Future Preventive Gene Therapy of Polygenic Diseases from a Population Genetics Perspective
Abstract
:1. Introduction
2. Results
2.1. Admixture of Populations with Matching Mean PRSs: To What Extent Can Causal Risk Alleles of Polygenic Diseases Differ between Populations?
2.2. Admixture of Populations with Differing PRSs
2.3. Lowering Polygenic Disease Prevalence by Editing Effect SNPs
2.4. Estimates of Population Genomic Parameters for Diseases Known to Have Large Risk Differences between Ethnic Groups
2.5. An Estimate of Preventive Gene Therapy for Early- to Middle-Age-Onset Polygenic Diseases
3. Discussion
4. Methods
4.1. Considerations for Liability Threshold Models
4.2. Conceptual Summary
4.3. Allele Genetic Architecture
4.4. Disease Prevalence Analysis
4.5. Simulating Gene Therapy under Population Stratification and Admixture Scenarios
5. Conclusions
Supplementary Materials
Funding
Acknowledgments
Conflicts of Interest
Abbreviations
AD | Alzheimer’s disease |
AFD | allele frequency difference statistic [97] |
CAD | coronary artery disease |
DD | Dupuytren’s disease |
EMOD | Early- to Middle-age-Onset polygenic Disease |
Fst | F-statistics, originally conceived as te fixation index by Wright, implemented here using Hudson’s method [96] |
GRS | genetic risk score; used synonymously with polygenic risk score, abbreviated below |
GWAS | genome-wide association study |
LE | lupus erythematosus |
LOD | late-onset disease; herein, analyzed LODs are exclusively polygenic |
MAF | minor allele frequency; customarily implies the effect allele frequency |
OR | odds ratio |
PRS | polygenic risk score; in this study, a normalized sum of logarithms of additional relative risk conferred by causal alleles |
RA | rheumatoid arthritis |
RR | relative risk or risk ratio |
SNP | single nucleotide polymorphism; in the context of this study, SNP is used synonymously with the term ’allele’ |
T2D | type 2 diabetes |
WGS | whole genome sequencing ff |
Appendix A. Ancillary Chapters and Figures
Appendix A.1. Population Stratification and Admixture from the Perspective of Polygenic Disease Risk
Appendix A.2. A Concise Summary of Gene-Editing Techniques
Appendix A.3. Implementation of Common Low-Effect Genetic Architecture
Appendix A.4. Ancillary Figures
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Fraction of Differing Causal SNPs | 100% | 65% | 33% | 20% |
---|---|---|---|---|
Second-generation prevalence increase, % | 1 | <1 | <1 | <1 |
Fifth-generation prevalence increase, % | 2.7 | 1.4 | 1.3 | 0.8 |
Asymptotic prevalence increase limit, % | 45 | 22 | 11 | 6.3 |
Disease | Prevalence in Pop 1 | Prevalence in Pop 2 | Admixed Prevalence | Relative Risk | PRS Change | Edited SNPs | SNPs in Disease Architecture |
---|---|---|---|---|---|---|---|
DD | 25% | 0.25% | 4.0% | 100 | 8.44 | 89.0 | 3575 |
RA | 3.0% | 0.30% | 1.0% | 10 | 2.62 | 27.6 | 1350 |
LE | 0.35% | 0.10% | 0.19% | 3.5 | 1.20 | 12.7 | 700 |
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Oliynyk, R.T. Future Preventive Gene Therapy of Polygenic Diseases from a Population Genetics Perspective. Int. J. Mol. Sci. 2019, 20, 5013. https://doi.org/10.3390/ijms20205013
Oliynyk RT. Future Preventive Gene Therapy of Polygenic Diseases from a Population Genetics Perspective. International Journal of Molecular Sciences. 2019; 20(20):5013. https://doi.org/10.3390/ijms20205013
Chicago/Turabian StyleOliynyk, Roman Teo. 2019. "Future Preventive Gene Therapy of Polygenic Diseases from a Population Genetics Perspective" International Journal of Molecular Sciences 20, no. 20: 5013. https://doi.org/10.3390/ijms20205013