Compressed Genotyping

Overview

Journal IEEE Trans Inf Theory

Date 2011 Apr 1

PMID 21451737

Citations 8

Authors

Yaniv Erlich

Assaf Gordon

Michael Brand

Gregory J Hannon

Partha P Mitra

Affiliations

Soon will be listed here.

Abstract

Over the past three decades we have steadily increased our knowledge on the genetic basis of many severe disorders. Nevertheless, there are still great challenges in applying this knowledge routinely in the clinic, mainly due to the relatively tedious and expensive process of genotyping. Since the genetic variations that underlie the disorders are relatively rare in the population, they can be thought of as a sparse signal. Using methods and ideas from compressed sensing and group testing, we have developed a cost-effective genotyping protocol to detect carriers for severe genetic disorders. In particular, we have adapted our scheme to a recently developed class of high throughput DNA sequencing technologies. The mathematical framework presented here has some important distinctions from the 'traditional' compressed sensing and group testing frameworks in order to address biological and technical constraints of our setting.

Citing Articles

Group testing via hypergraph factorization applied to COVID-19.

Hong D, Dey R, Lin X, Cleary B, Dobriban E Nat Commun. 2022; 13(1):1837.

PMID: 35383149 PMC: 8983763. DOI: 10.1038/s41467-022-29389-z.

COVID-19 Pandemic: Group Testing.

Nalbantoglu O, Gundogdu A Front Med (Lausanne). 2020; 7:522.

PMID: 32974372 PMC: 7461804. DOI: 10.3389/fmed.2020.00522.

An accurate clone-based haplotyping method by overlapping pool sequencing.

Li C, Cao C, Tu J, Sun X Nucleic Acids Res. 2016; 44(12):e112.

PMID: 27095193 PMC: 4937318. DOI: 10.1093/nar/gkw284.

Ensemble analysis of adaptive compressed genome sequencing strategies.

Taghavi Z BMC Bioinformatics. 2014; 15 Suppl 9:S13.

PMID: 25252999 PMC: 4221792. DOI: 10.1186/1471-2105-15-S9-S13.

iPipet: sample handling using a tablet.

Zielinski D, Gordon A, Zaks B, Erlich Y Nat Methods. 2014; 11(8):784-5.

PMID: 25075904 DOI: 10.1038/nmeth.3028.

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