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The Scientific World Journal
Volume 2013 (2013), Article ID 675851, 10 pages
http://dx.doi.org/10.1155/2013/675851
Review Article

Prediction of Deleterious Nonsynonymous Single-Nucleotide Polymorphism for Human Diseases

MOE Key Laboratory of Bioinformatics and Bioinformatics Division, TNLIST/Department of Automation, Tsinghua University, Beijing 100084, China

Received 27 October 2012; Accepted 11 December 2012

Academic Editors: C. Proctor and R. Rivas

Copyright © 2013 Jiaxin Wu and Rui Jiang. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

The identification of genetic variants that are responsible for human inherited diseases is a fundamental problem in human and medical genetics. As a typical type of genetic variation, nonsynonymous single-nucleotide polymorphisms (nsSNPs) occurring in protein coding regions may alter the encoded amino acid, potentially affect protein structure and function, and further result in human inherited diseases. Therefore, it is of great importance to develop computational approaches to facilitate the discrimination of deleterious nsSNPs from neutral ones. In this paper, we review databases that collect nsSNPs and summarize computational methods for the identification of deleterious nsSNPs. We classify the existing methods for characterizing nsSNPs into three categories (sequence based, structure based, and annotation based), and we introduce machine learning models for the prediction of deleterious nsSNPs. We further discuss methods for identifying deleterious nsSNPs in noncoding variants and those for dealing with rare variants.