Improved haplotype inference by exploiting long-range linking and allelic imbalance in RNA-seq datasets

Haplotype reconstruction of distant genetic variants is problematic in short-read sequencing. Here, the authors describe HapTree-X, a probabilistic framework that uses differential allele-specific expression to better reconstruct paternal haplotypes from diploid and polyploid genomes.

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Autores principales:	Emily Berger, Deniz Yorukoglu, Lillian Zhang, Sarah K. Nyquist, Alex K. Shalek, Manolis Kellis, Ibrahim Numanagić, Bonnie Berger
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2020
Materias:	Science Q
Acceso en línea:	https://doaj.org/article/c970eb7c1f7e4e68975f9e9fac639d5d
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spelling	oai:doaj.org-article:c970eb7c1f7e4e68975f9e9fac639d5d2021-12-02T15:16:00ZImproved haplotype inference by exploiting long-range linking and allelic imbalance in RNA-seq datasets10.1038/s41467-020-18320-z2041-1723https://doaj.org/article/c970eb7c1f7e4e68975f9e9fac639d5d2020-09-01T00:00:00Zhttps://doi.org/10.1038/s41467-020-18320-zhttps://doaj.org/toc/2041-1723Haplotype reconstruction of distant genetic variants is problematic in short-read sequencing. Here, the authors describe HapTree-X, a probabilistic framework that uses differential allele-specific expression to better reconstruct paternal haplotypes from diploid and polyploid genomes.Emily BergerDeniz YorukogluLillian ZhangSarah K. NyquistAlex K. ShalekManolis KellisIbrahim NumanagićBonnie BergerNature PortfolioarticleScienceQENNature Communications, Vol 11, Iss 1, Pp 1-9 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	Science Q
spellingShingle	Science Q Emily Berger Deniz Yorukoglu Lillian Zhang Sarah K. Nyquist Alex K. Shalek Manolis Kellis Ibrahim Numanagić Bonnie Berger Improved haplotype inference by exploiting long-range linking and allelic imbalance in RNA-seq datasets
description	Haplotype reconstruction of distant genetic variants is problematic in short-read sequencing. Here, the authors describe HapTree-X, a probabilistic framework that uses differential allele-specific expression to better reconstruct paternal haplotypes from diploid and polyploid genomes.
format	article
author	Emily Berger Deniz Yorukoglu Lillian Zhang Sarah K. Nyquist Alex K. Shalek Manolis Kellis Ibrahim Numanagić Bonnie Berger
author_facet	Emily Berger Deniz Yorukoglu Lillian Zhang Sarah K. Nyquist Alex K. Shalek Manolis Kellis Ibrahim Numanagić Bonnie Berger
author_sort	Emily Berger
title	Improved haplotype inference by exploiting long-range linking and allelic imbalance in RNA-seq datasets
title_short	Improved haplotype inference by exploiting long-range linking and allelic imbalance in RNA-seq datasets
title_full	Improved haplotype inference by exploiting long-range linking and allelic imbalance in RNA-seq datasets
title_fullStr	Improved haplotype inference by exploiting long-range linking and allelic imbalance in RNA-seq datasets
title_full_unstemmed	Improved haplotype inference by exploiting long-range linking and allelic imbalance in RNA-seq datasets
title_sort	improved haplotype inference by exploiting long-range linking and allelic imbalance in rna-seq datasets
publisher	Nature Portfolio
publishDate	2020
url	https://doaj.org/article/c970eb7c1f7e4e68975f9e9fac639d5d
work_keys_str_mv	AT emilyberger improvedhaplotypeinferencebyexploitinglongrangelinkingandallelicimbalanceinrnaseqdatasets AT denizyorukoglu improvedhaplotypeinferencebyexploitinglongrangelinkingandallelicimbalanceinrnaseqdatasets AT lillianzhang improvedhaplotypeinferencebyexploitinglongrangelinkingandallelicimbalanceinrnaseqdatasets AT sarahknyquist improvedhaplotypeinferencebyexploitinglongrangelinkingandallelicimbalanceinrnaseqdatasets AT alexkshalek improvedhaplotypeinferencebyexploitinglongrangelinkingandallelicimbalanceinrnaseqdatasets AT manoliskellis improvedhaplotypeinferencebyexploitinglongrangelinkingandallelicimbalanceinrnaseqdatasets AT ibrahimnumanagic improvedhaplotypeinferencebyexploitinglongrangelinkingandallelicimbalanceinrnaseqdatasets AT bonnieberger improvedhaplotypeinferencebyexploitinglongrangelinkingandallelicimbalanceinrnaseqdatasets
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Improved haplotype inference by exploiting long-range linking and allelic imbalance in RNA-seq datasets

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