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Jia G, Ping J, Guo X, Yang Y, Tao R, Li B, Ambs S, Barnard ME, Chen Y, Garcia-Closas M, Gu J, Hu JJ, Huo D, John EM, Li CI, Li JL, Nathanson KL, Nemesure B, Olopade OI, Pal T, Press MF, Sanderson M, Sandler DP, Shu XO, Troester MA, Yao S, Adejumo PO, Ahearn T, Brewster AM, Hennis AJM, Makumbi T, Ndom P, O'Brien KM, Olshan AF, Oluwasanu MM, Reid S, Butler EN, Huang M, Ntekim A, Qian H, Zhang H, Ambrosone CB, Cai Q, Long J, Palmer JR, Haiman CA, Zheng W. Genome-wide association analyses of breast cancer in women of African ancestry identify new susceptibility loci and improve risk prediction. Nat Genet 2024; 56:819-826. [PMID: 38741014 DOI: 10.1038/s41588-024-01736-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 03/25/2024] [Indexed: 05/16/2024]
Abstract
We performed genome-wide association studies of breast cancer including 18,034 cases and 22,104 controls of African ancestry. Genetic variants at 12 loci were associated with breast cancer risk (P < 5 × 10-8), including associations of a low-frequency missense variant rs61751053 in ARHGEF38 with overall breast cancer (odds ratio (OR) = 1.48) and a common variant rs76664032 at chromosome 2q14.2 with triple-negative breast cancer (TNBC) (OR = 1.30). Approximately 15.4% of cases with TNBC carried six risk alleles in three genome-wide association study-identified TNBC risk variants, with an OR of 4.21 (95% confidence interval = 2.66-7.03) compared with those carrying fewer than two risk alleles. A polygenic risk score (PRS) showed an area under the receiver operating characteristic curve of 0.60 for the prediction of breast cancer risk, which outperformed PRS derived using data from females of European ancestry. Our study markedly increases the population diversity in genetic studies for breast cancer and demonstrates the utility of PRS for risk prediction in females of African ancestry.
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Affiliation(s)
- Guochong Jia
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jie Ping
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Xingyi Guo
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yaohua Yang
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Center for Public Health Genomics, Department of Public Health Sciences, UVA Comprehensive Cancer Center, School of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Ran Tao
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Bingshan Li
- Department of Molecular Physiology & Biophysics, Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN, USA
| | - Stefan Ambs
- Laboratory of Human Carcinogenesis, Center of Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Yu Chen
- Division of Epidemiology, Department of Population Health, NYU Grossman School of Medicine, New York, NY, USA
| | | | - Jian Gu
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jennifer J Hu
- Department of Public Health Sciences, University of Miami School of Medicine, Miami, FL, USA
| | - Dezheng Huo
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
| | - Esther M John
- Departments of Epidemiology & Population Health and of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Christopher I Li
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - James L Li
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
| | - Katherine L Nathanson
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Basser Center for BRCA, Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Barbara Nemesure
- Department of Family, Population and Preventive Medicine, Renaissance School of Medicine, Stony Brook University, New York, NY, USA
| | - Olufunmilayo I Olopade
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Tuya Pal
- Division of Genetic Medicine, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Michael F Press
- Department of Pathology, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Maureen Sanderson
- Department of Family and Community Medicine, Meharry Medical College, Nashville, TN, USA
| | - Dale P Sandler
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Melissa A Troester
- Department of Epidemiology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Song Yao
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Elm & Carlton Streets, Buffalo, NY, USA
| | - Prisca O Adejumo
- Department of Nursing, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Thomas Ahearn
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Abenaa M Brewster
- Department of Clinical Cancer Prevention, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Anselm J M Hennis
- George Alleyne Chronic Disease Research Centre, University of the West Indies, Bridgetown, Barbados
- Department of Family, Population and Preventive Medicine, Stony Brook University, New York, NY, USA
| | | | - Paul Ndom
- Yaounde General Hospital, Yaounde, Cameroon
| | - Katie M O'Brien
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Andrew F Olshan
- Department of Epidemiology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Mojisola M Oluwasanu
- Department of Health Promotion and Education, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Sonya Reid
- Division of Hematology and Oncology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ebonee N Butler
- Department of Epidemiology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Maosheng Huang
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Atara Ntekim
- Department of Radiation Oncology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Huijun Qian
- Department of Statistics and Operation Research, University of North Carolina, Chapel Hill, NC, USA
| | - Haoyu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Christine B Ambrosone
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Elm & Carlton Streets, Buffalo, NY, USA
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Julie R Palmer
- Slone Epidemiology Center, Boston University, Boston, MA, USA
| | - Christopher A Haiman
- Department of Preventive Medicine, University of Southern California Keck School of Medicine, Los Angeles, CA, USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA.
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Luo J, Kibriya MG, Chen H, Kim K, Ahsan H, Olopade OI, Olopade CS, Aschebrook-Kilfoy B, Huo D. A metabolome-wide case-control study of african american breast cancer patients. BMC Cancer 2023; 23:183. [PMID: 36823587 PMCID: PMC9948520 DOI: 10.1186/s12885-023-10656-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 02/16/2023] [Indexed: 02/25/2023] Open
Abstract
BACKGROUND Breast cancer survivors face long-term sequelae compared to the general population, suggesting altered metabolic profiles after breast cancer. We used metabolomics approaches to investigate the metabolic differences between breast cancer patients and women in the general population, aiming to elaborate metabolic changes among breast cancer patients and identify potential targets for clinical interventions to mitigate long-term sequelae. METHODS Serum samples were retrieved from 125 breast cancer cases recruited from the Chicago Multiethnic Epidemiologic Breast Cancer Cohort (ChiMEC), and 125 healthy controls selected from Chicago Multiethnic Prevention and Surveillance Study (COMPASS). We used liquid chromatography-high resolution mass spectrometry to obtain untargeted metabolic profiles and partial least squares discriminant analysis (PLS-DA) combined with fold change to select metabolic features associated with breast cancer. Pathway analyses were conducted using Mummichog to identify differentially enriched metabolic pathways among cancer patients. As potential confounders we included age, marital status, tobacco smoking, alcohol drinking, type 2 diabetes, and area deprivation index in our model. Random effects of residence for intercept was also included in the model. We further conducted subgroup analysis by treatment timing (chemotherapy/radiotherapy/surgery), lymph node status, and cancer stages. RESULTS The entire study participants were African American. The average ages were 57.1 for cases and 58.0 for controls. We extracted 15,829 features in total, among which 507 features were eventually selected by our criteria. Pathway enrichment analysis of these 507 features identified three differentially enriched metabolic pathways related to prostaglandin, leukotriene, and glycerophospholipid. The three pathways demonstrated inconsistent patterns. Metabolic features in the prostaglandin and leukotriene pathways exhibited increased abundances among cancer patients. In contrast, metabolic intensity in the glycerolphospholipid pathway was deregulated among cancer patients. Subgroup analysis yielded consistent results. However, changes in these pathways were strengthened when only using cases with positive lymph nodes, and attenuated when only using cases with stage I disease. CONCLUSION Breast cancer in African American women is associated with increase in serum metabolites involved in prostaglandin and leukotriene pathways, but with decrease in serum metabolites in glycerolphospholipid pathway. Positive lymph nodes and advanced cancer stage may strengthen changes in these pathways.
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Affiliation(s)
- Jiajun Luo
- Department of Public Health Sciences, University of Chicago Biological Sciences, 5841 S. Maryland Ave. MC2000, 60637, Chicago, IL, USA.,Institute for Population and Precision Health, University of Chicago, Chicago, IL, USA.,Comprehensive Cancer Center, University of Chicago, Chicago, IL, USA
| | - Muhammad G Kibriya
- Department of Public Health Sciences, University of Chicago Biological Sciences, 5841 S. Maryland Ave. MC2000, 60637, Chicago, IL, USA.,Institute for Population and Precision Health, University of Chicago, Chicago, IL, USA
| | - Hui Chen
- Mass Spectrometry Core, University of Illinois at Chicago, Chicago, IL, USA
| | - Karen Kim
- Institute for Population and Precision Health, University of Chicago, Chicago, IL, USA.,Comprehensive Cancer Center, University of Chicago, Chicago, IL, USA.,Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Habibul Ahsan
- Department of Public Health Sciences, University of Chicago Biological Sciences, 5841 S. Maryland Ave. MC2000, 60637, Chicago, IL, USA.,Institute for Population and Precision Health, University of Chicago, Chicago, IL, USA.,Comprehensive Cancer Center, University of Chicago, Chicago, IL, USA
| | | | | | - Briseis Aschebrook-Kilfoy
- Department of Public Health Sciences, University of Chicago Biological Sciences, 5841 S. Maryland Ave. MC2000, 60637, Chicago, IL, USA. .,Institute for Population and Precision Health, University of Chicago, Chicago, IL, USA. .,Comprehensive Cancer Center, University of Chicago, Chicago, IL, USA.
| | - Dezheng Huo
- Department of Public Health Sciences, University of Chicago Biological Sciences, 5841 S. Maryland Ave. MC2000, 60637, Chicago, IL, USA. .,Institute for Population and Precision Health, University of Chicago, Chicago, IL, USA. .,Comprehensive Cancer Center, University of Chicago, Chicago, IL, USA. .,Department of Medicine, University of Chicago, Chicago, IL, USA.
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Ezeome ER, Yawe KDT, Ayandipo O, Badejo O, Adebamowo SN, Achusi B, Fowotade A, Ogun G, Adebamowo CA. The African Female Breast Cancer Epidemiology Study Protocol. Front Oncol 2022; 12:856182. [PMID: 35494056 PMCID: PMC9044037 DOI: 10.3389/fonc.2022.856182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 03/08/2022] [Indexed: 11/21/2022] Open
Abstract
Breast cancer is now the commonest cancer in most sub-Saharan African countries. Few studies of the epidemiology and genomics of breast cancer and its molecular subtypes in these countries have been done. The African Female Breast Cancer Epidemiology (AFBRECANE) study, a part of the Human Heredity and Health in Africa (H3Africa) initiative, is designed to study the genomics and epidemiology of breast cancer and its molecular subtypes in Nigerian women. We link recruitment of breast cancer cases at study sites with population-based cancer registries activities to enable ascertainment of the incidence of breast cancer and its molecular subtypes. We use centralized laboratory processing to characterize the histopathological and molecular diagnosis of breast cancer and its subtypes using multiple technologies. By combining genome-wide association study (GWAS) data from this study with that generated from 12,000 women participating in our prospective cohort study of cervical cancer, we conduct GWAS of breast cancer in an entirely indigenous African population. We test associations between dietary intakes and breast cancer and focus on vitamin D which we measure using dietary intakes, serum vitamin D, and Mendelian randomization. This paper describes the AFBRECANE project, its design, objectives and anticipated contributions to knowledge and understanding of breast cancer.
