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. 2016 Nov;25(11):1456-1463.
doi: 10.1158/1055-9965.EPI-16-0373. Epub 2016 Aug 2.

Rare Variation in TET2 Is Associated With Clinically Relevant Prostate Carcinoma in African Americans

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Free PMC article

Rare Variation in TET2 Is Associated With Clinically Relevant Prostate Carcinoma in African Americans

Daniel C Koboldt et al. Cancer Epidemiol Biomarkers Prev. .
Free PMC article

Abstract

Background: Common variants have been associated with prostate cancer risk. Unfortunately, few are reproducibly linked to aggressive disease, the phenotype of greatest clinical relevance. One possible explanation is that rare genetic variants underlie a significant proportion of the risk for aggressive disease.

Method: To identify such variants, we performed a two-stage approach using whole-exome sequencing followed by targeted sequencing of 800 genes in 652 aggressive prostate cancer patients and 752 disease-free controls in both African and European Americans. In each population, we tested rare variants for association using two gene-based aggregation tests. We established a study-wide significance threshold of 3.125 × 10-5 to correct for multiple testing.

Results: TET2 in African Americans was associated with aggressive disease, with 24.4% of cases harboring a rare deleterious variant compared with 9.6% of controls (FET P = 1.84 × 10-5, OR = 3.0; SKAT-O P = 2.74 × 10-5). We report 8 additional genes with suggestive evidence of association, including the DNA repair genes PARP2 and MSH6 Finally, we observed an excess of rare truncation variants in 5 genes, including the DNA repair genes MSH6, BRCA1, and BRCA2 This adds to the growing body of evidence that DNA repair pathway defects may influence susceptibility to aggressive prostate cancer.

Conclusions: Our findings suggest that rare variants influence risk of clinically relevant prostate cancer and, if validated, could serve to identify men for screening, prophylaxis, and treatment.

Impact: This study provides evidence that rare variants in TET2 may help identify African American men at increased risk for clinically relevant prostate cancer. Cancer Epidemiol Biomarkers Prev; 25(11); 1456-63. ©2016 AACR.

Figures

Figure 1
Figure 1
Selection of genes for targeted resequencing. (A) Genes nominated for sequencing by source. (B) Overlap of prostate cancer pathway genes from Acumenta and GeneGo. (C) Overlap of genes from candidate set (known, pathway) and discovery set (rare variant aggregation tests)
Figure 2
Figure 2
Rare variant aggregation test results for 800 genes. Top: Quantile-quantile plots for the African-American (A), European-American (C) and combined (E) sample sets. Bottom: Fraction of samples with at least one rare deleterious variant in each gene in African-American (B), European-American (D) and combined (F) sample sets. Genes with FET p-value <0.01 are marked in red.
Figure 3
Figure 3
Patterns of rare deleterious variants in selected genes. (A) Rare deleterious variants observed in TET2 in African-American cases (top) and controls (bottom). (B) Rare truncating variants observed in BRCA2 in European-American cases (top) and controls (bottom). (C) Rare deleterious variants in PARP2 observed in European-American cases (top) and controls (bottom).

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