Next Article in Journal
Pro12Ala PPAR-γ2 and +294T/C PPAR-δ Polymorphisms and Association with Metabolic Traits in Teenagers from Northern Mexico
Next Article in Special Issue
Sequencing Red Fox Y Chromosome Fragments to Develop Phylogenetically Informative SNP Markers and Glimpse Male-Specific Trans-Pacific Phylogeography
Previous Article in Journal
Mitochondrial PCK2 Missense Variant in Shetland Sheepdogs with Paroxysmal Exercise-Induced Dyskinesia (PED)
Article

Evolutionary History of the Risk of SNPs for Diffuse-Type Gastric Cancer in the Japanese Population

1
Department of Evolutionary Studies of Biosystems, SOKENDAI (The Graduate University for Advanced Studies), Kanagawa 240-0193, Japan
2
Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo 062-8517, Japan
3
Department of Anthropology, National Museum of Nature and Science, Ibaraki 305-0005, Japan
4
Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo 162-8655, Japan
*
Author to whom correspondence should be addressed.
Genes 2020, 11(7), 775; https://doi.org/10.3390/genes11070775
Received: 11 June 2020 / Revised: 2 July 2020 / Accepted: 8 July 2020 / Published: 10 July 2020
(This article belongs to the Collection Tools for Population and Evolutionary Genetics)
A genome wide association study reported that the T allele of rs2294008 in a cancer-related gene, PSCA, is a risk allele for diffuse-type gastric cancer. This allele has the highest frequency (0.63) in Japanese in Tokyo (JPT) among 26 populations in the 1000 Genomes Project database. FST ≈ 0.26 at this single nucleotide polymorphism is one of the highest between JPT and the genetically close Han Chinese in Beijing (CHB). To understand the evolutionary history of the alleles in PSCA, we addressed: (i) whether the C non-risk allele at rs2294008 is under positive selection, and (ii) why the mainland Japanese population has a higher T allele frequency than other populations. We found that haplotypes harboring the C allele are composed of two subhaplotypes. We detected that positive selection on both subhaplotypes has occurred in the East Asian lineage. However, the selection on one of the subhaplotypes in JPT seems to have been relaxed or ceased after divergence from the continental population; this may have caused the elevation of T allele frequency. Based on simulations under the dual structure model (a specific demography for the Japanese) and phylogenetic analysis with ancient DNA, the T allele at rs2294008 might have had high frequency in the Jomon people (one of the ancestral populations of the modern Japanese); this may explain the high T allele frequency in the extant Japanese. View Full-Text
Keywords: genetic differentiation; PSCA; diffuse-type gastric cancer; rs2294008; Japanese; dual-structure model; Jomon people; Yayoi people; soft sweep; hardening selective sweep; selection target change genetic differentiation; PSCA; diffuse-type gastric cancer; rs2294008; Japanese; dual-structure model; Jomon people; Yayoi people; soft sweep; hardening selective sweep; selection target change
Show Figures

Figure 1

MDPI and ACS Style

Iwasaki, R.L.; Ishiya, K.; Kanzawa-Kiriyama, H.; Kawai, Y.; Gojobori, J.; Satta, Y. Evolutionary History of the Risk of SNPs for Diffuse-Type Gastric Cancer in the Japanese Population. Genes 2020, 11, 775. https://doi.org/10.3390/genes11070775

AMA Style

Iwasaki RL, Ishiya K, Kanzawa-Kiriyama H, Kawai Y, Gojobori J, Satta Y. Evolutionary History of the Risk of SNPs for Diffuse-Type Gastric Cancer in the Japanese Population. Genes. 2020; 11(7):775. https://doi.org/10.3390/genes11070775

Chicago/Turabian Style

Iwasaki, Risa L., Koji Ishiya, Hideaki Kanzawa-Kiriyama, Yosuke Kawai, Jun Gojobori, and Yoko Satta. 2020. "Evolutionary History of the Risk of SNPs for Diffuse-Type Gastric Cancer in the Japanese Population" Genes 11, no. 7: 775. https://doi.org/10.3390/genes11070775

Find Other Styles
Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Article Access Map by Country/Region

1
Back to TopTop