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Affiliation(s)
- Emmanuel R. Ezeome
- Department of Surgery, College of Medicine, University of Nigeria, Enugu, Nigeria
- Oncology Center, University of Nigeria Teaching Hospital, Enugu, Nigeria
| | - King-David T. Yawe
- Department of Surgery, University of Abuja Teaching Hospital, Abuja, Nigeria
| | | | - Olawale Badejo
- Department of Pathology, National Hospital, Abuja, Nigeria
| | - Sally N. Adebamowo
- Department of Epidemiology and Public Health, and Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Benerdin Achusi
- Department of Anatomic Pathology, Federal Medical Center, Abuja, Nigeria
| | - Adeola Fowotade
- Department of Medical Microbiology, University College Hospital, Ibadan, Nigeria
| | - Gabriel Ogun
- Department of Pathology, University College Hospital, Ibadan, Nigeria
| | | | - Clement A. Adebamowo
- Department of Epidemiology and Public Health, and Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD, United States
- Institute of Human Virology Nigeria, Abuja, Nigeria
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4
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Scannell Bryan M, Ogundiran T, Ojengbede O, Zheng W, Blot W, Domcheck S, Hennis A, Nemesure B, Ambs S, Olopade OI, Huo D. Associations between age of menarche and genetic variation in women of African descent: genome-wide association study and polygenic score analysis. J Epidemiol Community Health 2021; 76:411-417. [PMID: 34706928 DOI: 10.1136/jech-2020-216000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 10/11/2021] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Many diseases of adulthood are associated with a woman's age at menarche. Genetic variation affects age at menarche, but it remains unclear whether in women of African ancestry the timing of menarche is regulated by genetic variants that were identified in predominantly European and East Asian populations. METHODS We explored the genetic architecture of age at menarche in 3145 women of African ancestry who live in the USA, Barbados and Nigeria. We undertook a genome-wide association study, and evaluated the performance of previously identified variants. RESULTS One variant was associated with age at menarche, a deletion at chromosome 2 (chr2:207216165) (p=1.14×10-8). 349 genotyped variants overlapped with these identified in populations of non-African ancestry; these replicated weakly, with 51.9% having concordant directions of effect. However, collectively, a polygenic score constructed of those previous variants was suggestively associated with age at menarche (beta=0.288 years; p=0.041). Further, this association was strong in women enrolled in the USA and Barbados (beta=0.445 years, p=0.008), but not in Nigerian women (beta=0.052 years; p=0.83). DISCUSSION This study suggests that in women of African ancestry the genetic drivers of age at menarche may differ from those identified in populations of non-African ancestry, and that these differences are more pronounced in women living in Nigeria, although some associated trait loci may be shared across populations. This highlights the need for well-powered ancestry-specific genetic studies to fully characterise the genetic influences of age at menarche.
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Affiliation(s)
- Molly Scannell Bryan
- Institute for Minority Health Research, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Temidayo Ogundiran
- Department of Surgery, College of Medicine, University of Ibadan, Ibadan, Nigeria, Ibadan, Nigeria
| | - Oladosu Ojengbede
- Center for Population and Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - William Blot
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Susan Domcheck
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Anselm Hennis
- Chronic Disease Research Centre, Tropical Medicine Research Institute, The University of the West Indies, Bridgetown, Barbados
| | - Barbara Nemesure
- Department of Preventative Medicine, State University of New York at Stony Brook, Stony Brook, New York, USA
| | - Stefan Ambs
- Laboratory of Human Carcinogenesis, National Cancer Institute, Bethesda, Maryland, USA
| | - Olufunmilayo I Olopade
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | - Dezheng Huo
- Department of Public Health Sciences, University of Chicago, Chicago, Illinois, USA
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5
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Blackman E, Ashing K, Gibbs D, Kuo YM, Andrews A, Ramakodi M, Devarajan K, Bucci J, Jean-Louis G, Richards-Waritay O, Wilson B, Bowen C, Edi E, Tolbert V, Noumbissi R, Cabral DN, Oliver J, Roberts R, Tulloch-Reid M, Ragin C. The Cancer Prevention Project of Philadelphia: preliminary findings examining diversity among the African diaspora. ETHNICITY & HEALTH 2021; 26:659-675. [PMID: 30453751 PMCID: PMC6526085 DOI: 10.1080/13557858.2018.1548695] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 10/22/2018] [Indexed: 06/09/2023]
Abstract
Objective: Cancer mortality inequity among persons of African Ancestry is remarkable. Yet, Black inclusion in cancer biology research is sorely lacking and warrants urgent attention. Epidemiologic research linking African Ancestry and the African Diaspora to disease susceptibility and outcomes is critical for understanding the significant and troubling health disparities among Blacks. Therefore, in a cohort of diverse Blacks, this study examined differences in genetic ancestry informative markers (AIMs) in the DNA repair pathway and the cancer related biomarker 4-(Methylnitrosamino)-1-(3-pyridyl)-1-butanol (NNAL).Methods: Participants completed a questionnaire and provided bio-specimens. AIMs in or around DNA repair pathway genes were analyzed to assess differences in minor allele frequency (MAF) across the 3 ethnic subgroups. NNAL concentration in urine was measured among current smokers.Results: To date the cohort includes 852 participants, 88.3% being Black. Of the 752 Blacks, 51.3% were US-born, 27.8% were Caribbean-born, and 19.6% were Africa-born. Current and former smokers represented 14.9% and 10.0%, respectively. US-born Blacks were more likely to be smokers and poor metabolizers of NNAL. Two-way hierarchical clustering revealed MAF of AIMs differed across the 3 ethnic subgroups.Conclusion: Our findings are consistent with the emerging literature demonstrating Black heterogeneity underscoring African Ancestry genetic subgroup differences - specifically relevant to cancer. Further investigations, with data harmonization and sharing, are urgently needed to begin to map African Ancestry cancer biomarkers as well as race, and race by place\region comparative biomarkers to inform cancer prevention and treatment in the era of precision medicine.
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Affiliation(s)
- Elizabeth Blackman
- Cancer Prevention and Control Program, Fox Chase Cancer Center-Temple Health, Philadelphia, USA
- Department of Epidemiology and Biostatistics, College of Public Health, Temple University, Philadelphia, USA
- African-Caribbean Cancer Consortium, Philadelphia, USA
| | - Kimlin Ashing
- Center of Community Alliance for Research & Education, Division of Health Equity, City of Hope Medical Center, Duarte, USA
| | - Denise Gibbs
- Cancer Prevention and Control Program, Fox Chase Cancer Center-Temple Health, Philadelphia, USA
- African-Caribbean Cancer Consortium, Philadelphia, USA
| | - Yin-Ming Kuo
- Cancer Epigenetics Program, Fox Chase Cancer Center-Temple Health, Philadelphia, USA
| | - Andrew Andrews
- Cancer Epigenetics Program, Fox Chase Cancer Center-Temple Health, Philadelphia, USA
| | - Meganathan Ramakodi
- Cancer Prevention and Control Program, Fox Chase Cancer Center-Temple Health, Philadelphia, USA
- African-Caribbean Cancer Consortium, Philadelphia, USA
- Department of Biology, Temple University, Philadelphia, USA
| | - Karthik Devarajan
- Biostatistics and Bioinformatics Facility, Fox Chase Cancer Center, Philadelphia, USA
| | - Jackie Bucci
- Nutrition Program, City University of New York at Hunter College, New York, USA
- Temple University and Hunter College Cancer Health Disparity Research Institute Cancer Research Training Program, Fox Chase Cancer Center, Philadelphia, USA
| | | | | | - Barbara Wilson
- Caribbean Festival & Cultural Organization of Pennsylvania, Philadelphia, USA
| | - Carlene Bowen
- Thomas Jefferson University Hospital, Philadelphia, USA
| | - Eric Edi
- The Coalition of African Communities (AFRICOM), Philadelphia, USA
| | - Vera Tolbert
- The Coalition of African Communities (AFRICOM), Philadelphia, USA
| | | | - Daramola N. Cabral
- African-Caribbean Cancer Consortium, Philadelphia, USA
- Department of Science, Math, and Technology, SUNY Empire State College, Brooklyn, USA
| | - JoAnn Oliver
- African-Caribbean Cancer Consortium, Philadelphia, USA
- Capstone College of Nursing, Tuscaloosa, USA
| | - Robin Roberts
- African-Caribbean Cancer Consortium, Philadelphia, USA
- School of Clinical Medicine & Research, University of the West Indies, Nassau, Bahamas
- Princess Margaret Hospital, Nassau, Bahamas
| | - Marshall Tulloch-Reid
- African-Caribbean Cancer Consortium, Philadelphia, USA
- Caribbean Institute for Health Research, University of the West Indies, Kingston, Jamaica
| | - Camille Ragin
- Cancer Prevention and Control Program, Fox Chase Cancer Center-Temple Health, Philadelphia, USA
- Department of Epidemiology and Biostatistics, College of Public Health, Temple University, Philadelphia, USA
- African-Caribbean Cancer Consortium, Philadelphia, USA
- Nutrition Program, City University of New York at Hunter College, New York, USA
- Department of Otolaryngology-Head and Neck Surgery, Lewis Katz School of Medicine, Temple University School of Medicine, Philadelphia, USA
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Shang L, Hattori M, Fleming G, Jaskowiak N, Hedeker D, Olopade OI, Huo D. Impact of post-diagnosis weight change on survival outcomes in Black and White breast cancer patients. Breast Cancer Res 2021; 23:18. [PMID: 33541403 PMCID: PMC7863526 DOI: 10.1186/s13058-021-01397-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 01/20/2021] [Indexed: 12/19/2022] Open
Abstract
PURPOSE To evaluate weight change patterns over time following the diagnosis of breast cancer and to examine the association of post-diagnosis weight change and survival outcomes in Black and White patients. METHODS The study included 2888 women diagnosed with non-metastatic breast cancer in 2000-2017 in Chicago. Longitudinal repeated measures of weight and height were collected, along with a questionnaire survey including questions on body size. Multilevel mixed-effects models were used to examine changes in body mass index (BMI). Delayed entry Cox proportional hazards models were used to investigate the impacts of changing slope of BMI on survival outcomes. RESULTS At diagnosis, most patients were overweight or obese with a mean BMI of 27.5 kg/m2 and 31.5 kg/m2 for Blacks and Whites, respectively. Notably, about 45% of the patients had cachexia before death and substantial weight loss started about 30 months before death. In multivariable-adjusted analyses, compared to stable weight, BMI loss (> 0.5 kg/m2/year) showed greater than 2-fold increased risk in overall survival (hazard ratio [HR] = 2.60, 95% CI 1.88-3.59), breast cancer-specific survival (HR = 3.05, 95% CI 1.91-4.86), and disease-free survival (HR = 2.12, 95% CI 1.52-2.96). The associations were not modified by race, age at diagnosis, and pre-diagnostic weight. BMI gain (> 0.5 kg/m2/year) was also related to worse survival, but the effect was weak (HR = 1.60, 95% CI 1.10-2.33 for overall survival). CONCLUSION BMI loss is a strong predictor of worse breast cancer outcomes. Growing prevalence of obesity may hide diagnosis of cancer cachexia, which can occur in a large proportion of breast cancer patients long before death.
