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Plos One : Ldx ; Estimation of Linkage Disequilibrium from High- Throughput Pooled Resequencing Data, Volume 7

By Wu, Rongling

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Book Id: WPLBN0003940072
Format Type: PDF eBook :
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Reproduction Date: 2015

Title: Plos One : Ldx ; Estimation of Linkage Disequilibrium from High- Throughput Pooled Resequencing Data, Volume 7  
Author: Wu, Rongling
Volume: Volume 7
Language: English
Subject: Journals, Science, Medical Science
Collections: Periodicals: Journal and Magazine Collection (Contemporary)
Historic
Publication Date:
Publisher: Plos

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Wu, R. (n.d.). Plos One : Ldx ; Estimation of Linkage Disequilibrium from High- Throughput Pooled Resequencing Data, Volume 7. Retrieved from http://netlibrary.net/


Description
Description : High-throughput pooled resequencing offers significant potential for whole genome population sequencing. However, its main drawback is the loss of haplotype information. In order to regain some of this information, we present LDx, a computational tool for estimating linkage disequilibrium (LD) from pooled resequencing data. LDx uses an approximate maximum likelihood approach to estimate LD (r2) between pairs of SNPs that can be observed within and among single reads. LDx also reports r2 estimates derived solely from observed genotype counts. We demonstrate that the LDx estimates are highly correlated with r2 estimated from individually resequenced strains. We discuss the performance of LDx using more stringent quality conditions and infer via simulation the degree to which performance can improve based on read depth. Finally we demonstrate two possible uses of LDx with real and simulated pooled resequencing data. First, we use LDx to infer genomewide patterns of decay of LD with physical distance in D. melanogaster population resequencing data. Second, we demonstrate that r2 estimates from LDx are capable of distinguishing alternative demographic models representing plausible demographic histories of D. melanogaster.

 

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