Using network clustering to predict copy number variations associated with health disparities

PeerJ
Yi JiangLi Yang

Abstract

Substantial health disparities exist between African Americans and Caucasians in the United States. Copy number variations (CNVs) are one form of human genetic variations that have been linked with complex diseases and often occur at different frequencies among African Americans and Caucasian populations. Here, we aimed to investigate whether CNVs with differential frequencies can contribute to health disparities from the perspective of gene networks. We inferred network clusters from human gene/protein networks based on two different data sources. We then evaluated each network cluster for the occurrences of known pathogenic genes and genes located in CNVs with different population frequencies, and used false discovery rates to rank network clusters. This approach let us identify five clusters enriched with known pathogenic genes and with genes located in CNVs with different frequencies between African Americans and Caucasians. These clustering patterns predict two candidate causal genes located in four population-specific CNVs that play potential roles in health disparities.

References

Jan 11, 2000·Nucleic Acids Research·S T SherryK Sirotkin
Apr 14, 2004·Archives of Ophthalmology·Nathan CongdonUNKNOWN Eye Diseases Prevalence Research Group
Feb 18, 2005·Nature Reviews. Genetics·Joel N Hirschhorn, Mark J Daly
Feb 18, 2005·Nature Reviews. Genetics·William Y S WangJohn A Todd
Dec 31, 2005·Nucleic Acids Research·Gopa R MishraAkhilesh Pandey
Jun 17, 2006·Bioinformatics·Stan Pounds, Cheng Cheng
Jun 27, 2006·American Journal of Physiology. Heart and Circulatory Physiology·Nitisha HiranandaniPaul M L Janssen
Sep 5, 2007·Nature Genetics·Steven A McCarroll, David M Altshuler
Jul 17, 2007·American Journal of Physiology. Heart and Circulatory Physiology·M A Hassan TalukderJay L Zweier
Nov 8, 2008·Nucleic Acids Research·T S Keshava PrasadAkhilesh Pandey
Mar 17, 2009·Human Molecular Genetics·Sergio E BaranziniMichael R Barnes
Mar 26, 2009·BMC Genetics·Joseph P McElroyJorge R Oksenberg
Apr 1, 2009·BMC Bioinformatics·James Vlasblom, Shoshana J Wodak
May 1, 2009·Nature·Joseph T GlessnerHakon Hakonarson
May 26, 2009·BMC Medical Genomics·Edward Ramos, Charles Rotimi
Dec 18, 2010·Nature Reviews. Genetics·Albert-László BarabásiJoseph Loscalzo
Mar 19, 2011·Cell·Marc VidalAlbert-László Barabási
Mar 1, 2012·IET Systems Biology·Z-P LiuL Chen
Mar 19, 2013·PLoS Computational Biology·Ekta KhuranaMark Gerstein
Jul 25, 2013·Molecular & Cellular Proteomics : MCP·Amitabh SharmaAlbert-László Barabási
Nov 12, 2013·Current Opinion in Genetics & Development·Nir AtiasRoded Sharan
Nov 26, 2013·Nucleic Acids Research·Donna KarolchikW James Kent
Nov 30, 2013·Current Opinion in Genetics & Development·Mark D M LeisersonBenjamin J Raphael
Aug 8, 2014·PLoS Genetics·Maggie C Y NgUNKNOWN MEta-analysis of type 2 DIabetes in African Americans Consortium

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OmimVarLocusIdSNP
MCL
MySQL
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MySQL API

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