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eLD: entropy-based linkage disequilibrium index between multiallelic sites

Quantification of linkage disequilibrium (LD) is a critical step in studies investigating human genome variations. Commonly used LD indices such as r(2) handle LD of biallelic variants for two sites. As shown in a previously introduced LD index of ε, normalized entropy difference of the haplotype fr...

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Autor principal: Okada, Yukinori
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6197273/
https://www.ncbi.nlm.nih.gov/pubmed/30374405
http://dx.doi.org/10.1038/s41439-018-0030-x
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author Okada, Yukinori
author_facet Okada, Yukinori
author_sort Okada, Yukinori
collection PubMed
description Quantification of linkage disequilibrium (LD) is a critical step in studies investigating human genome variations. Commonly used LD indices such as r(2) handle LD of biallelic variants for two sites. As shown in a previously introduced LD index of ε, normalized entropy difference of the haplotype frequency between LD and linkage equilibrium (LE) could be utilized to estimate LD of biallelic variants for multiple sites. Here, we developed eLD (entropy-based Linkage Disequilibrium index between multiallelic sites) as publicly available software to calculate ε of multiallelic variants for two sites. Application of eLD could dissect complex LD structures among multiple HLA genes (e.g., strong LD among HLA-DRB1, HLA-DQA1, and HLA-DQB1 in East Asians). Use of eLD is not restricted to haplotype-based LD; it is also applicable to genotype-based LD. Therefore, eLD enables estimation of trans-regional LD of SNP genotypes at two unlinked loci, such as the nonlinear LD between functional missense variants of ADH1B (rs1229984 [Arg47His]) and ALDH2 (rs671 [Glu504Lys]).
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spelling pubmed-61972732018-10-29 eLD: entropy-based linkage disequilibrium index between multiallelic sites Okada, Yukinori Hum Genome Var Software Report Quantification of linkage disequilibrium (LD) is a critical step in studies investigating human genome variations. Commonly used LD indices such as r(2) handle LD of biallelic variants for two sites. As shown in a previously introduced LD index of ε, normalized entropy difference of the haplotype frequency between LD and linkage equilibrium (LE) could be utilized to estimate LD of biallelic variants for multiple sites. Here, we developed eLD (entropy-based Linkage Disequilibrium index between multiallelic sites) as publicly available software to calculate ε of multiallelic variants for two sites. Application of eLD could dissect complex LD structures among multiple HLA genes (e.g., strong LD among HLA-DRB1, HLA-DQA1, and HLA-DQB1 in East Asians). Use of eLD is not restricted to haplotype-based LD; it is also applicable to genotype-based LD. Therefore, eLD enables estimation of trans-regional LD of SNP genotypes at two unlinked loci, such as the nonlinear LD between functional missense variants of ADH1B (rs1229984 [Arg47His]) and ALDH2 (rs671 [Glu504Lys]). Nature Publishing Group UK 2018-10-22 /pmc/articles/PMC6197273/ /pubmed/30374405 http://dx.doi.org/10.1038/s41439-018-0030-x Text en © The Author(s) 2018 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Software Report
Okada, Yukinori
eLD: entropy-based linkage disequilibrium index between multiallelic sites
title eLD: entropy-based linkage disequilibrium index between multiallelic sites
title_full eLD: entropy-based linkage disequilibrium index between multiallelic sites
title_fullStr eLD: entropy-based linkage disequilibrium index between multiallelic sites
title_full_unstemmed eLD: entropy-based linkage disequilibrium index between multiallelic sites
title_short eLD: entropy-based linkage disequilibrium index between multiallelic sites
title_sort eld: entropy-based linkage disequilibrium index between multiallelic sites
topic Software Report
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6197273/
https://www.ncbi.nlm.nih.gov/pubmed/30374405
http://dx.doi.org/10.1038/s41439-018-0030-x
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