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Connecting the dots: Potential of data integration to identify regulatory snps in late-onset alzheimer's disease GWAS findings

Rosenthal, SL and Barmada, MM and Wang, X and Demirci, FY and Kamboh, MI (2014) Connecting the dots: Potential of data integration to identify regulatory snps in late-onset alzheimer's disease GWAS findings. PLoS ONE, 9 (4).

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Abstract

Late-onset Alzheimer's disease (LOAD) is a multifactorial disorder with over twenty loci associated with disease risk. Given the number of genome-wide significant variants that fall outside of coding regions, it is possible that some of these variants alter some function of gene expression rather than tagging coding variants that alter protein structure and/or function. RegulomeDB is a database that annotates regulatory functions of genetic variants. In this study, we utilized RegulomeDB to investigate potential regulatory functions of lead single nucleotide polymorphisms (SNPs) identified in five genome-wide association studies (GWAS) of risk and age-at onset (AAO) of LOAD, as well as SNPs in LD (r2≥0.80) with the lead GWAS SNPs. Of a total 614 SNPs examined, 394 returned RegulomeDB scores of 1-6. Of those 394 variants, 34 showed strong evidence of regulatory function (RegulomeDB score ,3), and only 3 of them were genome-wide significant SNPs (ZCWPW1/ rs1476679, CLU/rs1532278 and ABCA7/rs3764650). This study further supports the assumption that some of the non-coding GWAS SNPs are true associations rather than tagged associations and demonstrates the application of RegulomeDB to GWAS data.©2014 Rosenthal et al.


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Details

Item Type: Article
Status: Published
Creators/Authors:
CreatorsEmailPitt UsernameORCID
Rosenthal, SLslr61@pitt.eduSLR61
Barmada, MMbarmada@pitt.eduBARMADA
Wang, Xxbw1@pitt.eduXBW1
Demirci, FYfyd1@pitt.eduFYD1
Kamboh, MIkamboh@pitt.eduKAMBOH
Contributors:
ContributionContributors NameEmailPitt UsernameORCID
EditorArendt, ThomasUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Centers: Other Centers, Institutes, Offices, or Units > Alzheimer's Disease Research Center
Date: 17 April 2014
Date Type: Publication
Journal or Publication Title: PLoS ONE
Volume: 9
Number: 4
DOI or Unique Handle: 10.1371/journal.pone.0095152
Schools and Programs: Graduate School of Public Health > Human Genetics
Refereed: Yes
Date Deposited: 23 Jun 2014 21:05
Last Modified: 05 Feb 2019 16:55
URI: http://d-scholarship.pitt.edu/id/eprint/21985

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