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Affiliation(s)
- Lihua Shang
- grid.412651.50000 0004 1808 3502Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Masaya Hattori
- grid.410800.d0000 0001 0722 8444Department of Breast Oncology, Aichi Cancer Center, Nagoya, Japan
| | - Gini Fleming
- grid.170205.10000 0004 1936 7822Section of Hematology and Oncology, Department of Medicine, University of Chicago, Chicago, IL USA
| | - Nora Jaskowiak
- grid.170205.10000 0004 1936 7822Department of Surgery, University of Chicago, Chicago, IL USA
| | - Donald Hedeker
- grid.170205.10000 0004 1936 7822Department of Public Health Sciences, University of Chicago, 5841 S. Maryland Avenue, MC 2000, Chicago, IL 60637 USA
| | - Olufunmilayo I. Olopade
- grid.170205.10000 0004 1936 7822Section of Hematology and Oncology, Department of Medicine, University of Chicago, Chicago, IL USA
| | - Dezheng Huo
- Section of Hematology and Oncology, Department of Medicine, University of Chicago, Chicago, IL, USA. .,Department of Public Health Sciences, University of Chicago, 5841 S. Maryland Avenue, MC 2000, Chicago, IL, 60637, USA.
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Afolaranmi O, Salako O, Okunade K, James A, Fagbenro G. Integrating genomics education into Nigerian undergraduate medical training - A narrative review. JOURNAL OF CLINICAL SCIENCES 2021. [DOI: 10.4103/jcls.jcls_6_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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8
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Critical Analysis of Genome-Wide Association Studies: Triple Negative Breast Cancer Quae Exempli Causa. Int J Mol Sci 2020; 21:ijms21165835. [PMID: 32823908 PMCID: PMC7461549 DOI: 10.3390/ijms21165835] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/10/2020] [Accepted: 08/11/2020] [Indexed: 12/14/2022] Open
Abstract
Genome-wide association studies (GWAS) are useful in assessing and analyzing either differences or variations in DNA sequences across the human genome to detect genetic risk factors of diseases prevalent within a target population under study. The ultimate goal of GWAS is to predict either disease risk or disease progression by identifying genetic risk factors. These risk factors will define the biological basis of disease susceptibility for the purposes of developing innovative, preventative, and therapeutic strategies. As single nucleotide polymorphisms (SNPs) are often used in GWAS, their relevance for triple negative breast cancer (TNBC) will be assessed in this review. Furthermore, as there are different levels and patterns of linkage disequilibrium (LD) present within different human subpopulations, a plausible strategy to evaluate known SNPs associated with incidence of breast cancer in ethnically different patient cohorts will be presented and discussed. Additionally, a description of GWAS for TNBC will be presented, involving various identified SNPs correlated with miRNA sites to determine their efficacies on either prognosis or progression of TNBC in patients. Although GWAS have identified multiple common breast cancer susceptibility variants that individually would result in minor risks, it is their combined effects that would likely result in major risks. Thus, one approach to quantify synergistic effects of such common variants is to utilize polygenic risk scores. Therefore, studies utilizing predictive risk scores (PRSs) based on known breast cancer susceptibility SNPs will be evaluated. Such PRSs are potentially useful in improving stratification for screening, particularly when combining family history, other risk factors, and risk prediction models. In conclusion, although interpretation of the results from GWAS remains a challenge, the use of SNPs associated with TNBC may elucidate and better contextualize these studies.
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9
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Afzaljavan F, Moezzi A, Vahednia E, Khorshid Shamshiri A, Vakili F, Homaei Shandiz F, Pasdar A. Predictive and prognostic value of LSP1 rs3817198 in sporadic breast cancer in northeastern population of Iran. Exp Mol Pathol 2020; 116:104514. [PMID: 32738313 DOI: 10.1016/j.yexmp.2020.104514] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 07/25/2020] [Accepted: 07/25/2020] [Indexed: 12/16/2022]
Affiliation(s)
- Fahimeh Afzaljavan
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Science, Mashhad, Iran; Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Atefeh Moezzi
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Science, Mashhad, Iran; Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Elham Vahednia
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Science, Mashhad, Iran
| | - Asma Khorshid Shamshiri
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Science, Mashhad, Iran; Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Fatemeh Vakili
- Midwifery department, Faculty of Nursing and Midwifery, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Alireza Pasdar
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Science, Mashhad, Iran; Division of Applied Medicine, Medical School, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK; Bioinformatics Research Group, Mashhad University of Medical Sciences, Mashhad, Iran.
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10
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Wang S, Pitt JJ, Zheng Y, Yoshimatsu TF, Gao G, Sanni A, Oluwasola O, Ajani M, Fitzgerald D, Odetunde A, Khramtsova G, Hurley I, Popoola A, Falusi A, Ogundiran T, Obafunwa J, Ojengbede O, Ibrahim N, Barretina J, White KP, Huo D, Olopade OI. Germline variants and somatic mutation signatures of breast cancer across populations of African and European ancestry in the US and Nigeria. Int J Cancer 2019; 145:3321-3333. [PMID: 31173346 PMCID: PMC6851589 DOI: 10.1002/ijc.32498] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 04/10/2019] [Accepted: 05/02/2019] [Indexed: 11/09/2022]
Abstract
Somatic mutation signatures may represent footprints of genetic and environmental exposures that cause different cancer. Few studies have comprehensively examined their association with germline variants, and none in an indigenous African population. SomaticSignatures was employed to extract mutation signatures based on whole-genome or whole-exome sequencing data from female patients with breast cancer (TCGA, training set, n = 1,011; Nigerian samples, validation set, n = 170), and to estimate contributions of signatures in each sample. Association between somatic signatures and common single nucleotide polymorphisms (SNPs) or rare deleterious variants were examined using linear regression. Nine stable signatures were inferred, and four signatures (APOBEC C>T, APOBEC C>G, aging and homologous recombination deficiency) were highly similar to known COSMIC signatures and explained the majority (60-85%) of signature contributions. There were significant heritable components associated with APOBEC C>T signature (h2 = 0.575, p = 0.010) and the combined APOBEC signatures (h2 = 0.432, p = 0.042). In TCGA dataset, seven common SNPs within or near GNB5 were significantly associated with an increased proportion (beta = 0.33, 95% CI = 0.21-0.45) of APOBEC signature contribution at genome-wide significance, while rare germline mutations in MTCL1 was also significantly associated with a higher contribution of this signature (p = 6.1 × 10-6 ). This is the first study to identify associations between germline variants and mutational patterns in breast cancer across diverse populations and geography. The findings provide evidence to substantiate causal links between germline genetic risk variants and carcinogenesis.
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Affiliation(s)
- Shengfeng Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing, China.,Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL
| | - Jason J Pitt
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL.,Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Yonglan Zheng
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL
| | - Toshio F Yoshimatsu
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL
| | - Guimin Gao
- Department of Public Health Sciences, University of Chicago, Chicago, IL
| | - Ayodele Sanni
- Department of Pathology & Forensic Medicine, Lagos State University Teaching Hospital, Lagos, Nigeria
| | | | - Mustapha Ajani
- Department of Pathology, University of Ibadan, Ibadan, Nigeria
| | - Dominic Fitzgerald
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL
| | - Abayomi Odetunde
- Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Galina Khramtsova
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL
| | - Ian Hurley
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL
| | - Abiodun Popoola
- Oncology Unit, Department of Radiology, Lagos State University, Lagos, Nigeria
| | - Adeyinka Falusi
- Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | | | - John Obafunwa
- Department of Pathology & Forensic Medicine, Lagos State University Teaching Hospital, Lagos, Nigeria
| | - Oladosu Ojengbede
- Centre for Population & Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Nasiru Ibrahim
- Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Jordi Barretina
- Girona Biomedical Research Institute (IDIBGI), Girona, Spain
| | | | - Dezheng Huo
- Department of Public Health Sciences, University of Chicago, Chicago, IL
| | - Olufunmilayo I Olopade
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL
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11
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Dutil J, Chen Z, Monteiro AN, Teer JK, Eschrich SA. An Interactive Resource to Probe Genetic Diversity and Estimated Ancestry in Cancer Cell Lines. Cancer Res 2019; 79:1263-1273. [PMID: 30894373 DOI: 10.1158/0008-5472.can-18-2747] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 11/08/2018] [Accepted: 12/26/2018] [Indexed: 12/21/2022]
Abstract
Recent work points to a lack of diversity in genomics studies from genome-wide association studies to somatic (tumor) genome analyses. Yet, population-specific genetic variation has been shown to contribute to health disparities in cancer risk and outcomes. Immortalized cancer cell lines are widely used in cancer research, from mechanistic studies to drug screening. Larger collections of cancer cell lines better represent the genomic heterogeneity found in primary tumors. Yet, the genetic ancestral origin of cancer cell lines is rarely acknowledged and often unknown. Using genome-wide genotyping data from 1,393 cancer cell lines from the Catalogue of Somatic Mutations in Cancer (COSMIC) and Cancer Cell Line Encyclopedia (CCLE), we estimated the genetic ancestral origin for each cell line. Our data indicate that cancer cell line collections are not representative of the diverse ancestry and admixture characterizing human populations. We discuss the implications of genetic ancestry and diversity of cellular models for cancer research and present an interactive tool, Estimated Cell Line Ancestry (ECLA), where ancestry can be visualized with reference populations of the 1000 Genomes Project. Cancer researchers can use this resource to identify cell line models for their studies by taking ancestral origins into consideration.
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Affiliation(s)
- Julie Dutil
- Cancer Biology Division, Ponce Research Institute, Ponce Health Sciences University, Ponce, Puerto Rico.
| | - Zhihua Chen
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Alvaro N Monteiro
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Jamie K Teer
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Steven A Eschrich
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida.
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12
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Jin TF, Zhang WT, Zhou ZF. The 6q25.1 rs2046210 polymorphism is associated with an elevated susceptibility to breast cancer: A meta-analysis of 261,703 subjects. Mol Genet Genomic Med 2019; 7:e553. [PMID: 30693664 PMCID: PMC6418377 DOI: 10.1002/mgg3.553] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 12/12/2018] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Several genome-wide association studies already explored the associations between 6q25.1 rs2046210 polymorphism and breast cancer (BC), but the results of these studies were not consistent. Thus, we conducted a meta-analysis of relevant studies to better analyze the effects of rs2046210 polymorphism on individual susceptibility to BC. METHODS PubMed, Web of Science, and Embase were searched for eligible studies. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated. RESULTS Totally 21 studies with 261,703 subjects were analyzed. A significant association with BC was observed for the rs2046210 polymorphism in GG versus GA +AA (dominant comparison, p < 0.0001, OR = 0.78, 95% CI 0.73-0.83), AA versus GG + GA (recessive comparison, p < 0.0001, OR = 1.21, 95% CI 1.18-1.24), GA versus GG + AA (overdominant comparison, p < 0.0001, OR = 1.12, 95% CI 1.08-1.16), and G versus A (allele comparison, p < 0.0001, OR = 0.86, 95% CI 0.82-0.89). Further subgroup analyses yielded similar positive results in both Asians and Caucasians. CONCLUSION In summary, our findings suggested that the rs2046210 polymorphism may serve as a potential genetic biomarker of BC in both Asians and Caucasians.
