Classification of genome-wide copy number variations and their associated SNP and gene networks analysis

Yang Liu*, Yiu Fai Lee, Kwok Po NG

*Corresponding author for this work

Research output: Chapter in book/report/conference proceedingConference contributionpeer-review

Abstract

Detection of genomic DNA copy number variations (CNVs) can provide a complete and more comprehensive view of human disease. In this paper, we incorporate DNA copy number variation data derived from SNP arrays into a computational shrunken model and formalize the detection of copy number variations as a case-control classification problem. By shrinkage, the number of relevant CNVs to disease can be determined. In order to understand relevant CNVs, we study their corresponding SNPs in the genome and find out the unique genes that those SNPs are located in. A gene-gene similarity value is computed using GOSemSim and gene pairs that has a similarity value being greater than a threshold are selected to construct several groups of genes. For the SNPs that involved in these groups of genes, a statistical software PLINK is employed to compute the pair-wise SNP-SNP interactions, and identify SNP networks based on their p-values. By using two real genome-wide data sets, we further demonstrate SNP and gene networks play a role in the biological process. An analysis shows that such networks have relationships directly or indirectly to disease study.

Original languageEnglish
Title of host publicationProceedings - 2010 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2010
Pages9-12
Number of pages4
DOIs
Publication statusPublished - 2010
Event2010 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2010 - Hong Kong, China
Duration: 18 Dec 201021 Dec 2010

Publication series

NameProceedings - 2010 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2010

Conference

Conference2010 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2010
Country/TerritoryChina
CityHong Kong
Period18/12/1021/12/10

Scopus Subject Areas

  • Biomedical Engineering
  • Health Informatics

User-Defined Keywords

  • Classification
  • Copy number variation
  • Genome-wide
  • Networks
  • Shrunken
  • Single nucleotide polymorphism

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