Erlich, Yaniv, Gordon, Assaf, Brand, Michael, Hannon, Gregory J, Mitra, Partha P (September 2009) Compressed Genotyping. IEEE Transactions on Information Theory. (Submitted)
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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.
| Item Type: | Paper |
|---|---|
| Subjects: | Investigative techniques and equipment > assays > next generation sequencing |
| CSHL Authors: | |
| Communities: | CSHL labs > Mitra lab School of Biological Sciences > Publications |
| SWORD Depositor: | CSHL Elements |
| Depositing User: | CSHL Elements |
| Date: | 21 September 2009 |
| Date Deposited: | 11 Oct 2023 15:10 |
| Last Modified: | 01 Mar 2024 16:18 |
| PMCID: | PMC3065185 |
| Related URLs: | |
| URI: | https://repository.cshl.edu/id/eprint/41178 |
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