Citations 3
PALB2, CHEK2 and ATM rare variants and cancer risk: data from COGS
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Journal of Medical Genetics | September 5, 2016 | Volume: 53 | Issue: 12 | Pages: 800-811
Background The rarity of mutations in PALB2, CHEK2 and ATM make it difficult to estimate precisely associated cancer risks. Population-based family studies have provided evidence that at least some of these mutations are associated with breast cancer risk as high as those associated with rare BRCA2 mutations. We aimed to estimate the relative risks associated with specific rare variants in PALB2, CHEK2 and ATM via a multicentre case-control study. Methods We genotyped 10 rare mutations using the custom iCOGS array: PALB2 c.1592delT, c.2816T>G and c.3113G>A, CHEK2 c.349A>G, c.538C>T, c.715G>A, c.1036C>T, c.1312G>T, and c.1343T>G and ATM c.7271T>G. We assessed associations with breast cancer risk (42 671 cases and 42 164 controls), as well as prostate (22 301 cases and 22 320 controls) and ovarian (14 542 cases and 23 491 controls) cancer risk, for each variant. Results For European women, strong evidence of association with breast cancer risk was observed for PALB2 c.1592delT OR 3.44 (95% CI 1.39 to 8.52, p=7.1×10−5), PALB2 c.3113G>A OR 4.21 (95% CI 1.84 to 9.60, p=6.9×10−8) and ATM c.7271T>G OR 11.0 (95% CI 1.42 to 85.7, p=0.0012). We also found evidence of association with breast cancer risk for three variants in CHEK2, c.349A>G OR 2.26 (95% CI 1.29 to 3.95), c.1036C>T OR 5.06 (95% CI 1.09 to 23.5) and c.538C>T OR 1.33 (95% CI 1.05 to 1.67) (p≤0.017). Evidence for prostate cancer risk was observed for CHEK2 c.1343T>G OR 3.03 (95% CI 1.53 to 6.03, p=0.0006) for African men and CHEK2 c.1312G>T OR 2.21 (95% CI 1.06 to 4.63, p=0.030) for European men. No evidence of association with ovarian cancer was found for any of these variants. Conclusions This report adds to accumulating evidence that at least some variants in these genes are associated with an increased risk of breast cancer that is clinically important.
The SNP rs6500843 in 16p13.3 is associated with survival specifically among chemotherapy-treated breast cancer patients
Fagerholm, Rainer, Khan, Sofia , Tapper, William , Aittomäki, Kristiina, Greco, Dario , Heikkinen, Tuomas , Muranen, Taru , Fasching, Peter A. , Janni, Wolfgang , Weinshilboum, Richard M. , Loehberg, Christian R. , Hopper, John L. , Southey, Melissa C. , Keeman, Renske , Lindblom, Annika , Margolin, Sara , Mannermaa, Arto, Chenevix‐Trench, Georgia , Investigators, kConFab, Lambrechts, Diether , Wildiers, Hans , Chang‐Claude, Jenny , Couch, Fergus J. , Andrulis, Irene L. , Knight, Julia A. , García‐Closas, Montserrat , Figueroa, Jonine D. , Hooning, Maartje J. , Jager, Agnes , Shah, Mitul , Perkins, Barbara, Hamann, Ute, Kabisch, Maria, Easton, Douglas F. , Liu, Jianjun , Eccles, Diana , Blomqvist, Carl , Lambrechts, Diether , Weinshilboum, Richard, Schmidt, Marjanka K. , Rafiq, Sajjad , Weinshilboum, Richard M. , Mannermaa, Arto, Kataja, Vesa , Seibold, Petra , Couch, Fergus J. , Olson, Janet E. , Hooning, Maartje J. , Luben, Robert , Czene, Kamila , Hall, Per N , Pharoah, Paul D.P. , Nevanlinna, Heli , Lambrechts, Diether , Eccles, Diana , Southey, Melissa C , Lambrechts, Diether , Muranen, Taru A , García-Closas, Montserrat , Chenevix-Trench, Georgia , Figueroa, Jonine D , Wildiers, Hans , Lindblom, Annika , Liu, Jing
Oncotarget | September 15, 2015 | Volume: 6 | Issue: 10 | Pages: 7390-7407
Identification of Inherited Genetic Variations Influencing Prognosis in Early-Onset Breast Cancer
Rafiq, Sajjad , Tapper, William , Collins, Andrew , Khan, Sofia , Politopoulos, Ioannis, Gerty, Sue, Blomqvist, Carl , Nevanlinna, Heli , Liu, Jianjun , Eccles, Diana , Couch, Fergus J. , Nevanlinna, H , Eccles, Diana , Liu, Jing
Cancer Research | January 14, 2013 | Volume: 73 | Issue: 6 | Pages: 1883-1891
Abstract Genome-Wide Association Studies (GWAS) have begun to investigate associations between inherited genetic variations and breast cancer prognosis. Here, we report our findings from a GWAS conducted in 536 patients with early-onset breast cancer aged 40 or less at diagnosis and with a mean follow-up period of 4.1 years (SD = 1.96). Patients were selected from the Prospective Study of Outcomes in Sporadic versus Hereditary breast cancer. A Bonferroni correction for multiple testing determined that a P value of 1.0 × 10−7 was a statistically significant association signal. Following quality control, we identified 487,496 single nucleotide polymorphisms (SNP) for association tests in stage 1. In stage 2, 35 SNPs with the most significant associations were genotyped in 1,516 independent cases from the same early-onset cohort. In stage 2, 11 SNPs remained associated in the same direction (P ≤ 0.05). Fixed effects meta-analysis models identified one SNP associated at close to genome wide level of significance 556 kb upstream of the ARRDC3 locus [HR = 1.61; 95% confidence interval (CI), 1.33–1.96; P = 9.5 × 10−7]. Four further associations at or close to the PBX1, RORα, NTN1, and SYT6 loci also came close to genome-wide significance levels (P = 10−6). In the first ever GWAS for the identification of SNPs associated with prognosis in patients with early-onset breast cancer, we report a SNP upstream of the ARRDC3 locus as potentially associated with prognosis (median follow-up time for genotypes: CC = 4 years, CT = 3 years, and TT = 2.7 years; Wilcoxon rank-sum test CC vs. CT, P = 4 × 10−4 and CT vs. TT, P = 0.76). Four further loci may also be associated with prognosis. Cancer Res; 73(6); 1883–91. ©2012 AACR.