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Genomic Scans of Zygotic Disequilibrium and Epistatic SNPs in HapMap Phase III Populations

Previous theory indicates that zygotic linkage disequilibrium (LD) is more informative than gametic or composite digenic LD in revealing natural population history. Further, the difference between the composite digenic and maximum zygotic LDs can be used to detect epistatic selection for fitness. He...

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Autores principales: Hu, Xin-Sheng, Hu, Yang
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4488364/
https://www.ncbi.nlm.nih.gov/pubmed/26126177
http://dx.doi.org/10.1371/journal.pone.0131039
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author Hu, Xin-Sheng
Hu, Yang
author_facet Hu, Xin-Sheng
Hu, Yang
author_sort Hu, Xin-Sheng
collection PubMed
description Previous theory indicates that zygotic linkage disequilibrium (LD) is more informative than gametic or composite digenic LD in revealing natural population history. Further, the difference between the composite digenic and maximum zygotic LDs can be used to detect epistatic selection for fitness. Here we corroborate the theory by investigating genome-wide zygotic LDs in HapMap phase III human populations. Results show that non-Africa populations have much more significant zygotic LDs than do Africa populations. Africa populations (ASW, LWK, MKK, and YRI) possess more significant zygotic LDs for the double-homozygotes (D(AABB)) than any other significant zygotic LDs (D(AABb), D(AaBB), and D(AaBb)), while non-Africa populations generally have more significant D(AaBb)’s than any other significant zygotic LDs (D(AABB), D(AABb), and D(AaBB)). Average r-squares for any significant zygotic LDs increase generally in an order of populations YRI, MKK, CEU, CHB, LWK, JPT, CHD, TSI, GIH, ASW, and MEX. Average r-squares are greater for D(AABB) and D(AaBb) than for D(AaBB) and D(AABb) in each population. YRI and MKK can be separated from LWK and ASW in terms of the pattern of average r-squares. All population divergences in zygotic LDs can be interpreted with the model of Out of Africa for modern human origins. We have also detected 19735-95921 SNP pairs exhibiting strong signals of epistatic selection in different populations. Gene-gene interactions for some epistatic SNP pairs are evident from empirical findings, but many more epistatic SNP pairs await evidence. Common epistatic SNP pairs rarely exist among all populations, but exist in distinct regions (Africa, Europe, and East Asia), which helps to understand geographical genomic medicine.
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spelling pubmed-44883642015-07-02 Genomic Scans of Zygotic Disequilibrium and Epistatic SNPs in HapMap Phase III Populations Hu, Xin-Sheng Hu, Yang PLoS One Research Article Previous theory indicates that zygotic linkage disequilibrium (LD) is more informative than gametic or composite digenic LD in revealing natural population history. Further, the difference between the composite digenic and maximum zygotic LDs can be used to detect epistatic selection for fitness. Here we corroborate the theory by investigating genome-wide zygotic LDs in HapMap phase III human populations. Results show that non-Africa populations have much more significant zygotic LDs than do Africa populations. Africa populations (ASW, LWK, MKK, and YRI) possess more significant zygotic LDs for the double-homozygotes (D(AABB)) than any other significant zygotic LDs (D(AABb), D(AaBB), and D(AaBb)), while non-Africa populations generally have more significant D(AaBb)’s than any other significant zygotic LDs (D(AABB), D(AABb), and D(AaBB)). Average r-squares for any significant zygotic LDs increase generally in an order of populations YRI, MKK, CEU, CHB, LWK, JPT, CHD, TSI, GIH, ASW, and MEX. Average r-squares are greater for D(AABB) and D(AaBb) than for D(AaBB) and D(AABb) in each population. YRI and MKK can be separated from LWK and ASW in terms of the pattern of average r-squares. All population divergences in zygotic LDs can be interpreted with the model of Out of Africa for modern human origins. We have also detected 19735-95921 SNP pairs exhibiting strong signals of epistatic selection in different populations. Gene-gene interactions for some epistatic SNP pairs are evident from empirical findings, but many more epistatic SNP pairs await evidence. Common epistatic SNP pairs rarely exist among all populations, but exist in distinct regions (Africa, Europe, and East Asia), which helps to understand geographical genomic medicine. Public Library of Science 2015-06-30 /pmc/articles/PMC4488364/ /pubmed/26126177 http://dx.doi.org/10.1371/journal.pone.0131039 Text en © 2015 Hu, Hu http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Hu, Xin-Sheng
Hu, Yang
Genomic Scans of Zygotic Disequilibrium and Epistatic SNPs in HapMap Phase III Populations
title Genomic Scans of Zygotic Disequilibrium and Epistatic SNPs in HapMap Phase III Populations
title_full Genomic Scans of Zygotic Disequilibrium and Epistatic SNPs in HapMap Phase III Populations
title_fullStr Genomic Scans of Zygotic Disequilibrium and Epistatic SNPs in HapMap Phase III Populations
title_full_unstemmed Genomic Scans of Zygotic Disequilibrium and Epistatic SNPs in HapMap Phase III Populations
title_short Genomic Scans of Zygotic Disequilibrium and Epistatic SNPs in HapMap Phase III Populations
title_sort genomic scans of zygotic disequilibrium and epistatic snps in hapmap phase iii populations
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4488364/
https://www.ncbi.nlm.nih.gov/pubmed/26126177
http://dx.doi.org/10.1371/journal.pone.0131039
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