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5 results on '"Hammet F"'

1. VTRNA2-1 : Genetic Variation, Heritable Methylation and Disease Association.

Author

Dugué PA, Yu C, McKay T, Wong EM, Joo JE, Tsimiklis H, Hammet F, Mahmoodi M, Theys D, kConFab, Hopper JL, Giles GG, Milne RL, Steen JA, Dowty JG, Nguyen-Dumont T, and Southey MC

Subjects
Aged, Breast Neoplasms genetics, Case-Control Studies, CpG Islands genetics, Female, Genome-Wide Association Study methods, Humans, Male, Middle Aged, Prospective Studies, Quantitative Trait Loci genetics, DNA Methylation genetics, MicroRNAs genetics, Polymorphism, Single Nucleotide genetics
Abstract

VTRNA2-1 is a metastable epiallele with accumulating evidence that methylation at this region is heritable, modifiable and associated with disease including risk and progression of cancer. This study investigated the influence of genetic variation and other factors such as age and adult lifestyle on blood DNA methylation in this region. We first sequenced the VTRNA2-1 gene region in multiple-case breast cancer families in which VTRNA2-1 methylation was identified as heritable and associated with breast cancer risk. Methylation quantitative trait loci (mQTL) were investigated using a prospective cohort study (4500 participants with genotyping and methylation data). The cis -mQTL analysis (334 variants ± 50 kb of the most heritable CpG site) identified 43 variants associated with VTRNA2-1 methylation ( p < 1.5 × 10 -4 ); however, these explained little of the methylation variation (R 2 < 0.5% for each of these variants). No genetic variants elsewhere in the genome were found to strongly influence VTRNA2-1 methylation. SNP-based heritability estimates were consistent with the mQTL findings (h 2 = 0, 95%CI: -0.14 to 0.14). We found no evidence that age, sex, country of birth, smoking, body mass index, alcohol consumption or diet influenced blood DNA methylation at VTRNA2-1 . Genetic factors and adult lifestyle play a minimal role in explaining methylation variability at the heritable VTRNA2-1 cluster.

Published
2021
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2. Using SNP genotypes to improve the discrimination of a simple breast cancer risk prediction model.

Author

Dite GS, Mahmoodi M, Bickerstaffe A, Hammet F, Macinnis RJ, Tsimiklis H, Dowty JG, Apicella C, Phillips KA, Giles GG, Southey MC, and Hopper JL

Subjects
Adult, Area Under Curve, Australia epidemiology, Breast Neoplasms epidemiology, Breast Neoplasms metabolism, Case-Control Studies, Confidence Intervals, Female, Genetic Predisposition to Disease, Humans, Middle Aged, Receptors, Estrogen metabolism, Receptors, Progesterone metabolism, Risk Assessment, Breast Neoplasms genetics, Models, Genetic, Polymorphism, Single Nucleotide
Abstract

It has been shown that, for women aged 50 years or older, the discriminatory accuracy of the Breast Cancer Risk Prediction Tool (BCRAT) can be modestly improved by the inclusion of information on common single nucleotide polymorphisms (SNPs) that are associated with increased breast cancer risk. We aimed to determine whether a similar improvement is seen for earlier onset disease. We used the Australian Breast Cancer Family Registry to study a population-based sample of 962 cases aged 35-59 years, and 463 controls frequency matched for age and for whom genotyping data was available. Overall, the inclusion of data on seven SNPs improved the area under the receiver operating characteristic curve (AUC) from 0.58 (95 % confidence interval [CI] 0.55-0.61) for BCRAT alone to 0.61 (95 % CI 0.58-0.64) for BCRAT and SNP data combined (p < 0.001). For women aged 35-39 years at interview, the corresponding improvement in AUC was from 0.61 (95 % CI 0.56-0.66) to 0.65 (95 % CI 0.60-0.70; p = 0.03), while for women aged 40-49 years at diagnosis, the AUC improved from 0.61 (95 % CI 0.55-0.66) to 0.63 (95 % CI 0.57-0.69; p = 0.04). Using previously used classifications of low, intermediate and high risk, 2.1 % of cases and none of the controls aged 35-39 years, and 10.9 % of cases and 4.0 % of controls aged 40-49 years were classified into a higher risk group. Including information on seven SNPs associated with breast cancer risk, improves the discriminatory accuracy of BCRAT for women aged 35-39 years and 40-49 years. Given, the low absolute risk for women in these age groups, only a small proportion are reclassified into a higher category for predicted 5-year risk of breast cancer.

Published
2013
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3. Genome-wide association studies identify four ER negative-specific breast cancer risk loci.