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Affiliation(s)
- Tie-Feng Jin
- The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Wen-Ting Zhang
- The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Zhen-Feng Zhou
- Department of Anesthesiology, Zhejiang Provincial People's Hospital, Hangzhou, Zhejiang, China
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13
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Pitt JJ, Riester M, Zheng Y, Yoshimatsu TF, Sanni A, Oluwasola O, Veloso A, Labrot E, Wang S, Odetunde A, Ademola A, Okedere B, Mahan S, Leary R, Macomber M, Ajani M, Johnson RS, Fitzgerald D, Grundstad AJ, Tuteja JH, Khramtsova G, Zhang J, Sveen E, Hwang B, Clayton W, Nkwodimmah C, Famooto B, Obasi E, Aderoju V, Oludara M, Omodele F, Akinyele O, Adeoye A, Ogundiran T, Babalola C, MacIsaac K, Popoola A, Morrissey MP, Chen LS, Wang J, Olopade CO, Falusi AG, Winckler W, Haase K, Van Loo P, Obafunwa J, Papoutsakis D, Ojengbede O, Weber B, Ibrahim N, White KP, Huo D, Olopade OI, Barretina J. Characterization of Nigerian breast cancer reveals prevalent homologous recombination deficiency and aggressive molecular features. Nat Commun 2018; 9:4181. [PMID: 30327465 PMCID: PMC6191428 DOI: 10.1038/s41467-018-06616-0] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Accepted: 09/13/2018] [Indexed: 02/08/2023] Open
Abstract
Racial/ethnic disparities in breast cancer mortality continue to widen but genomic studies rarely interrogate breast cancer in diverse populations. Through genome, exome, and RNA sequencing, we examined the molecular features of breast cancers using 194 patients from Nigeria and 1037 patients from The Cancer Genome Atlas (TCGA). Relative to Black and White cohorts in TCGA, Nigerian HR + /HER2 - tumors are characterized by increased homologous recombination deficiency signature, pervasive TP53 mutations, and greater structural variation-indicating aggressive biology. GATA3 mutations are also more frequent in Nigerians regardless of subtype. Higher proportions of APOBEC-mediated substitutions strongly associate with PIK3CA and CDH1 mutations, which are underrepresented in Nigerians and Blacks. PLK2, KDM6A, and B2M are also identified as previously unreported significantly mutated genes in breast cancer. This dataset provides novel insights into potential molecular mechanisms underlying outcome disparities and lay a foundation for deployment of precision therapeutics in underserved populations.
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Affiliation(s)
- Jason J Pitt
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL 60637, USA.,Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore, 117599, Singapore
| | - Markus Riester
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Yonglan Zheng
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Toshio F Yoshimatsu
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Ayodele Sanni
- Department of Pathology and Forensic Medicine, Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria
| | | | - Artur Veloso
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Emma Labrot
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Shengfeng Wang
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL 60637, USA.,Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing, 100191, China
| | - Abayomi Odetunde
- Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Adeyinka Ademola
- Department of Surgery, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Babajide Okedere
- Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Scott Mahan
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Rebecca Leary
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Maura Macomber
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Mustapha Ajani
- Department of Pathology, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Ryan S Johnson
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Dominic Fitzgerald
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL 60637, USA
| | - A Jason Grundstad
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL 60637, USA
| | - Jigyasa H Tuteja
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL 60637, USA
| | - Galina Khramtsova
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Jing Zhang
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Elisabeth Sveen
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Bryce Hwang
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Wendy Clayton
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | | | - Bisola Famooto
- Department of Surgery, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Esther Obasi
- Department of Pathology and Forensic Medicine, Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria
| | - Victor Aderoju
- Department of Surgery, Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria
| | - Mobolaji Oludara
- Department of Surgery, Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria
| | - Folusho Omodele
- Department of Surgery, Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria
| | - Odunayo Akinyele
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Adewunmi Adeoye
- Department of Pathology, University of Ibadan, Ibadan, Oyo, Nigeria
| | | | - Chinedum Babalola
- Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria.,Department of Pharmaceutical Chemistry, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Kenzie MacIsaac
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Abiodun Popoola
- Oncology Unit, Department of Radiology, Lagos State University, Ikeja, Lagos, Nigeria
| | | | - Lin S Chen
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Jiebiao Wang
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Christopher O Olopade
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Adeyinka G Falusi
- Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Wendy Winckler
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Kerstin Haase
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Peter Van Loo
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,Department of Human Genetics, University of Leuven, Oude Markt 13, Leuven, 3000, Belgium
| | - John Obafunwa
- Department of Pathology and Forensic Medicine, Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria
| | | | - Oladosu Ojengbede
- Centre for Population and Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Barbara Weber
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Nasiru Ibrahim
- Department of Surgery, Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria
| | - Kevin P White
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL 60637, USA. .,Tempus Labs Inc., Chicago, IL, USA.
| | - Dezheng Huo
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL 60637, USA. .,Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA.
| | - Olufunmilayo I Olopade
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL 60637, USA. .,Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL 60637, USA.
| | - Jordi Barretina
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA. .,Girona Biomedical Research Institute (IDIBGI), Girona, 17007, Spain.
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14
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Wang S, Huo D, Ogundiran TO, Ojengbede O, Zheng W, Nathanson KL, Nemesure B, Ambs S, Olopade OI, Zheng Y. Genetic variation in the Hippo pathway and breast cancer risk in women of African ancestry. Mol Carcinog 2018; 57:1311-1318. [PMID: 29873413 DOI: 10.1002/mc.22845] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 05/18/2018] [Accepted: 06/01/2018] [Indexed: 12/14/2022]
Abstract
Gene expression changes within the Hippo pathway were found to be associated with large tumor size and metastasis in breast cancer. The combined effect of genetic variants in genes of this pathway may have a causal role in breast cancer development. We examined 7086 SNPs that were not highly correlated (r2 < 0.8) in 35 Hippo pathway genes using data from the genome-wide association study of breast cancer from the Root Consortium, which includes 3686 participants of African ancestry from Nigeria, United States of America, and Barbados: 1657 cases (403 estrogen receptor-positive [ER+], 374 ER-) and 2029 controls. Gene-level analyses were conducted using improved AdaJoint test for large-scale genetic association studies adjusting for age, study site and the first four eigenvectors from the principal component analysis. SNP-level analyses were conducted with logistic regression. The Hippo pathway was significantly associated with risk of ER+ breast cancer (pathway-level P = 0.019), with WWC1 (Padj = 0.04) being the leading gene. The pathway-level significance was lost without WWC1 (P = 0.12). rs147106204 in the WWC1 gene was the most statistically significant SNP after gene-level adjustment for multiple comparisons (OR = 0.53, 95%CI = 0.41-0.70, Padj = 0.025). We found evidence of an association between genetic variations in the Hippo pathway and ER+ breast cancer. Moreover, WWC1 was identified as the most important genetic susceptibility locus highlighting the importance of genetic epidemiology studies of breast cancer in understudied populations.
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Affiliation(s)
- Shengfeng Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing, China.,Center for Clinical Cancer Genetics and Global Health, Department of Medicine, University of Chicago, Chicago, Illinois
| | - Dezheng Huo
- Department of Public Health Sciences, University of Chicago, Chicago, Illinois
| | - Temidayo O Ogundiran
- Department of Surgery, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Oladosu Ojengbede
- Center for Population and Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee
| | | | - Barbara Nemesure
- Department of Preventive Medicine, State University of New York at Stony Brook, Stony Brook, New York
| | - Stefan Ambs
- Laboratory of Human Carcinogenesis, National Cancer Institute, Bethesda, Maryland
| | - Olufunmilayo I Olopade
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, University of Chicago, Chicago, Illinois
| | - Yonglan Zheng
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, University of Chicago, Chicago, Illinois
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15
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Lilyquist J, Ruddy KJ, Vachon CM, Couch FJ. Common Genetic Variation and Breast Cancer Risk-Past, Present, and Future. Cancer Epidemiol Biomarkers Prev 2018; 27:380-394. [PMID: 29382703 PMCID: PMC5884707 DOI: 10.1158/1055-9965.epi-17-1144] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 01/05/2018] [Accepted: 01/11/2018] [Indexed: 11/16/2022] Open
Abstract
Breast cancer is the most common cancer among women in the United States, with up to 30% of those diagnosed displaying a family history of breast cancer. To date, 18% of the familial risk of breast cancer can be explained by SNPs. This review summarizes the discovery of risk-associated SNPs using candidate gene and genome-wide association studies (GWAS), including discovery and replication in large collaborative efforts such as The Collaborative Oncologic Gene-environment Study and OncoArray. We discuss the evolution of GWAS studies, efforts to discover additional SNPs, and methods for identifying causal variants. We summarize findings associated with overall breast cancer, pathologic subtypes, and mutation carriers (BRCA1, BRCA2, and CHEK2). In addition, we summarize the development of polygenic risk scores (PRS) using the risk-associated SNPs and show how PRS can contribute to estimation of individual risks for developing breast cancer. Cancer Epidemiol Biomarkers Prev; 27(4); 380-94. ©2018 AACRSee all articles in this CEBP Focus section, "Genome-Wide Association Studies in Cancer."
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Affiliation(s)
- Jenna Lilyquist
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | | | - Celine M Vachon
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Fergus J Couch
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota.
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
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16
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Jiang C, Yu S, Qian P, Guo R, Zhang R, Ao Z, Li Q, Wu G, Chen Y, Li J, Wang C, Yao W, Xu J, Qian G, Ji F. The breast cancer susceptibility-related polymorphisms at the TOX3/LOC643714 locus associated with lung cancer risk in a Han Chinese population. Oncotarget 2018; 7:59742-59753. [PMID: 27486757 PMCID: PMC5312345 DOI: 10.18632/oncotarget.10874] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 07/09/2016] [Indexed: 11/25/2022] Open
Abstract
It has been well established that besides environmental factors, genetic factors are also associated with lung cancer risk. However, to date, the prior identified genetic variants and loci only explain a small fraction of the familial risk of lung cancer. Hence it is vital to investigate the remaining missing heritability to understand the development and process of lung cancer. In the study, to test our hypothesis that the previously identified breast cancer risk-associated genetic polymorphisms at the TOX3/LOC643714 locus might contribute to lung cancer risk, 16 SNPs at the TOX3/LOC643714 locus were evaluated in a Han Chinese population based on a case-control study. Pearson's chi-square test or Fisher's exact test revealed that rs9933638, rs12443621, and rs3104746 were significantly associated with lung cancer risk (P < 0.001, P < 0.001, and P = 0.005, respectively). Logistic regression analyses displayed that lung cancer risk of individuals with rs9933638(GG+GA) were 1.89 times higher than that of rs9933638AA carriers (OR = 1.893, 95% CI = 1.308-2.741, P = 0.001). Similar findings were manifested for rs12443621 (OR = 1.824, 95% CI = 1.272-2.616, P = 0.001, rs12443621(GG+GA) carriers vs. rs12443621AA carriers) and rs3104746 (OR = 1.665, 95% CI = 1.243-2.230, P = 0.001, rs3104746TT carriers vs. rs3104746(TA+AA) carriers). The study discovered for the first time that three SNPs (rs9933638, rs12443621, and rs3104746) at the TOX3/LOC643714 locus contributed to lung cancer risk, providing new evidences that lung cancer and breast cancer are linked at the molecular and genetic level to a certain extent.
