Compressed genotyping

Yaniv Erlich, Assaf Gordon, Michael Brand, Greg J Hannon, Partha P Mitra

Research output: Contribution to journalArticleResearchpeer-review

37 Citations (Scopus)

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.
Original languageEnglish
Pages (from-to)706 - 723
Number of pages18
JournalIEEE Transactions on Information Theory
Volume56
Issue number2
DOIs
Publication statusPublished - 2010
Externally publishedYes

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