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Similarity-based disease risk assessment for personal genomes: proof of concept.

Authors
  • Woo, Jung Hoon1
  • Lai, Albert M
  • Chung, Wendy K
  • Weng, Chunhua
  • 1 Department of Biomedical Informatics, Columbia University, New York, NY 10032, USA.
Type
Published Article
Journal
AMIA ... Annual Symposium proceedings. AMIA Symposium
Publication Date
Jan 01, 2011
Volume
2011
Pages
1524–1531
Identifiers
PMID: 22195217
Source
Medline
License
Unknown

Abstract

The increasing availability of personal genome data has led to escalating needs by consumers to understand the implications of their gene sequences. At present, poorly integrated genetic knowledge has not met these needs. This proof-of-concept study proposes a similarity-based approach to assess the disease risk predisposition for personal genomes. We hypothesize that the semantic similarity between a personal genome and a disease can indicate the disease risks in the person. We developed a knowledge network that integrates existing knowledge of genes, diseases, and symptoms from six sources using the Semantic Web standard, Resource Description Framework (RDF). We then used latent relationships between genes and diseases derived from our knowledge network to measure the semantic similarity between a personal genome and a genetic disease. For demonstration, we showed the feasibility of assessing the disease risks in one personal genome and discussed related methodology issues.

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