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Affiliation(s)
- Chaowen Jiang
- Institute of Human Respiratory Disease, Xinqiao Hospital, The Third Military Medical University, Chongqing 400037, China
| | - Shilong Yu
- Institute of Human Respiratory Disease, Xinqiao Hospital, The Third Military Medical University, Chongqing 400037, China
| | - Pin Qian
- Institute of Human Respiratory Disease, Xinqiao Hospital, The Third Military Medical University, Chongqing 400037, China
| | - Ruiling Guo
- Department of Respiratory Diseases, 324th Hospital of People's Liberation Army (No.324 Hospital of PLA), Chongqing 400020, China
| | - Ruijie Zhang
- Department of Respiratory Medicine, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Zhi Ao
- Institute of Human Respiratory Disease, Xinqiao Hospital, The Third Military Medical University, Chongqing 400037, China
| | - Qi Li
- Institute of Human Respiratory Disease, Xinqiao Hospital, The Third Military Medical University, Chongqing 400037, China
| | - Guoming Wu
- Institute of Human Respiratory Disease, Xinqiao Hospital, The Third Military Medical University, Chongqing 400037, China
| | - Yan Chen
- Institute of Human Respiratory Disease, Xinqiao Hospital, The Third Military Medical University, Chongqing 400037, China
| | - Jin Li
- Institute of Human Respiratory Disease, Xinqiao Hospital, The Third Military Medical University, Chongqing 400037, China
| | - Changzheng Wang
- Institute of Human Respiratory Disease, Xinqiao Hospital, The Third Military Medical University, Chongqing 400037, China
| | - Wei Yao
- Institute of Human Respiratory Disease, Xinqiao Hospital, The Third Military Medical University, Chongqing 400037, China
| | - Jiancheng Xu
- Institute of Human Respiratory Disease, Xinqiao Hospital, The Third Military Medical University, Chongqing 400037, China
| | - Guisheng Qian
- Institute of Human Respiratory Disease, Xinqiao Hospital, The Third Military Medical University, Chongqing 400037, China
| | - Fuyun Ji
- Institute of Human Respiratory Disease, Xinqiao Hospital, The Third Military Medical University, Chongqing 400037, China
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17
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Huo D, Feng Y, Haddad S, Zheng Y, Yao S, Han YJ, Ogundiran TO, Adebamowo C, Ojengbede O, Falusi AG, Zheng W, Blot W, Cai Q, Signorello L, John EM, Bernstein L, Hu JJ, Ziegler RG, Nyante S, Bandera EV, Ingles SA, Press MF, Deming SL, Rodriguez-Gil JL, Nathanson KL, Domchek SM, Rebbeck TR, Ruiz-Narváez EA, Sucheston-Campbell LE, Bensen JT, Simon MS, Hennis A, Nemesure B, Leske MC, Ambs S, Chen LS, Qian F, Gamazon ER, Lunetta KL, Cox NJ, Chanock SJ, Kolonel LN, Olshan AF, Ambrosone CB, Olopade OI, Palmer JR, Haiman CA. Genome-wide association studies in women of African ancestry identified 3q26.21 as a novel susceptibility locus for oestrogen receptor negative breast cancer. Hum Mol Genet 2018; 25:4835-4846. [PMID: 28171663 DOI: 10.1093/hmg/ddw305] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 07/21/2016] [Accepted: 08/26/2016] [Indexed: 12/20/2022] Open
Abstract
Multiple breast cancer loci have been identified in previous genome-wide association studies, but they were mainly conducted in populations of European ancestry. Women of African ancestry are more likely to have young-onset and oestrogen receptor (ER) negative breast cancer for reasons that are unknown and understudied. To identify genetic risk factors for breast cancer in women of African descent, we conducted a meta-analysis of two genome-wide association studies of breast cancer; one study consists of 1,657 cases and 2,029 controls genotyped with Illumina’s HumanOmni2.5 BeadChip and the other study included 3,016 cases and 2,745 controls genotyped using Illumina Human1M-Duo BeadChip. The top 18,376 single nucleotide polymorphisms (SNP) from the meta-analysis were replicated in the third study that consists of 1,984 African Americans cases and 2,939 controls. We found that SNP rs13074711, 26.5 Kb upstream of TNFSF10 at 3q26.21, was significantly associated with risk of oestrogen receptor (ER)-negative breast cancer (odds ratio [OR]=1.29, 95% CI: 1.18-1.40; P = 1.8 × 10 − 8). Functional annotations suggest that the TNFSF10 gene may be involved in breast cancer aetiology, but further functional experiments are needed. In addition, we confirmed SNP rs10069690 was the best indicator for ER-negative breast cancer at 5p15.33 (OR = 1.30; P = 2.4 × 10 − 10) and identified rs12998806 as the best indicator for ER-positive breast cancer at 2q35 (OR = 1.34; P = 2.2 × 10 − 8) for women of African ancestry. These findings demonstrated additional susceptibility alleles for breast cancer can be revealed in diverse populations and have important public health implications in building race/ethnicity-specific risk prediction model for breast cancer.
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Affiliation(s)
- Dezheng Huo
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
| | - Ye Feng
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Stephen Haddad
- Slone Epidemiology Center, Boston University, Boston, MA, USA
| | - Yonglan Zheng
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Song Yao
- Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Yoo-Jeong Han
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Temidayo O Ogundiran
- Department of Surgery, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Clement Adebamowo
- Department of Epidemiology & Preventive Medicine, University of Maryland, Baltimore, MD, USA
| | - Oladosu Ojengbede
- Center for Population and Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Adeyinka G Falusi
- Institute for Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN, USA
| | - William Blot
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN, USA
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN, USA
| | - Lisa Signorello
- Cancer Prevention Fellowship Program, National Cancer Institute, Bethesda, MD, USA
| | - Esther M John
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN, USA.,Cancer Prevention Fellowship Program, National Cancer Institute, Bethesda, MD, USA
| | - Leslie Bernstein
- Division of Cancer Etiology, Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Jennifer J Hu
- Sylvester Comprehensive Cancer Center and Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Regina G Ziegler
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MA, USA
| | - Sarah Nyante
- Department of Epidemiology, Gillings School of Global Public Health, and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | | | - Sue A Ingles
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Michael F Press
- Department of Pathology, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Sandra L Deming
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN, USA
| | - Jorge L Rodriguez-Gil
- Sylvester Comprehensive Cancer Center and Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL, USA
| | | | - Susan M Domchek
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Timothy R Rebbeck
- Dana Farber Cancer Institute & Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | | | | | - Jeannette T Bensen
- Department of Epidemiology, Gillings School of Global Public Health, and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Michael S Simon
- Karmanos Cancer Institute, Department of Oncology, Wayne State University, Detroit, MI, USA
| | - Anselm Hennis
- Division of Cancer Etiology, Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA.,Sylvester Comprehensive Cancer Center and Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Barbara Nemesure
- Department of Preventive Medicine, State University of New York at Stony Brook, Stony Brook, NY, USA
| | - M Cristina Leske
- Department of Preventive Medicine, State University of New York at Stony Brook, Stony Brook, NY, USA
| | - Stefan Ambs
- Laboratory of Human Carcinogenesis, National Cancer Institute, Bethesda, MD, USA
| | - Lin S Chen
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
| | - Frank Qian
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Eric R Gamazon
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MA, USA.,Department of Epidemiology, Gillings School of Global Public Health, and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Kathryn L Lunetta
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Nancy J Cox
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University, Nashville, TN, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MA, USA
| | - Laurence N Kolonel
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Andrew F Olshan
- Department of Epidemiology, Gillings School of Global Public Health, and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | | | - Olufunmilayo I Olopade
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Julie R Palmer
- Slone Epidemiology Center, Boston University, Boston, MA, USA
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
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18
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Smith CJ, Minas TZ, Ambs S. Analysis of Tumor Biology to Advance Cancer Health Disparity Research. THE AMERICAN JOURNAL OF PATHOLOGY 2017; 188:304-316. [PMID: 29137948 DOI: 10.1016/j.ajpath.2017.06.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 06/24/2017] [Accepted: 06/29/2017] [Indexed: 12/20/2022]
Abstract
Cancer mortality rates in the United States continue to decline. Reductions in tobacco use, uptake of preventive measures, adoption of early detection methods, and better treatments have resulted in improved cancer outcomes for men and women. Despite this progress, some population groups continue to experience an excessive cancer burden when compared with other population groups. One of the most prominent cancer health disparities exists in prostate cancer. Prostate cancer mortality rates are highest among men of African ancestry when compared with other men, both in the United States and globally. This disparity and other cancer health disparities are largely explained by differences in access to health care, diet, lifestyle, cultural barriers, and disparate exposures to carcinogens and pathogens. Dietary and lifestyle factors, pathogens, and ancestry-related factors can modify tumor biology and induce a more aggressive disease. There are numerous examples of how environmental exposures, like tobacco, chronic stress, or dietary factors, induce an adverse tumor biology, leading to a more aggressive disease and decreased patient survival. Because of population differences in the exposure to these risk factors, they can be the cause of cancer disparities. In this review, we will summarize recent advances in our understanding of prostate and breast cancer disparities in the United States and discuss how the analysis of tumor biology can advance health disparity research.
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Affiliation(s)
- Cheryl J Smith
- Laboratory of Human Carcinogenesis, Center of Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Tsion Z Minas
- Laboratory of Human Carcinogenesis, Center of Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Stefan Ambs
- Laboratory of Human Carcinogenesis, Center of Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland.