Author

Garcia-Closas M, Couch FJ, Lindstrom S, Michailidou K, Schmidt MK, Brook MN, Orr N, Rhie SK, Riboli E, Feigelson HS, Le Marchand L, Buring JE, Eccles D, Miron P, Fasching PA, Brauch H, Chang-Claude J, Carpenter J, Godwin AK, Nevanlinna H, Giles GG, Cox A, Hopper JL, Bolla MK, Wang Q, Dennis J, Dicks E, Howat WJ, Schoof N, Bojesen SE, Lambrechts D, Broeks A, Andrulis IL, Guénel P, Burwinkel B, Sawyer EJ, Hollestelle A, Fletcher O, Winqvist R, Brenner H, Mannermaa A, Hamann U, Meindl A, Lindblom A, Zheng W, Devillee P, Goldberg MS, Lubinski J, Kristensen V, Swerdlow A, Anton-Culver H, Dörk T, Muir K, Matsuo K, Wu AH, Radice P, Teo SH, Shu XO, Blot W, Kang D, Hartman M, Sangrajrang S, Shen CY, Southey MC, Park DJ, Hammet F, Stone J, Veer LJ, Rutgers EJ, Lophatananon A, Stewart-Brown S, Siriwanarangsan P, Peto J, Schrauder MG, Ekici AB, Beckmann MW, Dos Santos Silva I, Johnson N, Warren H, Tomlinson I, Kerin MJ, Miller N, Marme F, Schneeweiss A, Sohn C, Truong T, Laurent-Puig P, Kerbrat P, Nordestgaard BG, Nielsen SF, Flyger H, Milne RL, Perez JI, Menéndez P, Müller H, Arndt V, Stegmaier C, Lichtner P, Lochmann M, Justenhoven C, Ko YD, Muranen TA, Aittomäki K, Blomqvist C, Greco D, Heikkinen T, Ito H, Iwata H, Yatabe Y, Antonenkova NN, Margolin S, Kataja V, Kosma VM, Hartikainen JM, Balleine R, Tseng CC, Berg DV, Stram DO, Neven P, Dieudonné AS, Leunen K, Rudolph A, Nickels S, Flesch-Janys D, Peterlongo P, Peissel B, Bernard L, Olson JE, Wang X, Stevens K, Severi G, Baglietto L, McLean C, Coetzee GA, Feng Y, Henderson BE, Schumacher F, Bogdanova NV, Labrèche F, Dumont M, Yip CH, Taib NA, Cheng CY, Shrubsole M, Long J, Pylkäs K, Jukkola-Vuorinen A, Kauppila S, Knight JA, Glendon G, Mulligan AM, Tollenaar RA, Seynaeve CM, Kriege M, Hooning MJ, van den Ouweland AM, van Deurzen CH, Lu W, Gao YT, Cai H, Balasubramanian SP, Cross SS, Reed MW, Signorello L, Cai Q, Shah M, Miao H, Chan CW, Chia KS, Jakubowska A, Jaworska K, Durda K, Hsiung CN, Wu PE, Yu JC, Ashworth A, Jones M, Tessier DC, González-Neira A, Pita G, Alonso MR, Vincent D, Bacot F, Ambrosone CB, Bandera EV, John EM, Chen GK, Hu JJ, Rodriguez-Gil JL, Bernstein L, Press MF, Ziegler RG, Millikan RM, Deming-Halverson SL, Nyante S, Ingles SA, Waisfisz Q, Tsimiklis H, Makalic E, Schmidt D, Bui M, Gibson L, Müller-Myhsok B, Schmutzler RK, Hein R, Dahmen N, Beckmann L, Aaltonen K, Czene K, Irwanto A, Liu J, Turnbull C, Rahman N, Meijers-Heijboer H, Uitterlinden AG, Rivadeneira F, Olswold C, Slager S, Pilarski R, Ademuyiwa F, Konstantopoulou I, Martin NG, Montgomery GW, Slamon DJ, Rauh C, Lux MP, Jud SM, Bruning T, Weaver J, Sharma P, Pathak H, Tapper W, Gerty S, Durcan L, Trichopoulos D, Tumino R, Peeters PH, Kaaks R, Campa D, Canzian F, Weiderpass E, Johansson M, Khaw KT, Travis R, Clavel-Chapelon F, Kolonel LN, Chen C, Beck A, Hankinson SE, Berg CD, Hoover RN, Lissowska J, Figueroa JD, Chasman DI, Gaudet MM, Diver WR, Willett WC, Hunter DJ, Simard J, Benitez J, Dunning AM, Sherman ME, Chenevix-Trench G, Chanock SJ, Hall P, Pharoah PD, Vachon C, Easton DF, Haiman CA, and Kraft P

