Compressed sensing-based pooling experiments using next generation sequencing

Noam Shental*, Amnon Amir, Or Zuk

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

Abstract

Screening for carriers of rare variants by resequencing is important for the identification of individuals carrying disease alleles. Rapid sequencing by new technologies enables low-cost resequencing of target regions, although it is still prohibitive to test more than a few individuals. Pooling designs can enable detection of carriers of rare alleles in groups of individuals in a more economical manner. Previous pooling strategies were shown only for a relatively low number of individuals in a pool, and required the design of pooling schemes for particular cases. We propose a novel pooling design, based on a compressed sensing approach, which is general, simple and efficient. We model the experimental procedure and show via computer simulations our ability to recover rare allele carriers in larger groups than were possible before, especially when high coverage is obtained for each individual.

Original languageAmerican English
Title of host publication2010 Information Theory and Applications Workshop, ITA 2010 - Conference Proceedings
Pages446-447
Number of pages2
DOIs
StatePublished - 2010
Externally publishedYes
Event2010 Information Theory and Applications Workshop, ITA 2010 - San Diego, CA, United States
Duration: 31 Jan 20105 Feb 2010

Publication series

Name2010 Information Theory and Applications Workshop, ITA 2010 - Conference Proceedings

Conference

Conference2010 Information Theory and Applications Workshop, ITA 2010
Country/TerritoryUnited States
CitySan Diego, CA
Period31/01/105/02/10

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