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19
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Gao G, Pierce BL, Olopade OI, Im HK, Huo D. Trans-ethnic predicted expression genome-wide association analysis identifies a gene for estrogen receptor-negative breast cancer. PLoS Genet 2017; 13:e1006727. [PMID: 28957356 PMCID: PMC5619687 DOI: 10.1371/journal.pgen.1006727] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 03/30/2017] [Indexed: 01/22/2023] Open
Abstract
Genome-wide association studies (GWAS) have identified more than 90 susceptibility loci for breast cancer, but the underlying biology of those associations needs to be further elucidated. More genetic factors for breast cancer are yet to be identified but sample size constraints preclude the identification of individual genetic variants with weak effects using traditional GWAS methods. To address this challenge, we utilized a gene-level expression-based method, implemented in the MetaXcan software, to predict gene expression levels for 11,536 genes using expression quantitative trait loci and examine the genetically-predicted expression of specific genes for association with overall breast cancer risk and estrogen receptor (ER)-negative breast cancer risk. Using GWAS datasets from a Challenge launched by National Cancer Institute, we identified TP53INP2 (tumor protein p53-inducible nuclear protein 2) at 20q11.22 to be significantly associated with ER-negative breast cancer (Z = -5.013, p = 5.35×10−7, Bonferroni threshold = 4.33×10−6). The association was consistent across four GWAS datasets, representing European, African and Asian ancestry populations. There are 6 single nucleotide polymorphisms (SNPs) included in the prediction of TP53INP2 expression and five of them were associated with estrogen-receptor negative breast cancer, although none of the SNP-level associations reached genome-wide significance. We conducted a replication study using a dataset outside of the Challenge, and found the association between TP53INP2 and ER-negative breast cancer was significant (p = 5.07x10-3). Expression of HP (16q22.2) showed a suggestive association with ER-negative breast cancer in the discovery phase (Z = 4.30, p = 1.70x10-5) although the association was not significant after Bonferroni adjustment. Of the 249 genes that are 250 kb within known breast cancer susceptibility loci identified from previous GWAS, 20 genes (8.0%) were statistically significant associated with ER-negative breast cancer (p<0.05), compared to 582 (5.2%) of 11,287 genes that are not close to previous GWAS loci. This study demonstrated that expression-based gene mapping is a promising approach for identifying cancer susceptibility genes. Although individual genetic variant-based genome-wide association studies have greatly increased our understanding of the genetic susceptibility to breast cancer, the genetic variants identified to date account for a relatively small proportion of the heritability. Shifting the focus of analysis from individual genetic variants to genes or gene sets could lead to the identification of novel genes involved in breast cancer risk. Here, we take advantage of a recently developed gene-level expression-based association method MetaXcan to examine the association of genetically-predicted expression levels for 11,536 genes across the human genome with breast cancer risk. The MetaXcan method uses external information on the effects of genetic variants on gene expression. We show that the TP53INP2 gene on human chromosome 20 is significantly associated with estrogen-receptor negative breast cancer (P = 5.35×10−7, Bonferroni threshold = 4.33×10−6). The association is consistent across analyses of four datasets, representing European, African and Asian ancestry populations. As a downstream gene of p53, TP53INP2 may affect breast cancer risk through p53 signaling pathway. Furthermore, TP53INP2, also known as DOR (Diabetes And Obesity-Regulated Gene), has been linked to obesity and diabetes, suggesting a novel biological pathway for the known association between obesity and breast cancer risk.
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Affiliation(s)
- Guimin Gao
- Department of Public Health Sciences, University of Chicago, Chicago, United States of America
| | - Brandon L. Pierce
- Department of Public Health Sciences, University of Chicago, Chicago, United States of America
- Department of Human Genetics, University of Chicago, Chicago, United States of America
| | - Olufunmilayo I. Olopade
- Section of Hematology and Oncology, Department of Medicine, University of Chicago, Chicago, United States of America
| | - Hae Kyung Im
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, United States of America
| | - Dezheng Huo
- Department of Public Health Sciences, University of Chicago, Chicago, United States of America
- * E-mail:
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20
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Yao S, Hong CC, Bandera EV, Zhu Q, Liu S, Cheng TYD, Zirpoli G, Haddad SA, Lunetta KL, Ruiz-Narvaez EA, McCann SE, Troester MA, Rosenberg L, Palmer JR, Olshan AF, Ambrosone CB. Demographic, lifestyle, and genetic determinants of circulating concentrations of 25-hydroxyvitamin D and vitamin D-binding protein in African American and European American women. Am J Clin Nutr 2017; 105:1362-1371. [PMID: 28424184 PMCID: PMC5445669 DOI: 10.3945/ajcn.116.143248] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 03/15/2017] [Indexed: 12/29/2022] Open
Abstract
Background: Vitamin D may have anticancer activities. The high prevalence of vitamin D deficiency in African Americans (AAs) may be a contributing factor to the cancer health disparities between AAs and European Americans (EAs).Objectives: We compared concentrations of 25(OH)D and vitamin D-binding protein (VDBP) in AA and EA women and investigated determinants of the vitamin D-biomarker concentrations in both populations.Design: We used data and biospecimens from 909 AA and 847 EA healthy control subjects from the Carolina Breast Cancer Study (CBCS) and the Women's Circle of Health Study (WCHS) in the African American Breast Cancer Epidemiology and Risk Consortium. We measured plasma 25(OH)D and VDBP concentrations in all participants and genotyped 67 vitamin D-related genes in AA women only.Results: AA women had lower 25(OH)D concentrations than did EA women (mean ± SD: 14.2 ± 8.1 compared with 21.1 ± 11.5 ng/mL, respectively; P < 0.0001) but similar concentrations of VDBP (mean ± SD: 344 ± 133 compared with 336 ± 124 μg/mL, respectively; P = 0.25). With VDBP and other factors controlled for, the observed racial difference in 25(OH)D concentrations did not diminish. Relations of demographic and lifestyle factors with 25(OH)D were similar between AA and EA women. Although none of the genetic variants that have been identified in previous genome-wide association studies of 25(OH)D concentrations in EAs were significant (P > 0.05) in AAs, AA women who carried the allele of a functional single nucleotide polymorphism rs4988235, which has been previously associated with lactase expression and lactose tolerance, had higher dietary vitamin D intake and higher measured 25(OH)D concentrations.Conclusions: AA women have lower concentrations of total 25(OH)D than EA women do, but both groups have similar VDBP concentrations, suggesting that there are lower concentrations of free 25(OH)D in AAs. Although demographic and lifestyle determinants of 25(OH)D concentrations are similar between the 2 groups, genetic determinants may be ethnicity specific. Larger studies in AAs will be needed to fully elucidate the underlying determinants of low vitamin D concentrations in AA populations.
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Affiliation(s)
- Song Yao
- Departments of Cancer Prevention and Control and
| | | | - Elisa V Bandera
- Cancer Prevention and Control Program, Rutgers Cancer Institute of New Jersey, The State University of New Jersey, New Brunswick, NJ
| | - Qianqian Zhu
- Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY
| | - Song Liu
- Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY
| | | | - Gary Zirpoli
- Departments of Cancer Prevention and Control and
| | | | - Kathryn L Lunetta
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA; and
| | | | | | - Melissa A Troester
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | | | - Andrew F Olshan
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC
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21
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Hu X, Jiang L, Tang C, Ju Y, Jiu L, Wei Y, Guo L, Zhao Y. Association of three single nucleotide polymorphisms of ESR1with breast cancer susceptibility: a meta-analysis. J Biomed Res 2017; 31:213-225. [PMID: 28808214 PMCID: PMC5460609 DOI: 10.7555/jbr.31.20160087] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Expression of estrogen receptors is correlated with breast cancer risk, but inconsistent results have been reported. To clarify potential estrogen receptor (ESR)-related breast cancer risk, we analyzed genetic variants of ESR1 in association with breast cancer susceptibility. We performed a meta-analysis to investigate the association between rs2234693, rs1801132, and rs2046210 (single nucleotide polymorphisms of ESR1 ), and breast cancer risk. Our analysis included 44 case-control studies. For rs2234693, the CC genotype had a higher risk of breast cancer compared to the TT or CT genotype. For rs2046210, the AA, GA, or GA+ GG genotype had a much higher risk compared to the GG genotype. No significant association was found for the rs1801132 polymorphism with breast cancer risk. This meta-analysis demonstrates association between the rs2234693 and rs2046210 polymorphisms of ESR1 and breast cancer risk. The correlation strength between rs2234693 and breast cancer susceptibility differs in subgroup assessment by ethnicity.
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Affiliation(s)
- Xu Hu
- Department of Biotechnology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Linfei Jiang
- Department of Biotechnology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Chenhui Tang
- Department of Biotechnology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Yuehong Ju
- Department of Biotechnology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Li Jiu
- School of International Pharmaceutical Business, China Pharmaceutical University, Nanjing, Jiangsu 211198, China
| | - Yongyue Wei
- Department of Biostatistics, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing, Jiangsu 211166, China
| | - Li Guo
- School of Geographic and Biologic Information, Nanjing University of Posts and Telecommunications, Nanjing, Jiangsu 210046, China
| | - Yang Zhao
- Department of Biostatistics, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing, Jiangsu 211166, China
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Abstract
A coding region polymorphism exists in the TP53 gene (Pro47Ser; rs1800371) in individuals of African descent, which reduces p53 tumor suppressor function in a mouse model. It has been unclear whether this functionally significant polymorphism alters cancer risk in humans. This analysis included 6907 women with breast cancer and 7644 controls from the AMBER, ROOT, and AABC consortia. We used multivariable logistic regression to estimate associations between the TP53 Pro47Ser allele and overall breast cancer risk. Because polymorphisms in TP53 tend to be associated with cancer risk in pre-menopausal women, we also limited our analyses to this population in the AMBER and ROOT consortia, where menopausal status was known, and conducted a fixed effects meta-analysis. In an analysis of all women in the AMBER, ROOT, and AABC consortia, we found no evidence for association of the Pro47Ser variant with breast cancer risk. However, when we restricted our analysis to only pre-menopausal women from the AMBER and ROOT consortia, there was a per allele odds ratio of 1.72 (95% confidence interval 1.08-2.76; p-value = 0.023). Although the Pro47Ser variant was not associated with overall breast cancer risk, it may increase risk among pre-menopausal women of African ancestry. Following up on more studies in human populations may better elucidate the role of this variant in breast cancer etiology. However, because of the low frequency of the polymorphism in women of African ancestry, its impact at a population level may be minimal.
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23
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Zhu Q, Shepherd L, Lunetta KL, Yao S, Liu Q, Hu Q, Haddad SA, Sucheston-Campbell L, Bensen JT, Bandera EV, Rosenberg L, Liu S, Haiman CA, Olshan AF, Palmer JR, Ambrosone CB. Trans-ethnic follow-up of breast cancer GWAS hits using the preferential linkage disequilibrium approach. Oncotarget 2016; 7:83160-83176. [PMID: 27825120 PMCID: PMC5341253 DOI: 10.18632/oncotarget.13075] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 10/12/2016] [Indexed: 12/22/2022] Open
Abstract
Leveraging population-distinct linkage equilibrium (LD) patterns, trans-ethnic follow-up of variants discovered from genome-wide association studies (GWAS) has proved to be useful in facilitating the identification of bona fide causal variants. We previously developed the preferential LD approach, a novel method that successfully identified causal variants driving the GWAS signals within European-descent populations even when the causal variants were only weakly linked with the GWAS-discovered variants. To evaluate the performance of our approach in a trans-ethnic setting, we applied it to follow up breast cancer GWAS hits identified mostly from populations of European ancestry in African Americans (AA). We evaluated 74 breast cancer GWAS variants in 8,315 AA women from the African American Breast Cancer Epidemiology and Risk (AMBER) consortium. Only 27% of them were associated with breast cancer risk at significance level α=0.05, suggesting race-specificity of the identified breast cancer risk loci. We followed up on those replicated GWAS hits in the AMBER consortium utilizing the preferential LD approach, to search for causal variants or better breast cancer markers from the 1000 Genomes variant catalog. Our approach identified stronger breast cancer markers for 80% of the GWAS hits with at least nominal breast cancer association, and in 81% of these cases, the marker identified was among the top 10 of all 1000 Genomes variants in the corresponding locus. The results support trans-ethnic application of the preferential LD approach in search for candidate causal variants, and may have implications for future genetic research of breast cancer in AA women.
