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.
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 School of Biological Sciences > 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: | https://repository.cshl.edu/id/eprint/15407 |
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