Inclusion of Population-specific Reference Panel from India to the 1000 Genomes Phase 3 Panel Improves Imputation Accuracy

Abstract Imputation is a computational method based on the principle of haplotype sharing allowing enrichment of genome-wide association study datasets. It depends on the haplotype structure of the population and density of the genotype data. The 1000 Genomes Project led to the generation of imputat...

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Autores principales:	Meraj Ahmad, Anubhav Sinha, Sreya Ghosh, Vikrant Kumar, Sonia Davila, Chittaranjan S. Yajnik, Giriraj R. Chandak
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/5aaeda6a90ea4c0fa5f3e7dade8f0cee
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spelling	oai:doaj.org-article:5aaeda6a90ea4c0fa5f3e7dade8f0cee2021-12-02T12:32:05ZInclusion of Population-specific Reference Panel from India to the 1000 Genomes Phase 3 Panel Improves Imputation Accuracy10.1038/s41598-017-06905-62045-2322https://doaj.org/article/5aaeda6a90ea4c0fa5f3e7dade8f0cee2017-07-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-06905-6https://doaj.org/toc/2045-2322Abstract Imputation is a computational method based on the principle of haplotype sharing allowing enrichment of genome-wide association study datasets. It depends on the haplotype structure of the population and density of the genotype data. The 1000 Genomes Project led to the generation of imputation reference panels which have been used globally. However, recent studies have shown that population-specific panels provide better enrichment of genome-wide variants. We compared the imputation accuracy using 1000 Genomes phase 3 reference panel and a panel generated from genome-wide data on 407 individuals from Western India (WIP). The concordance of imputed variants was cross-checked with next-generation re-sequencing data on a subset of genomic regions. Further, using the genome-wide data from 1880 individuals, we demonstrate that WIP works better than the 1000 Genomes phase 3 panel and when merged with it, significantly improves the imputation accuracy throughout the minor allele frequency range. We also show that imputation using only South Asian component of the 1000 Genomes phase 3 panel works as good as the merged panel, making it computationally less intensive job. Thus, our study stresses that imputation accuracy using 1000 Genomes phase 3 panel can be further improved by including population-specific reference panels from South Asia.Meraj AhmadAnubhav SinhaSreya GhoshVikrant KumarSonia DavilaChittaranjan S. YajnikGiriraj R. ChandakNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-8 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Meraj Ahmad Anubhav Sinha Sreya Ghosh Vikrant Kumar Sonia Davila Chittaranjan S. Yajnik Giriraj R. Chandak Inclusion of Population-specific Reference Panel from India to the 1000 Genomes Phase 3 Panel Improves Imputation Accuracy
description	Abstract Imputation is a computational method based on the principle of haplotype sharing allowing enrichment of genome-wide association study datasets. It depends on the haplotype structure of the population and density of the genotype data. The 1000 Genomes Project led to the generation of imputation reference panels which have been used globally. However, recent studies have shown that population-specific panels provide better enrichment of genome-wide variants. We compared the imputation accuracy using 1000 Genomes phase 3 reference panel and a panel generated from genome-wide data on 407 individuals from Western India (WIP). The concordance of imputed variants was cross-checked with next-generation re-sequencing data on a subset of genomic regions. Further, using the genome-wide data from 1880 individuals, we demonstrate that WIP works better than the 1000 Genomes phase 3 panel and when merged with it, significantly improves the imputation accuracy throughout the minor allele frequency range. We also show that imputation using only South Asian component of the 1000 Genomes phase 3 panel works as good as the merged panel, making it computationally less intensive job. Thus, our study stresses that imputation accuracy using 1000 Genomes phase 3 panel can be further improved by including population-specific reference panels from South Asia.
format	article
author	Meraj Ahmad Anubhav Sinha Sreya Ghosh Vikrant Kumar Sonia Davila Chittaranjan S. Yajnik Giriraj R. Chandak
author_facet	Meraj Ahmad Anubhav Sinha Sreya Ghosh Vikrant Kumar Sonia Davila Chittaranjan S. Yajnik Giriraj R. Chandak
author_sort	Meraj Ahmad
title	Inclusion of Population-specific Reference Panel from India to the 1000 Genomes Phase 3 Panel Improves Imputation Accuracy
title_short	Inclusion of Population-specific Reference Panel from India to the 1000 Genomes Phase 3 Panel Improves Imputation Accuracy
title_full	Inclusion of Population-specific Reference Panel from India to the 1000 Genomes Phase 3 Panel Improves Imputation Accuracy
title_fullStr	Inclusion of Population-specific Reference Panel from India to the 1000 Genomes Phase 3 Panel Improves Imputation Accuracy
title_full_unstemmed	Inclusion of Population-specific Reference Panel from India to the 1000 Genomes Phase 3 Panel Improves Imputation Accuracy
title_sort	inclusion of population-specific reference panel from india to the 1000 genomes phase 3 panel improves imputation accuracy
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/5aaeda6a90ea4c0fa5f3e7dade8f0cee
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_version_	1718394158344830976

Inclusion of Population-specific Reference Panel from India to the 1000 Genomes Phase 3 Panel Improves Imputation Accuracy

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