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Affiliation(s)
- Qianqian Zhu
- Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Lori Shepherd
- Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Kathryn L. Lunetta
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Song Yao
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Qian Liu
- Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Qiang Hu
- Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY, USA
| | | | - Lara Sucheston-Campbell
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Jeannette T. Bensen
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Elisa V. Bandera
- Cancer Prevention and Control, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Lynn Rosenberg
- Slone Epidemiology Center, Boston University, Boston, MA, USA
| | - Song Liu
- Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Christopher A. Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Andrew F. Olshan
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Julie R. Palmer
- Slone Epidemiology Center, Boston University, Boston, MA, USA
| | - Christine B. Ambrosone
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, NY, USA
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Chen Y, Fu F, Lin Y, Qiu L, Lu M, Zhang J, Qiu W, Yang P, Wu N, Huang M, Wang C. The precision relationships between eight GWAS-identified genetic variants and breast cancer in a Chinese population. Oncotarget 2016; 7:75457-75467. [PMID: 27705907 PMCID: PMC5342752 DOI: 10.18632/oncotarget.12255] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 09/16/2016] [Indexed: 11/25/2022] Open
Abstract
Some of the new breast cancer susceptibility loci discovered in recent Genome-wide association studies (GWASs) have not been confirmed in Chinese populations. To determine whether eight novel Single-Nucleotide Polymorphisms (SNPs) have associations with breast cancer risk in women from southeast China, we conducted a case-control study of 1,156 breast cancer patients and 1,256 healthy controls. We first validated that the SNPs rs12922061, rs2290203, and rs2981578 were associated with overall breast cancer risk in southeast Chinese women, with the per-allele OR of 1.209 (95%CI: 1.064-1.372), 1.176 (95%CI: 1.048-1.320), and 0.852 (95%CI: 0.759-0.956), respectively. Rs12922061 and rs2290203 even passed the threshold for Bonferroni correction (P value: 0.00625). In stratified analysis, we found another three SNPs were significantly associated within different subgroups. However, after Bonferroni correction (P value: 0.000446), there were no statistically significant was observed. In gene-environment interaction analysis, we observed gene-environment interactions played a potential role of in the risk of breast cancer. These findings provide new insight into the associations between the genetic susceptibility and fine classifications of breast cancer. Based on these results, we encourage further large series studies and functional research to confirm these finding.
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Affiliation(s)
- Yazhen Chen
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian Province, 350001, China
| | - Fangmeng Fu
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian Province, 350001, China
| | - Yuxiang Lin
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian Province, 350001, China
| | - Lin Qiu
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian Province, 350001, China
| | - Minjun Lu
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian Province, 350001, China
| | - Jiantang Zhang
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian Province, 350001, China
| | - Wei Qiu
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian Province, 350001, China
| | - Peidong Yang
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian Province, 350001, China
| | - Na Wu
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian Province, 350001, China
| | - Meng Huang
- Fujian Center for Disease Control and Prevention, Fuzhou, Fujian Province, 350001, China
| | - Chuan Wang
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian Province, 350001, China
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25
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Han YJ, Zhang J, Zheng Y, Huo D, Olopade OI. Genetic and Epigenetic Regulation of TOX3 Expression in Breast Cancer. PLoS One 2016; 11:e0165559. [PMID: 27806084 PMCID: PMC5091860 DOI: 10.1371/journal.pone.0165559] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 10/13/2016] [Indexed: 01/09/2023] Open
Abstract
Genome wide association studies (GWAS) have identified low penetrance and high frequency single nucleotide polymorphisms (SNPs) that contribute to genetic susceptibility of breast cancer. The SNPs at 16q12, close to the TOX3 and CASC16 genes, represent one of the susceptibility loci identified by GWAS, showing strong evidence for breast cancer association across various populations. To examine molecular mechanisms of TOX3 regulation in breast cancer, we investigated both genetic and epigenetic factors using cell lines and datasets derived from primary breast tumors available through The Cancer Genome Atlas (TCGA). TOX3 expression is highly up-regulated in luminal subtype tumors compared to normal breast tissues or basal-like tumors. Expression quantitative trait loci (eQTL) analyses revealed significant associations of rs3803662 and rs4784227 genotypes with TOX3 expression in breast tumors. Bisulfite sequencing of four CpG islands in the TOX3 promoter showed a clear difference between luminal and basal-like cancer cell lines. 5-Aza-2’-deoxycytidine treatment of a basal-like cancer cell line increased expression of TOX3. TCGA dataset verified significantly lower levels of methylation of the promoter in luminal breast tumors with an inverse correlation between methylation and expression of TOX3. Methylation QTL (mQTL) analyses showed a weak or no correlation of rs3803662 or rs4784227 with TOX3 promoter methylation in breast tumors, indicating an independent relationship between the genetic and epigenetic events. These data suggest a complex system of TOX3 regulation in breast tumors, driven by germline variants and somatic epigenetic modifications in a subtype specific manner.
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Affiliation(s)
- Yoo-Jeong Han
- Center for Clinical Cancer Genetics and Global Health; and Section of Hematology and Oncology, Department of Medicine, University of Chicago, Chicago, IL 60637, United States of America
- * E-mail: (OIO); (YJH)
| | - Jing Zhang
- Center for Clinical Cancer Genetics and Global Health; and Section of Hematology and Oncology, Department of Medicine, University of Chicago, Chicago, IL 60637, United States of America
| | - Yonglan Zheng
- Center for Clinical Cancer Genetics and Global Health; and Section of Hematology and Oncology, Department of Medicine, University of Chicago, Chicago, IL 60637, United States of America
| | - Dezheng Huo
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, United States of America
| | - Olufunmilayo I. Olopade
- Center for Clinical Cancer Genetics and Global Health; and Section of Hematology and Oncology, Department of Medicine, University of Chicago, Chicago, IL 60637, United States of America
- * E-mail: (OIO); (YJH)
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26
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Qian F, Feng Y, Zheng Y, Ogundiran TO, Ojengbede O, Zheng W, Blot W, Ambrosone CB, John EM, Bernstein L, Hu JJ, Ziegler RG, Nyante S, Bandera EV, Ingles SA, Press MF, Nathanson KL, Hennis A, Nemesure B, Ambs S, Kolonel LN, Olopade OI, Haiman CA, Huo D. Genetic variants in microRNA and microRNA biogenesis pathway genes and breast cancer risk among women of African ancestry. Hum Genet 2016; 135:1145-59. [PMID: 27380242 DOI: 10.1007/s00439-016-1707-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 06/25/2016] [Indexed: 10/21/2022]
Abstract
MicroRNAs (miRNA) regulate breast biology by binding to specific RNA sequences, leading to RNA degradation and inhibition of translation of their target genes. While germline genetic variations may disrupt some of these interactions between miRNAs and their targets, studies assessing the relationship between genetic variations in the miRNA network and breast cancer risk are still limited, particularly among women of African ancestry. We systematically put together a list of 822 and 10,468 genetic variants among primary miRNA sequences and 38 genes in the miRNA biogenesis pathway, respectively; and examined their association with breast cancer risk in the ROOT consortium which includes women of African ancestry. Findings were replicated in an independent consortium. Logistic regression was used to estimate the odds ratio (OR) and 95 % confidence intervals (CI). For overall breast cancer risk, three single-nucleotide polymorphisms (SNPs) in miRNA biogenesis genes DROSHA rs78393591 (OR = 0.69, 95 % CI: 0.55-0.88, P = 0.003), ESR1 rs523736 (OR = 0.88, 95 % CI: 0.82-0.95, P = 3.99 × 10(-4)), and ZCCHC11 rs114101502 (OR = 1.33, 95 % CI: 1.11-1.59, P = 0.002), and one SNP in primary miRNA sequence (rs116159732 in miR-6826, OR = 0.74, 95 % CI: 0.63-0.89, P = 0.001) were found to have significant associations in both discovery and validation phases. In a subgroup analysis, two SNPs were associated with risk of estrogen receptor (ER)-negative breast cancer, and three SNPs were associated with risk of ER-positive breast cancer. Several variants in miRNA and miRNA biogenesis pathway genes were associated with breast cancer risk. Risk associations varied by ER status, suggesting potential new mechanisms in etiology.
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Affiliation(s)
- Frank Qian
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Ye Feng
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Yonglan Zheng
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Temidayo O Ogundiran
- Department of Surgery, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Oladosu Ojengbede
- Center for Population and Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN, USA
| | - William Blot
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN, USA
| | | | - Esther M John
- Cancer Prevention Institute of California, Fremont, CA, USA.,Department of Health Research and Policy (Epidemiology) and Stanford Cancer Institute, Stanford University School of Medicine Stanford, Stanford, CA, USA
| | - Leslie Bernstein
- Division of Cancer Etiology, Department of Population Science, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Jennifer J Hu
- Sylvester Comprehensive Cancer Center and Department of Epidemiology and Public Health, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Regina G Ziegler
- Epidemiology and Biostatistics Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, DC, USA
| | - Sarah Nyante
- Department of Epidemiology, Gillings School of Global Public Health and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Elisa V Bandera
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Sue A Ingles
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Michael F Press
- Department of Pathology, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | | | - Anselm Hennis
- Chronic Disease Research Centre and Tropical Medicine Research Institute, University of the West Indies, Bridgetown, Barbados
| | - Barbara Nemesure
- Department of Preventive Medicine, State University of New York at Stony Brook, Stony Brook, NY, USA
| | - Stefan Ambs
- Laboratory of Human Carcinogenesis, National Cancer Institute, Bethesda, MD, USA
| | - Laurence N Kolonel
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | | | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Dezheng Huo
- Department of Public Health Sciences, University of Chicago, 5841 S. Maryland Ave., MC 2007, Chicago, IL, 60637, USA.
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27
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Haddad SA, Ruiz-Narváez EA, Haiman CA, Sucheston-Campbell LE, Bensen JT, Zhu Q, Liu S, Yao S, Bandera EV, Rosenberg L, Olshan AF, Ambrosone CB, Palmer JR, Lunetta KL. An exome-wide analysis of low frequency and rare variants in relation to risk of breast cancer in African American Women: the AMBER Consortium. Carcinogenesis 2016; 37:870-877. [PMID: 27267999 DOI: 10.1093/carcin/bgw067] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 05/30/2016] [Indexed: 01/14/2023] Open
Abstract
A large percentage of breast cancer heritability remains unaccounted for, and most of the known susceptibility loci have been established in European and Asian populations. Rare variants may contribute to the unexplained heritability of this disease, including in women of African ancestry (AA). We conducted an exome-wide analysis of rare variants in relation to risk of overall and subtype-specific breast cancer in the African American Breast Cancer Epidemiology and Risk (AMBER) Consortium, which includes data from four large studies of AA women. Genotyping on the Illumina Human Exome Beadchip yielded data for 170 812 SNPs and 8287 subjects: 3629 cases (1093 estrogen receptor negative (ER-), 1968 ER+, 568 ER unknown) and 4658 controls, the largest exome chip study to date for AA breast cancer. Pooled gene-based association analyses were performed using the unified optimal sequence kernel association test (SKAT-O) for variants with minor allele frequency (MAF) ≤ 5%. In addition, each variant with MAF >0.5% was tested for association using logistic regression. There were no significant associations with overall breast cancer. However, a novel gene, FBXL22 (P = 8.2×10(-6)), and a gene previously identified in GWAS of European ancestry populations, PDE4D (P = 1.2×10(-6)), were significantly associated with ER- breast cancer after correction for multiple testing. Cases with the associated rare variants were also negative for progesterone and human epidermal growth factor receptors-thus, triple-negative cancer. Replication is required to confirm these gene-level associations, which are based on very small counts at extremely rare SNPs.
