White KL, Rider DN, Kalli KR, Knutson KL, Jarvik GP, Goode EL. Genomics of the NF-κB signaling pathway: hypothesized role in ovarian cancer.
Cancer Causes Control 2011;
22:785-801. [PMID:
21359843 DOI:
10.1007/s10552-011-9745-4]
[Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2010] [Accepted: 02/09/2011] [Indexed: 12/17/2022]
Abstract
OBJECTIVE
We sought to review evidence linking nuclear factor-kappa B (NF-κB) to ovarian cancer and to identify genetic variants involved in NF-κB signaling.
METHODS
PubMed was reviewed to inform on ovarian cancer biology and NF-κB signaling and to identify key genes. Public linkage disequilibrium (LD) data were analyzed to identify informative inherited variants (tagSNPs) using ldSelect.
RESULTS
We identified 319 key NF-κB genes including five NF-κB subunits, 167 activating genes, and 55 inhibiting genes. We found that the 1000 Genomes Project was the most informative LD source for most genes (92.8%), and we identified 13,027 LD bins (r (2) ≥ 0.9, minor allele frequency ≥ 0.05) and 1,018 putative-functional variants worthy of investigation. We also report that reliance on a commonly used genome-wide SNP array and genotype imputation with HapMap Phase II data provides data on only 74% of the common inherited NF-κB SNPs of interest.
CONCLUSIONS
Compelling evidence suggests that NF-κB plays a critical role in ovarian cancer, yet inherited variation in these genes has not been thoroughly assessed in relation to disease risk or outcome. We present a collection of variants in key genes and suggest creation of a custom genotyping array as an optimal approach.
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