Subjects
Breast Neoplasms metabolism, Breast Neoplasms pathology, Case-Control Studies, Cooperative Behavior, Female, Genome-Wide Association Study, Genotype, Humans, Meta-Analysis as Topic, Oligonucleotide Array Sequence Analysis, Receptors, Estrogen genetics, Risk Factors, Breast Neoplasms etiology, Genetic Loci genetics, Genetic Predisposition to Disease, Polymorphism, Single Nucleotide genetics, Receptors, Estrogen metabolism
Abstract

Estrogen receptor (ER)-negative tumors represent 20-30% of all breast cancers, with a higher proportion occurring in younger women and women of African ancestry. The etiology and clinical behavior of ER-negative tumors are different from those of tumors expressing ER (ER positive), including differences in genetic predisposition. To identify susceptibility loci specific to ER-negative disease, we combined in a meta-analysis 3 genome-wide association studies of 4,193 ER-negative breast cancer cases and 35,194 controls with a series of 40 follow-up studies (6,514 cases and 41,455 controls), genotyped using a custom Illumina array, iCOGS, developed by the Collaborative Oncological Gene-environment Study (COGS). SNPs at four loci, 1q32.1 (MDM4, P = 2.1 × 10(-12) and LGR6, P = 1.4 × 10(-8)), 2p24.1 (P = 4.6 × 10(-8)) and 16q12.2 (FTO, P = 4.0 × 10(-8)), were associated with ER-negative but not ER-positive breast cancer (P > 0.05). These findings provide further evidence for distinct etiological pathways associated with invasive ER-positive and ER-negative breast cancers.

Published
2013
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4. Associations of common variants at 1p11.2 and 14q24.1 (RAD51L1) with breast cancer risk and heterogeneity by tumor subtype: findings from the Breast Cancer Association Consortium.

Author

Figueroa JD, Garcia-Closas M, Humphreys M, Platte R, Hopper JL, Southey MC, Apicella C, Hammet F, Schmidt MK, Broeks A, Tollenaar RA, Van't Veer LJ, Fasching PA, Beckmann MW, Ekici AB, Strick R, Peto J, dos Santos Silva I, Fletcher O, Johnson N, Sawyer E, Tomlinson I, Kerin M, Burwinkel B, Marme F, Schneeweiss A, Sohn C, Bojesen S, Flyger H, Nordestgaard BG, Benítez J, Milne RL, Ignacio Arias J, Zamora MP, Brenner H, Müller H, Arndt V, Rahman N, Turnbull C, Seal S, Renwick A, Brauch H, Justenhoven C, Brüning T, Chang-Claude J, Hein R, Wang-Gohrke S, Dörk T, Schürmann P, Bremer M, Hillemanns P, Nevanlinna H, Heikkinen T, Aittomäki K, Blomqvist C, Bogdanova N, Antonenkova N, Rogov YI, Karstens JH, Bermisheva M, Prokofieva D, Gantcev SH, Khusnutdinova E, Lindblom A, Margolin S, Chenevix-Trench G, Beesley J, Chen X, Mannermaa A, Kosma VM, Soini Y, Kataja V, Lambrechts D, Yesilyurt BT, Chrisiaens MR, Peeters S, Radice P, Peterlongo P, Manoukian S, Barile M, Couch F, Lee AM, Diasio R, Wang X, Giles GG, Severi G, Baglietto L, Maclean C, Offit K, Robson M, Joseph V, Gaudet M, John EM, Winqvist R, Pylkäs K, Jukkola-Vuorinen A, Grip M, Andrulis I, Knight JA, Mulligan AM, O'Malley FP, Brinton LA, Sherman ME, Lissowska J, Chanock SJ, Hooning M, Martens JW, van den Ouweland AM, Collée JM, Hall P, Czene K, Cox A, Brock IW, Reed MW, Cross SS, Pharoah P, Dunning AM, Kang D, Yoo KY, Noh DY, Ahn SH, Jakubowska A, Lubinski J, Jaworska K, Durda K, Sangrajrang S, Gaborieau V, Brennan P, McKay J, Shen CY, Ding SL, Hsu HM, Yu JC, Anton-Culver H, Ziogas A, Ashworth A, Swerdlow A, Jones M, Orr N, Trentham-Dietz A, Egan K, Newcomb P, Titus-Ernstoff L, Easton D, and Spurdle AB

