (p<0.0003). This SNP is located in the ALDH2 gene. The mutant A allele is associated with increased side effects after alcohol intake. The frequency of the GG genotype (wild type) was higher in the Okinawa Japanese (78.7%) than in mainland Japanese (34.7%; Bonferroni corrected P<0.001). For 31 (63.3%) of the mainland Japanese and 42 (89.4%) of Okinawa Japanese, the highest population likelihood was obtained with the Japanese reference population. However, only in a few individuals, the likelihoods were significantly different from those calculated using reference data from neighboring populations. The likelihoods for mainland Japanese and Okinawa Japanese were not significantly different from each other for any of the investigated individuals. STRUCTURE and PCA analyses showed that mainland Japanese, Okinawa Japanese, and East Asians could not be differentiated with the Precision ID Ancestry Panel.
AB - We typed 165 AIMs in 49 mainland Japanese and 47 Okinawa Japanese using the Precision ID Ancestry Panel (Thermo Fisher Scientific). None of the 165 SNPs showed significant deviation from Hardy-Weinberg equilibrium in the mainland Japanese. One SNP (rs3943253) showed significant deviation from Hardy-Weinberg equilibrium in Okinawa Japanese. Fisher's exact tests showed that the genotype frequencies of 14 loci were significantly different (p<0.05) between the two populations before correction for multiple testing. After Bonferroni correction, only rs671 remained statistically significant (p<0.0003). This SNP is located in the ALDH2 gene. The mutant A allele is associated with increased side effects after alcohol intake. The frequency of the GG genotype (wild type) was higher in the Okinawa Japanese (78.7%) than in mainland Japanese (34.7%; Bonferroni corrected P<0.001). For 31 (63.3%) of the mainland Japanese and 42 (89.4%) of Okinawa Japanese, the highest population likelihood was obtained with the Japanese reference population. However, only in a few individuals, the likelihoods were significantly different from those calculated using reference data from neighboring populations. The likelihoods for mainland Japanese and Okinawa Japanese were not significantly different from each other for any of the investigated individuals. STRUCTURE and PCA analyses showed that mainland Japanese, Okinawa Japanese, and East Asians could not be differentiated with the Precision ID Ancestry Panel.
KW - Journal Article
KW - Ancestry informative markers
KW - Massive parallel sequencing
KW - Okinawan Japanese
KW - Precision ID ancestry panel
KW - Mainland japanese
KW - Genetics, Population
KW - DNA Fingerprinting
KW - Gene Frequency
KW - Humans
KW - Japan
KW - Genotype
KW - Multiplex Polymerase Chain Reaction
KW - Asian Continental Ancestry Group/genetics
KW - Likelihood Functions
KW - High-Throughput Nucleotide Sequencing/instrumentation
KW - Polymorphism, Single Nucleotide
UR - http://www.scopus.com/inward/record.url?scp=85037609102&partnerID=8YFLogxK
U2 - 10.1016/j.fsigen.2017.12.004
DO - 10.1016/j.fsigen.2017.12.004
M3 - Journal article
C2 - 29223883
SN - 1872-4973
VL - 33
SP - 106
EP - 109
JO - Forensic Science International: Genetics
JF - Forensic Science International: Genetics
IS - March
ER -