Compressed Genotyping

DOI10.1109/TIT.2009.2037043zbMATH Open1366.92078DBLPjournals/tit/ErlichGBHM10arXiv0909.3691WikidataQ42013661 ScholiaQ42013661MaRDI QIDQ4976005FDOQ4976005

Michael Brand, P. P. Mitra, Assaf Gordon, Gregory J. Hannon, Yaniv Erlich

Publication date: 27 July 2017

Published in: IEEE Transactions on Information Theory (Search for Journal in Brave)

Abstract: Significant volumes of knowledge have been accumulated in recent years linking subtle genetic variations to a wide variety of medical disorders from Cystic Fibrosis to mental retardation. Nevertheless, there are still great challenges in applying this knowledge routinely in the clinic, largely due to the relatively tedious and expensive process of DNA sequencing. Since the genetic polymorphisms that underlie these disorders are relatively rare in the human population, the presence or absence of a disease-linked polymorphism 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. In particular, we have adapted our scheme to a recently developed class of high throughput DNA sequencing technologies, and assembled a mathematical framework that has some important distinctions from 'traditional' compressed sensing ideas in order to address different biological and technical constraints.

Full work available at URL: https://arxiv.org/abs/0909.3691

Mathematics Subject Classification ID

Genetics and epigenetics (92D10)

Cited In (6)

• Compression of Whole Genome Alignments
• Bayesian clustering of DNA sequences using Markov chains and a stochastic partition model
• Data Rotation Improves Genomotyping Efficiency
• De Novo NGS Data Compression
• Superimposed Codes and Threshold Group Testing
• Search for Sparse Active Inputs: A Review

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