Subjects
Alleles, Case-Control Studies, Confidence Intervals, Female, Genetic Heterogeneity, Genetic Predisposition to Disease, Humans, Odds Ratio, Receptor, ErbB-2 metabolism, Receptors, Estrogen metabolism, Receptors, Progesterone metabolism, Risk Factors, Breast Neoplasms classification, Breast Neoplasms genetics, Chromosomes, Human, Pair 1 genetics, Chromosomes, Human, Pair 14 genetics, DNA-Binding Proteins genetics, Genome-Wide Association Study, Polymorphism, Single Nucleotide genetics
Abstract

A genome-wide association study (GWAS) identified single-nucleotide polymorphisms (SNPs) at 1p11.2 and 14q24.1 (RAD51L1) as breast cancer susceptibility loci. The initial GWAS suggested stronger effects for both loci for estrogen receptor (ER)-positive tumors. Using data from the Breast Cancer Association Consortium (BCAC), we sought to determine whether risks differ by ER, progesterone receptor (PR), human epidermal growth factor receptor 2 (HER2), grade, node status, tumor size, and ductal or lobular morphology. We genotyped rs11249433 at 1p.11.2, and two highly correlated SNPs rs999737 and rs10483813 (r(2)= 0.98) at 14q24.1 (RAD51L1), for up to 46 036 invasive breast cancer cases and 46 930 controls from 39 studies. Analyses by tumor characteristics focused on subjects reporting to be white women of European ancestry and were based on 25 458 cases, of which 87% had ER data. The SNP at 1p11.2 showed significantly stronger associations with ER-positive tumors [per-allele odds ratio (OR) for ER-positive tumors was 1.13, 95% CI = 1.10-1.16 and, for ER-negative tumors, OR was 1.03, 95% CI = 0.98-1.07, case-only P-heterogeneity = 7.6 × 10(-5)]. The association with ER-positive tumors was stronger for tumors of lower grade (case-only P= 6.7 × 10(-3)) and lobular histology (case-only P= 0.01). SNPs at 14q24.1 were associated with risk for most tumor subtypes evaluated, including triple-negative breast cancers, which has not been described previously. Our results underscore the need for large pooling efforts with tumor pathology data to help refine risk estimates for SNP associations with susceptibility to different subtypes of breast cancer.

Published
2011
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5. Breast cancer risk and 6q22.33: Combined results from breast cancer association consortium and consortium of investigators on modifiers of brca1/2

Author

Kirchhoff, T., Gaudet, M.M., Antoniou, A.C., McGuffog, L., Humphreys, M.K., Dunning, A.M., Bojesen, S.E., Nordestgaard, B.G., Flyger, H., Kang, D., Yoo, K.Y., Noh, D.Y., Ahn, S.H., Dork, T., Schurmann, P., Karstens, J.H., Hillemanns, P., Couch, F.J., Olson, J., Vachon, C., Wang, X.S., Cox, A., Brock, I., Elliott, G., Reed, M.W.R., Burwinkel, B., Meindl, A., Brauch, H., Hamann, U., Ko, Y.D., Broeks, A., Schmidt, M.K., Veer, L.J. van 't, Braaf, L.M., Johnson, N., Fletcher, O., Gibson, L., Peto, J., Turnbull, C., Seal, S., Renwick, A., Rahman, N., Wu, P.E., Yu, J.C., Hsiung, C.N., Shen, C.Y., Southey, M.C., Hopper, J.L., Hammet, F., Dorpe, T. van, Dieudonne, A.S., Hatse, S., Lambrechts, D., Andrulis, I.L., Bogdanova, N., Antonenkova, N., Rogov, J.I., Prokofieva, D., Bermisheva, M., Khusnutdinova, E., Asperen, C.J. van, Tollenaar, R.A.E.M., Hooning, M.J., Devilee, P., Margolin, S., Lindblom, A., Milne, R.L., Arias, J.I., Zamora, M.P., Benitez, J., Severi, G., Baglietto, L., Giles, G.G., Spurdle, A.B., Beesley, J., Chen, X.Q., Holland, H., Healey, S., Wang-Gohrke, S., Chang-Claude, J., Mannermaa, A., Kosma, V.M., Kauppinen, J., Kataja, V., Agnarsson, B.A., Caligo, M.A., Godwin, A.K., Nevanlinna, H., Heikkinen, T., Fredericksen, Z., Lindor, N., Nathanson, K.L., Domchek, S.M., Loman, N., Karlsson, P., Askmalm, M.S., Melin, B., Wachenfeldt, A. von, Hogervorst, F.B.L., Verheus, M., Rookus, M.A., Seynaeve, C., Oldenburg, R.A., Ligtenberg, M.J., Ausems, M.G.E.M., Aalfs, C.M., Gille, H.J.P., Wijnen, J.T., Garcia, E.B.G., Peock, S., Cook, M., Oliver, C.T., Frost, D., Luccarini, C., Pichert, G., Davidson, R., Chu, C., Eccles, D., Ong, K.R., Cook, J., Douglas, F., Hodgson, S., Evans, D.G., Eeles, R., Gold, B., Pharoah, P.D.P., Offit, K., Chenevix-Trench, G., Easton, D.F., GENICA Network, kConFab, AOCS Study Grp, SWE-BRCA, HEBON, EMBRACE, BCAC-CIMBA, Medical Oncology, Clinical Genetics, Genetica & Celbiologie, RS: GROW - School for Oncology and Reproduction, Human genetics, CCA - Oncogenesis, Department of Obstetrics and Gynecology, Women's Health Research Program, Human Genetics, Cancer Center Amsterdam, and Amsterdam Reproduction & Development (AR&D)

