Compressed Genotyping

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 g...

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Bibliographic Details
Published in:IEEE transactions on information theory Vol. 56; no. 2; pp. 706 - 723
Main Authors: Erlich, Y., Gordon, A., Brand, M., Hannon, G.J., Mitra, P.P.
Format: Journal Article
Language:English
Published: New York, NY IEEE 01.02.2010
Institute of Electrical and Electronics Engineers
The Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subjects:
Applied sciences
Bioinformatics
Biological variation
Carriers
Compressed
Compressed sensing
Data compression
Deoxyribonucleic acid
Detection
Disorders
DNA
Exact sciences and technology
Genetics
Genomics
Genotype & phenotype
genotyping
group testing
Humans
Information theory
Information, signal and communications theory
Large-scale systems
Mathematical analysis
Protocols
Sequencing
Systems, networks and services of telecommunications
Telecommunications
Telecommunications and information theory
Testing
Throughput
Transmission and modulation (techniques and equipments)
Information rate
group testing
Information transmission
DNA
Compressed sensing
genotyping
ISSN:0018-9448, 1557-9654
Online Access:Get full text
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Summary: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.
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ISSN:0018-9448
1557-9654
DOI:10.1109/TIT.2009.2037043