Compressed genotyping

Erlich, Y., Gordon, A., Brand, M., Hannon, G. J., Mitra, P. P. (February 2010) Compressed genotyping. IEEE Transactions on Information Theory, 56 (2). pp. 706-723.

URL: http://www.ncbi.nlm.nih.gov/pubmed/21451737
DOI: 10.1109/TIT.2009.2037043

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. © 2006 IEEE.

Item Type: Paper
Uncontrolled Keywords: Compressed sensing DNA Genotyping Group testing
Subjects: bioinformatics > quantitative biology
bioinformatics > genomics and proteomics > annotation > sequence annotation
bioinformatics > genomics and proteomics > analysis and processing > Sequence Data Processing
bioinformatics > genomics and proteomics > Mapping and Rendering > Sequence Rendering
CSHL Authors:
Communities: CSHL labs > Hannon lab
CSHL labs > Mitra lab
Watson School > Publications
Depositing User: CSHL Librarian
Date: February 2010
Date Deposited: 29 Sep 2011 14:53
Last Modified: 22 Sep 2014 19:18
PMCID: PMC3065185
URI: http://repository.cshl.edu/id/eprint/15407

Actions (login required)

Administrator's edit/view item Administrator's edit/view item
CSHL HomeAbout CSHLResearchEducationNews & FeaturesCampus & Public EventsCareersGiving