Evolutionary History of the Risk of SNPs for Diffuse-Type Gastric Cancer in the Japanese Population
Abstract
:1. Introduction
2. Materials and Methods
2.1. Strategy of Analysis
2.2. Human SNP Data
2.3. FST
2.4. Linkage Disequilibrium Analysis
2.5. Neutrality Tests
2.5.1. Haplotype-Based Tests (EHH, nSL, and H12)
2.5.2. Site Frequency Spectrum-Based Tests (Tajima’s D and Fay and Wu’s H)
2.5.3. Nucleotide Diversity (π)
2.5.4. Two-Dimensional Site Frequency Spectrum (2D SFS)
2.5.5. Application of Population Branch Statistics (PBS)
2.6. Forward Simulation Using Japanese Demographic Model
2.6.1. Demographic Parameters in Simulations
2.6.2. Investigating Possible Causes of Large FST
2.7. Analysis using Ancient DNA Sequences from the Jomon People
3. Results
3.1. The T Allele at rs2294008 is Highly Differentiated between JPT and CHB
3.2. Exploring the Signal of Natural Selection Acting on rs2294008
3.3. Two-Dimensional Site Frequency Spectrum (2D SFS)
3.3.1. Detection of Positive Selection in CHB, but not in JPT
3.3.2. Selection Mode in CHB and JPT
3.3.3. History of Natural Selection in JPT and CHB
3.4. Examination of Whether Genetic Drift Can Explain the High FST Using Forward Simulation
3.5. Phylogenic Position of Jomon Haplotypes in the Network of Extant JPT and CHB
4. Discussion
- (i)
- Selection operated on the C allele (the non-risk allele) in the common ancestor of the Han Chinese and the Jomon people. The mode of positive selection in the Japanese is complex; selection on the A-G subhaplotype ceased or relaxed at some point along the Japanese lineage, but ongoing selection occurred on the C-A suphaplotype. Relaxation or cessation of positive selection on the A-G subhaplotype may have led to low frequency of the C allele in the extant JPT.
- (ii)
- The ancestral population (the Jomon people) had a high T allele frequency, which led to a high T allele frequency in the extant Japanese, even though the Jomon people experienced admixture with immigrant Yayoi farmers. These factors result in the large T/C allele frequency difference between JPT and CHB.
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Population | JPT | CHB | ||
---|---|---|---|---|
Core Region | 143755915- 143770914 | 143755876- 143771875 | ||
n # | 208 (C = 77, T = 131) | 206 (C = 155, T = 51) | ||
S † | 91 | 88 | ||
Tested Allele | C | T | C | T |
Allele Frequency | 0.370 | 0.630 | 0.752 | 0.248 |
Fc § | 0.167 (0.834) | 0.833 (>0.999) | 0.352 × 10−1 (0.223 × 10−2) ** | 0.869 (>0.999) |
Gc0 | 9.60 (0.693) | 31.84 (0.975) | 1.84 (0.167 × 10−2) ** | 25.13 (>0.999) |
Lc0 | 0.178 × 10−1 (0.708) | 0.259 (>0.999) | 0.565 × 10−2 (>0.167 × 10−2) ** | 0.130 (>0.999) |
G*c0 | 22.50 | 46.23 | 5.00 | 30.69 |
γ*(10) | 0.500 | 0.700 | 0.000 | 0.962 |
imax | 40 | 130 | 8 | 50 |
i*max | 0 | 29 | 75 | 21 |
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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
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 StyleIwasaki, 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