Subjects
Oncology, Genetics and Molecular Biology (all), Medicin och hälsovetenskap, Alleles, BRCA1 Protein, BRCA2 Protein, Breast Neoplasms, Chromosomes, Human, Pair 6, Confidence Intervals, Female, Genetic Association Studies, Heterozygote, Humans, Middle Aged, Odds Ratio, Polymorphism, Single Nucleotide, Proportional Hazards Models, Receptors, Estrogen, Risk Factors, Genetic Predisposition to Disease, Medicine (all), Biochemistry, Genetics and Molecular Biology (all), Agricultural and Biological Sciences (all), Epidemiology, Genome-wide association study, VARIANTS, Bioinformatics, Medical and Health Sciences, Biochemistry, 0302 clinical medicine, Breast Tumors, Genotype, Receptors, skin and connective tissue diseases, GeneralLiterature_REFERENCE(e.g.,dictionaries,encyclopedias,glossaries), 0303 health sciences, education.field_of_study, variants, Multidisciplinary, Cancer Risk Factors, Obstetrics and Gynecology, Single Nucleotide, 3. Good health, Genetic Epidemiology, 030220 oncology & carcinogenesis, alleles, Medicine, Pair 6, Cancer Epidemiology, Research Article, Human, medicine.medical_specialty, SUSCEPTIBILITY LOCI, Science, Genetic Causes of Cancer, Population, Hereditary cancer and cancer-related syndromes Genetics and epigenetic pathways of disease [ONCOL 1], education, Single-nucleotide polymorphism, Chromosomes, 03 medical and health sciences, Breast cancer, SDG 3 - Good Health and Well-being, Translational research [ONCOL 3], Internal medicine, Breast Cancer, Genetics, Cancer Genetics, Genome-Wide Association Studies, medicine, GENOME-WIDE ASSOCIATION, Polymorphism, Genetics and epigenetic pathways of disease Translational research [NCMLS 6], gene, Biology, 030304 developmental biology, Cancer och onkologi, Population Biology, Hereditary cancer and cancer-related syndromes [ONCOL 1], Proportional hazards model, business.industry, Cancers and Neoplasms, Odds ratio, medicine.disease, GENE, Estrogen, susceptibility loci, Minor allele frequency, Cancer and Oncology, FGFR2, genome-wide association, 3111 Biomedicine, business
Abstract

Recently, a locus on chromosome 6q22.33 (rs2180341) was reported to be associated with increased breast cancer risk in the Ashkenazi Jewish (AJ) population, and this association was also observed in populations of non-AJ European ancestry. In the present study, we performed a large replication analysis of rs2180341 using data from 31,428 invasive breast cancer cases and 34,700 controls collected from 25 studies in the Breast Cancer Association Consortium (BCAC). In addition, we evaluated whether rs2180341 modifies breast cancer risk in 3,361 BRCA1 and 2,020 BRCA2 carriers from 11 centers in the Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA). Based on the BCAC data from women of European ancestry, we found evidence for a weak association with breast cancer risk for rs2180341 (per-allele odds ratio (OR) = 1.03, 95% CI 1.00-1.06, p = 0.023). There was evidence for heterogeneity in the ORs among studies (I-2 = 49.3%; p = less than0.004). In CIMBA, we observed an inverse association with the minor allele of rs2180341 and breast cancer risk in BRCA1 mutation carriers (per-allele OR = 0.89, 95% CI 0.80-1.00, p = 0.048), indicating a potential protective effect of this allele. These data suggest that that 6q22.33 confers a weak effect on breast cancer risk.

Published
2012
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