Cancer Specific Non-Synonymous Single Nucleotide Polymorphism Prediction in the Context of Haplotype and Protein Interacting Sites - Journal of Biomedical Science and Engineering

JBiSE > Vol.10 No.5, May 2017

Cancer Specific Non-Synonymous Single Nucleotide Polymorphism Prediction in the Context of Haplotype and Protein Interacting Sites ()

HTML XML

Download as PDF (Size: 471KB) PP. 28-44

DOI: 10.4236/jbise.2017.105B004 1,576 Downloads 2,786 Views Citations

Author(s)

Pakeeza Akram, Li Liao

Affiliation(s)

Computer and Information Sciences, University of Delaware, Newark, Delaware, USA.

ABSTRACT

In this work, we study predicting the effect of non-synonymous SNPs on several cancers. We trained classifiers on both sequential and structural features extracted from the affected genes and assessed the predictions made by the trained classifiers using cross validation. Specifically, we investigated how the prediction performance can be improved by connecting SNPs in the context of haplotype and interacting sites of proteins encoded by affected genes. We found that accuracy was consistently enhanced by combining sequential and structural features, with increase ranging from a few percentage points up to more than 20 percentage points. The results for putting SNPs in the context of interacting sites were less consistent. Compared to individual SNPs, these that appear together in haplotype showed stronger correlation with one another and with the phenotype, and therefore led to significant improvement inprediction performance, with ROC score increased from 0.81 to 0.95. Although some similar effect has been expected for connecting SNPs to interacting sites in proteins, the performance actually got worse. This decrease in prediction accuracy may be caused by the small data set being used in the study, as many affected proteins in the study do not have known interacting sites.

KEYWORDS

Single Nucleotide Polymorphism, Haplotype, Interaction Sites, Prediction, Cancer

Share and Cite:

Akram, P. and Liao, L. (2017) Cancer Specific Non-Synonymous Single Nucleotide Polymorphism Prediction in the Context of Haplotype and Protein Interacting Sites. Journal of Biomedical Science and Engineering, 10, 28-44. doi: 10.4236/jbise.2017.105B004.

Journals Menu

Follow SCIRP

	+1 323-425-8868
	customer@scirp.org
	+86 18163351462(WhatsApp)
	1655362766

	Paper Publishing WeChat

Journals Menu

Home

About SCIRP

Service

Policies