Document Detail


Analysis of 60 reported glioma risk SNPs replicates published GWAS findings but fails to replicate associations from published candidate-gene studies.
MedLine Citation:
PMID:  23280628     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
Genomewide association studies (GWAS) and candidate-gene studies have implicated single-nucleotide polymorphisms (SNPs) in at least 45 different genes as putative glioma risk factors. Attempts to validate these associations have yielded variable results and few genetic risk factors have been consistently replicated. We conducted a case-control study of Caucasian glioma cases and controls from the University of California San Francisco (810 cases, 512 controls) and the Mayo Clinic (852 cases, 789 controls) in an attempt to replicate previously reported genetic risk factors for glioma. Sixty SNPs selected from the literature (eight from GWAS and 52 from candidate-gene studies) were successfully genotyped on an Illumina custom genotyping panel. Eight SNPs in/near seven different genes (TERT, EGFR, CCDC26, CDKN2A, PHLDB1, RTEL1, TP53) were significantly associated with glioma risk in the combined dataset (P < 0.05), with all associations in the same direction as in previous reports. Several SNP associations showed considerable differences across histologic subtype. All eight successfully replicated associations were first identified by GWAS, although none of the putative risk SNPs from candidate-gene studies was associated in the full case-control sample (all P values > 0.05). Although several confirmed associations are located near genes long known to be involved in gliomagenesis (e.g., EGFR, CDKN2A, TP53), these associations were first discovered by the GWAS approach and are in noncoding regions. These results highlight that the deficiencies of the candidate-gene approach lay in selecting both appropriate genes and relevant SNPs within these genes.
Authors:
Kyle M Walsh; Erik Anderson; Helen M Hansen; Paul A Decker; Matt L Kosel; Thomas Kollmeyer; Terri Rice; Shichun Zheng; Yuanyuan Xiao; Jeffrey S Chang; Lucie S McCoy; Paige M Bracci; Joe L Wiemels; Alexander R Pico; Ivan Smirnov; Daniel H Lachance; Hugues Sicotte; Jeanette E Eckel-Passow; John K Wiencke; Robert B Jenkins; Margaret R Wrensch
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Publication Detail:
Type:  Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, P.H.S.     Date:  2012-12-31
Journal Detail:
Title:  Genetic epidemiology     Volume:  37     ISSN:  1098-2272     ISO Abbreviation:  Genet. Epidemiol.     Publication Date:  2013 Feb 
Date Detail:
Created Date:  2013-01-11     Completed Date:  2013-09-16     Revised Date:  2014-02-03    
Medline Journal Info:
Nlm Unique ID:  8411723     Medline TA:  Genet Epidemiol     Country:  United States    
Other Details:
Languages:  eng     Pagination:  222-8     Citation Subset:  IM    
Copyright Information:
© 2012 WILEY PERIODICALS, INC.
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MeSH Terms
Descriptor/Qualifier:
Aged
California
Case-Control Studies
Central Nervous System Neoplasms / genetics*
DNA Helicases / genetics
European Continental Ancestry Group / genetics
Female
Genes, p16
Genes, p53
Genetic Predisposition to Disease*
Genome-Wide Association Study*
Glioma / genetics*
Humans
Intracellular Signaling Peptides and Proteins / genetics
Male
Middle Aged
Nerve Tissue Proteins / genetics
Polymorphism, Single Nucleotide*
Receptor, Epidermal Growth Factor / genetics
Telomerase / genetics
Grant Support
ID/Acronym/Agency:
1U58 DP000807-01/DP/NCCDPHP CDC HHS; P30 CA15083/CA/NCI NIH HHS; P50 CA108961/CA/NCI NIH HHS; P50CA097257/CA/NCI NIH HHS; P50CA108961/CA/NCI NIH HHS; R01 CA052689/CA/NCI NIH HHS; R01CA52689/CA/NCI NIH HHS; R25 CA112355/CA/NCI NIH HHS; R25CA112355/CA/NCI NIH HHS; RC1NS068222Z/NS/NINDS NIH HHS
Chemical
Reg. No./Substance:
0/CCDC26 protein, human; 0/Intracellular Signaling Peptides and Proteins; 0/Nerve Tissue Proteins; 0/PHLDB1 protein, human; EC 2.7.10.1/EGFR protein, human; EC 2.7.10.1/Receptor, Epidermal Growth Factor; EC 2.7.7.49/TERT protein, human; EC 2.7.7.49/Telomerase; EC 3.6.1.-/RTEL1 protein, human; EC 3.6.4.-/DNA Helicases
Comments/Corrections

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