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Genetic variants improve breast cancer risk prediction on mammograms.

ABSTRACT: Several recent genome-wide association studies have identified genetic variants associated with breast cancer. However, how much these genetic variants may help advance breast cancer risk prediction based on other clinical features, like mammographic findings, is unknown. We conducted a retrospective case-control study, collecting mammographic findings and high-frequency/low-penetrance genetic variants from an existing personalized medicine data repository. A Bayesian network was developed using Tree Augmented Naive Bayes (TAN) by training on the mammographic findings, with and without the 22 genetic variants collected. We analyzed the predictive performance using the area under the ROC curve, and found that the genetic variants significantly improved breast cancer risk prediction on mammograms. We also identified the interaction effect between the genetic variants and collected mammographic findings in an attempt to link genotype to mammographic phenotype to better understand disease patterns, mechanisms, and/or natural history.

SUBMITTER: Liu J

PROVIDER: S-EPMC3900221 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature

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Genetic variants improve breast cancer risk prediction on mammograms.

Liu Jie J Page David D Nassif Houssam H Shavlik Jude J Peissig Peggy P McCarty Catherine C Onitilo Adedayo A AA Burnside Elizabeth E

AMIA ... Annual Symposium proceedings. AMIA Symposium 20131116

Several recent genome-wide association studies have identified genetic variants associated with breast cancer. However, how much these genetic variants may help advance breast cancer risk prediction based on other clinical features, like mammographic findings, is unknown. We conducted a retrospective case-control study, collecting mammographic findings and high-frequency/low-penetrance genetic variants from an existing personalized medicine data repository. A Bayesian network was developed using ...[more]

PMID: 24551380

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Project description:IntroductionBreast cancer in situ (BCIS) diagnoses, a precursor lesion for invasive breast cancer, comprise about 20 % of all breast cancers (BC) in countries with screening programs. Family history of BC is considered one of the strongest risk factors for BCIS.MethodsTo evaluate the association of BC susceptibility loci with BCIS risk, we genotyped 39 single nucleotide polymorphisms (SNPs), associated with risk of invasive BC, in 1317 BCIS cases, 10,645 invasive BC cases, and 14,006 healthy controls in the National Cancer Institute's Breast and Prostate Cancer Cohort Consortium (BPC3). Using unconditional logistic regression models adjusted for age and study, we estimated the association of SNPs with BCIS using two different comparison groups: healthy controls and invasive BC subjects to investigate whether BCIS and BC share a common genetic profile.ResultsWe found that five SNPs (CDKN2BAS-rs1011970, FGFR2-rs3750817, FGFR2-rs2981582, TNRC9-rs3803662, 5p12-rs10941679) were significantly associated with BCIS risk (P value adjusted for multiple comparisons <0.0016). Comparing invasive BC and BCIS, the largest difference was for CDKN2BAS-rs1011970, which showed a positive association with BCIS (OR = 1.24, 95 % CI: 1.11-1.38, P = 1.27 x 10(-4)) and no association with invasive BC (OR = 1.03, 95 % CI: 0.99-1.07, P = 0.06), with a P value for case-case comparison of 0.006. Subgroup analyses investigating associations with ductal carcinoma in situ (DCIS) found similar associations, albeit less significant (OR = 1.25, 95 % CI: 1.09-1.42, P = 1.07 x 10(-3)). Additional risk analyses showed significant associations with invasive disease at the 0.05 level for 28 of the alleles and the OR estimates were consistent with those reported by other studies.ConclusionsOur study adds to the knowledge that several of the known BC susceptibility loci are risk factors for both BCIS and invasive BC, with the possible exception of rs1011970, a putatively functional SNP situated in the CDKN2BAS gene that may be a specific BCIS susceptibility locus.

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Genetic variants improve breast cancer risk prediction on mammograms.

Publications

Genetic variants improve breast cancer risk prediction on mammograms.

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