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Analysis of 60 reported glioma risk SNPs replicates published GWAS findings but fails to replicate associations from published candidate-gene studies.

Publication ,  Journal Article
Walsh, KM; Anderson, E; Hansen, HM; Decker, PA; Kosel, ML; Kollmeyer, T; Rice, T; Zheng, S; Xiao, Y; Chang, JS; McCoy, LS; Bracci, PM ...
Published in: Genet Epidemiol
February 2013

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.

Duke Scholars

Published In

Genet Epidemiol

DOI

EISSN

1098-2272

Publication Date

February 2013

Volume

37

Issue

2

Start / End Page

222 / 228

Location

United States

Related Subject Headings

  • White People
  • Telomerase
  • RNA, Long Noncoding
  • Polymorphism, Single Nucleotide
  • Nerve Tissue Proteins
  • Middle Aged
  • Male
  • Intracellular Signaling Peptides and Proteins
  • Humans
  • Glioma
 

Citation

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Walsh, K. M., Anderson, E., Hansen, H. M., Decker, P. A., Kosel, M. L., Kollmeyer, T., … Wrensch, M. R. (2013). Analysis of 60 reported glioma risk SNPs replicates published GWAS findings but fails to replicate associations from published candidate-gene studies. Genet Epidemiol, 37(2), 222–228. https://doi.org/10.1002/gepi.21707
Walsh, Kyle M., Erik Anderson, Helen M. Hansen, Paul A. Decker, Matt L. Kosel, Thomas Kollmeyer, Terri Rice, et al. “Analysis of 60 reported glioma risk SNPs replicates published GWAS findings but fails to replicate associations from published candidate-gene studies.Genet Epidemiol 37, no. 2 (February 2013): 222–28. https://doi.org/10.1002/gepi.21707.
Walsh KM, Anderson E, Hansen HM, Decker PA, Kosel ML, Kollmeyer T, et al. Analysis of 60 reported glioma risk SNPs replicates published GWAS findings but fails to replicate associations from published candidate-gene studies. Genet Epidemiol. 2013 Feb;37(2):222–8.
Walsh, Kyle M., et al. “Analysis of 60 reported glioma risk SNPs replicates published GWAS findings but fails to replicate associations from published candidate-gene studies.Genet Epidemiol, vol. 37, no. 2, Feb. 2013, pp. 222–28. Pubmed, doi:10.1002/gepi.21707.
Walsh KM, Anderson E, Hansen HM, Decker PA, Kosel ML, Kollmeyer T, Rice T, Zheng S, Xiao Y, Chang JS, McCoy LS, Bracci PM, Wiemels JL, Pico AR, Smirnov I, Lachance DH, Sicotte H, Eckel-Passow JE, Wiencke JK, Jenkins RB, Wrensch MR. Analysis of 60 reported glioma risk SNPs replicates published GWAS findings but fails to replicate associations from published candidate-gene studies. Genet Epidemiol. 2013 Feb;37(2):222–228.
Journal cover image

Published In

Genet Epidemiol

DOI

EISSN

1098-2272

Publication Date

February 2013

Volume

37

Issue

2

Start / End Page

222 / 228

Location

United States

Related Subject Headings

  • White People
  • Telomerase
  • RNA, Long Noncoding
  • Polymorphism, Single Nucleotide
  • Nerve Tissue Proteins
  • Middle Aged
  • Male
  • Intracellular Signaling Peptides and Proteins
  • Humans
  • Glioma