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Published on: January 12, 2020
Candidate gene analysis using imputed genotypes: cell cycle single-nucleotide polymorphisms and ovarian cancer risk
Ellen L Goode1, Brooke L Fridley, Robert A Vierkant
1Department of Health Sciences Research, Mayo Clinic College of Medicine, 200 First Street Southwest, Rochester, MN 55905, USA. egoode@mayo.edu
Genetic variations in cell cycle genes are linked to ovarian cancer risk. This study combined data from five ovarian cancer studies, using imputation to analyze single nucleotide polymorphisms (SNPs) and identify key genes associated with cancer development.
Area of Science:
- Genetics
- Oncology
- Molecular Biology
Background:
- Polymorphisms in cell cycle control genes are potential risk factors for ovarian cancer.
- Previous studies used varying sets of single nucleotide polymorphisms (SNPs), limiting comprehensive analysis.
Purpose of the Study:
- To conduct a combined analysis of five independent ovarian cancer studies.
- To maximize information from existing genotype data by using imputation for SNP analysis.
Main Methods:
- Combined genotype data from up to 2,120 cases and 3,382 controls across five studies.
- Assayed 123 tagging SNPs in 11 cell cycle genes and one gene region (CDKN2A-CDKN2B).
- Performed multiple imputation using fastPHASE with HapMap and NIEHS SNPs data, followed by logistic regression.
Main Results:
- Strengthened association signals were observed after imputation, particularly for SNPs in CDKN2A-CDKN2B, CCND1, CDK2, and CCNE1.
- Identified specific SNPs (e.g., CDKN2A-CDKN2B rs3731239, CCND1 rs602652) with notable associations.
Conclusions:
- Imputation is a valuable tool for enhancing candidate gene studies.
- Provides evidence supporting the role of cell cycle genes in ovarian cancer etiology.
- Suggests a refined set of SNPs for future ovarian cancer genetic association studies.
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