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Candidate gene analysis using imputed genotypes: cell cycle single-nucleotide polymorphisms and ovarian cancer risk.

Publication ,  Journal Article
Goode, EL; Fridley, BL; Vierkant, RA; Cunningham, JM; Phelan, CM; Anderson, S; Rider, DN; White, KL; Pankratz, VS; Song, H; Hogdall, E ...
Published in: Cancer Epidemiol Biomarkers Prev
March 2009

Polymorphisms in genes critical to cell cycle control are outstanding candidates for association with ovarian cancer risk; numerous genes have been interrogated by multiple research groups using differing tagging single-nucleotide polymorphism (SNP) sets. To maximize information gleaned from existing genotype data, we conducted a combined analysis of five independent studies of invasive epithelial ovarian cancer. Up to 2,120 cases and 3,382 controls were genotyped in the course of two collaborations at a variety of SNPs in 11 cell cycle genes (CDKN2C, CDKN1A, CCND3, CCND1, CCND2, CDKN1B, CDK2, CDK4, RB1, CDKN2D, and CCNE1) and one gene region (CDKN2A-CDKN2B). Because of the semi-overlapping nature of the 123 assayed tagging SNPs, we performed multiple imputation based on fastPHASE using data from White non-Hispanic study participants and participants in the international HapMap Consortium and National Institute of Environmental Health Sciences SNPs Program. Logistic regression assuming a log-additive model was done on combined and imputed data. We observed strengthened signals in imputation-based analyses at several SNPs, particularly CDKN2A-CDKN2B rs3731239; CCND1 rs602652, rs3212879, rs649392, and rs3212891; CDK2 rs2069391, rs2069414, and rs17528736; and CCNE1 rs3218036. These results exemplify the utility of imputation in candidate gene studies and lend evidence to a role of cell cycle genes in ovarian cancer etiology, suggest a reduced set of SNPs to target in additional cases and controls.

Duke Scholars

Published In

Cancer Epidemiol Biomarkers Prev

DOI

ISSN

1055-9965

Publication Date

March 2009

Volume

18

Issue

3

Start / End Page

935 / 944

Location

United States

Related Subject Headings

  • Risk
  • Registries
  • Polymorphism, Single Nucleotide
  • Ovarian Neoplasms
  • Oncogene Proteins
  • North Carolina
  • Neoplasm Invasiveness
  • Minnesota
  • Middle Aged
  • Markov Chains
 

Citation

APA
Chicago
ICMJE
MLA
NLM
Goode, E. L., Fridley, B. L., Vierkant, R. A., Cunningham, J. M., Phelan, C. M., Anderson, S., … Sellers, T. A. (2009). Candidate gene analysis using imputed genotypes: cell cycle single-nucleotide polymorphisms and ovarian cancer risk. Cancer Epidemiol Biomarkers Prev, 18(3), 935–944. https://doi.org/10.1158/1055-9965.EPI-08-0860
Goode, Ellen L., Brooke L. Fridley, Robert A. Vierkant, Julie M. Cunningham, Catherine M. Phelan, Stephanie Anderson, David N. Rider, et al. “Candidate gene analysis using imputed genotypes: cell cycle single-nucleotide polymorphisms and ovarian cancer risk.Cancer Epidemiol Biomarkers Prev 18, no. 3 (March 2009): 935–44. https://doi.org/10.1158/1055-9965.EPI-08-0860.
Goode EL, Fridley BL, Vierkant RA, Cunningham JM, Phelan CM, Anderson S, et al. Candidate gene analysis using imputed genotypes: cell cycle single-nucleotide polymorphisms and ovarian cancer risk. Cancer Epidemiol Biomarkers Prev. 2009 Mar;18(3):935–44.
Goode, Ellen L., et al. “Candidate gene analysis using imputed genotypes: cell cycle single-nucleotide polymorphisms and ovarian cancer risk.Cancer Epidemiol Biomarkers Prev, vol. 18, no. 3, Mar. 2009, pp. 935–44. Pubmed, doi:10.1158/1055-9965.EPI-08-0860.
Goode EL, Fridley BL, Vierkant RA, Cunningham JM, Phelan CM, Anderson S, Rider DN, White KL, Pankratz VS, Song H, Hogdall E, Kjaer SK, Whittemore AS, DiCioccio R, Ramus SJ, Gayther SA, Schildkraut JM, Pharaoh PPD, Sellers TA. Candidate gene analysis using imputed genotypes: cell cycle single-nucleotide polymorphisms and ovarian cancer risk. Cancer Epidemiol Biomarkers Prev. 2009 Mar;18(3):935–944.

Published In

Cancer Epidemiol Biomarkers Prev

DOI

ISSN

1055-9965

Publication Date

March 2009

Volume

18

Issue

3

Start / End Page

935 / 944

Location

United States

Related Subject Headings

  • Risk
  • Registries
  • Polymorphism, Single Nucleotide
  • Ovarian Neoplasms
  • Oncogene Proteins
  • North Carolina
  • Neoplasm Invasiveness
  • Minnesota
  • Middle Aged
  • Markov Chains