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Affiliation(s)
| | | | - Christopher A Haiman
- Department of Preventive Medicine , Keck School of Medicine , University of Southern California/Norris Comprehensive Cancer Center , Los Angeles, CA 90033 , USA
| | - Lara E Sucheston-Campbell
- Department of Cancer Prevention and Control , Roswell Park Cancer Institute , Buffalo, NY 14263 , USA
| | - Jeannette T Bensen
- Department of Epidemiology , Gillings School of Global Public Health , University of North Carolina at Chapel Hill , Chapel Hill , NC 27599 , USA
| | - Qianqian Zhu
- Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute , Buffalo, NY 14263 , USA
| | - Song Liu
- Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute , Buffalo, NY 14263 , USA
| | - Song Yao
- Department of Cancer Prevention and Control , Roswell Park Cancer Institute , Buffalo, NY 14263 , USA
| | - Elisa V Bandera
- Cancer Prevention and Control, Rutgers Cancer Institute of New Jersey , New Brunswick, NJ 08903 , USA and
| | | | - Andrew F Olshan
- Department of Epidemiology , Gillings School of Global Public Health , University of North Carolina at Chapel Hill , Chapel Hill , NC 27599 , USA
| | - Christine B Ambrosone
- Department of Cancer Prevention and Control , Roswell Park Cancer Institute , Buffalo, NY 14263 , USA
| | | | - Kathryn L Lunetta
- Department of Biostatistics, Boston University School of Public Health , Boston, MA 02118 , USA
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28
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Young EL, Feng BJ, Stark AW, Damiola F, Durand G, Forey N, Francy TC, Gammon A, Kohlmann WK, Kaphingst KA, McKay-Chopin S, Nguyen-Dumont T, Oliver J, Paquette AM, Pertesi M, Robinot N, Rosenthal JS, Vallee M, Voegele C, Hopper JL, Southey MC, Andrulis IL, John EM, Hashibe M, Gertz J, Le Calvez-Kelm F, Lesueur F, Goldgar DE, Tavtigian SV. Multigene testing of moderate-risk genes: be mindful of the missense. J Med Genet 2016; 53:366-76. [PMID: 26787654 PMCID: PMC4893078 DOI: 10.1136/jmedgenet-2015-103398] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 12/18/2015] [Indexed: 12/13/2022]
Abstract
BACKGROUND Moderate-risk genes have not been extensively studied, and missense substitutions in them are generally returned to patients as variants of uncertain significance lacking clearly defined risk estimates. The fraction of early-onset breast cancer cases carrying moderate-risk genotypes and quantitative methods for flagging variants for further analysis have not been established. METHODS We evaluated rare missense substitutions identified from a mutation screen of ATM, CHEK2, MRE11A, RAD50, NBN, RAD51, RINT1, XRCC2 and BARD1 in 1297 cases of early-onset breast cancer and 1121 controls via scores from Align-Grantham Variation Grantham Deviation (GVGD), combined annotation dependent depletion (CADD), multivariate analysis of protein polymorphism (MAPP) and PolyPhen-2. We also evaluated subjects by polygenotype from 18 breast cancer risk SNPs. From these analyses, we estimated the fraction of cases and controls that reach a breast cancer OR≥2.5 threshold. RESULTS Analysis of mutation screening data from the nine genes revealed that 7.5% of cases and 2.4% of controls were carriers of at least one rare variant with an average OR≥2.5. 2.1% of cases and 1.2% of controls had a polygenotype with an average OR≥2.5. CONCLUSIONS Among early-onset breast cancer cases, 9.6% had a genotype associated with an increased risk sufficient to affect clinical management recommendations. Over two-thirds of variants conferring this level of risk were rare missense substitutions in moderate-risk genes. Placement in the estimated OR≥2.5 group by at least two of these missense analysis programs should be used to prioritise variants for further study. Panel testing often creates more heat than light; quantitative approaches to variant prioritisation and classification may facilitate more efficient clinical classification of variants.
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Affiliation(s)
- E L Young
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, USA
| | - B J Feng
- Department of Dermatology, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, USA
| | - A W Stark
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, USA
| | - F Damiola
- Breast Cancer Genetics Group, Cancer Research Centre of Lyon, Centre Léon Bérard, Lyon, France
| | - G Durand
- Genetic Cancer Susceptibility group, International Agency for Research on Cancer, Lyon, France
| | - N Forey
- Genetic Cancer Susceptibility group, International Agency for Research on Cancer, Lyon, France
| | - T C Francy
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, USA
| | - A Gammon
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, USA
| | - W K Kohlmann
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, USA
| | - K A Kaphingst
- Department of Communication and Huntsman Cancer Institute, University of Utah
| | - S McKay-Chopin
- Genetic Cancer Susceptibility group, International Agency for Research on Cancer, Lyon, France
| | - T Nguyen-Dumont
- Genetic Epidemiology Laboratory, The University of Melbourne, Melbourne, Victoria, Australia
| | - J Oliver
- Instituto de Ciencias Básicas y Medicina Experimental del Hospital Italiano de Buenos Aires, Buenos Aires, Argentina
| | - A M Paquette
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, USA
| | - M Pertesi
- Genetic Cancer Susceptibility group, International Agency for Research on Cancer, Lyon, France
| | - N Robinot
- Genetic Cancer Susceptibility group, International Agency for Research on Cancer, Lyon, France
| | - J S Rosenthal
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, USA
| | - M Vallee
- Cancer Genomics Laboratory, CHUQ Research Center, Quebec City, Canada
| | - C Voegele
- Genetic Cancer Susceptibility group, International Agency for Research on Cancer, Lyon, France
| | - J L Hopper
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia Department of Epidemiology (Genome Epidemiology Lab), Seoul National University School of Public Health, Seoul, Korea
| | - M C Southey
- Department of Communication and Huntsman Cancer Institute, University of Utah
| | - I L Andrulis
- Department of Molecular Genetics, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - E M John
- Cancer Prevention Institute of California, Fremont, California, USA Department of Health Research and Policy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California, USA
| | - M Hashibe
- Department of Family and Preventive Medicine, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, USA
| | - J Gertz
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, USA
| | - F Le Calvez-Kelm
- Genetic Cancer Susceptibility group, International Agency for Research on Cancer, Lyon, France
| | - F Lesueur
- Genetic Epidemiology of Cancer Team, Inserm, U900, Institut Curie, Paris, France
| | - D E Goldgar
- Department of Dermatology, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, USA
| | - S V Tavtigian
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, USA
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29
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Amrani I, Bulatova N, Awidi A, Yousef AM, Melhem JM, Al-Masri M, Tahoun LA. Lack of Association between CYP1A1 M2 and M4 Polymorphisms and Breast Carcinoma in Jordanian Women: a Case-Control Study. Asian Pac J Cancer Prev 2016; 17:387-93. [DOI: 10.7314/apjcp.2016.17.1.387] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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30
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Fernandes GC, Michelli RAD, Scapulatempo-Neto C, Palmero EI. Association of polymorphisms with a family history of cancer and the presence of germline mutations in the BRCA1/BRCA2 genes. Hered Cancer Clin Pract 2016; 14:2. [PMID: 26770289 PMCID: PMC4712611 DOI: 10.1186/s13053-015-0042-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 12/04/2015] [Indexed: 11/10/2022] Open
Abstract
Introduction Breast cancer (BC) is an important public health problem worldwide. In Brazil, breast cancer is the most frequently diagnosed tumor and the leading cause of cancer death in women. Hereditary cancer represents approximately 5 to 10 % of BC cases. Even outside the hereditary cancer context, the presence of polymorphisms acting as genetic modifiers may contribute to a better or worse prognosis. Not much is known about the hereditary BC epidemiology in Brazil or about the influence of polymorphisms on hereditary predisposition. Objective This study examined the role of five different polymorphisms in four groups of women with BC: Group 1: women with a germline mutation in the BRCA1/2 genes; Group 2: women with variants of uncertain significance in BRCA1/2 and Group 3: women with no mutations in BRCA1/2. Patients and methods The women included in groups 1, 2 and 3 were patients from the Department of Oncogenetics of the Barretos Cancer Hospital who had undergone genetic testing because of a clinical suspicion of hereditary predisposition syndrome. The constitutive DNA was analyzed for the presence of polymorphisms at rs2981582 (FGFR2 gene); rs3803662 (TNRC9); rs889312 (MAP3K1); rs3817198 (LSP1 gene); and rs13281615 (8q24). The analyses were performed using PCR amplification and bi-directional sequencing. Results No differences were identified in the frequency of the polymorphisms that were analyzed among the three groups. However, some associations were identified, such as the occurrence of bilateral breast cancer and homozygosity for the G allele in rs13281615 as well as the correlation between the SNPs rs2981582 and rs13281615 and the number of cancer cases in the family. Regarding the G allele of rs13281615, we observed that the proportion of individuals who were homozygous for this allele increased with the number of generations affected by cancer, regardless of the group where the patients were included. Concerning the rs2981582 we could observe that individuals from group 1 and homozygous CC had fewer cancer (and also fewer breast cancer) cases. Regarding the hormone receptors, we observed an increased frequency in C homozygotes (rs3803662) among estrogen receptor-negative individuals from groups 1 and 3. For rs2981582 (FGFR2), we observed an increased frequency of the T allele in women who were positive for the estrogen and progesterone receptors regardless of the BRCA1/2 mutational status (p = 0.020 and p = 0.014, respectively). Conclusion The results presented here provide interesting data on the modifying effect of polymorphisms on a family history of cancer; this may be a variable to consider in the analysis of tumor diversity, and of the family history observed in families with hereditary breast cancer (even in those harboring the same type of genetic alteration). Electronic supplementary material The online version of this article (doi:10.1186/s13053-015-0042-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gabriela C Fernandes
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil ; Post-Graduate Program in Oncology, Barretos Cancer Hospital, Barretos, Brazil
| | | | - Cristovam Scapulatempo-Neto
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil ; Post-Graduate Program in Oncology, Barretos Cancer Hospital, Barretos, Brazil ; Pathology Department, Barretos Cancer Hospital, Barretos, Brazil
| | - Edenir I Palmero
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil ; Post-Graduate Program in Oncology, Barretos Cancer Hospital, Barretos, Brazil ; Oncogenetics Department, Barretos Cancer Hospital, Barretos, Brazil ; Barretos School of Health Sciences, Dr. Paulo Prata - FACISB, Barretos, Brazil
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Variants of FGFR2 and their associations with breast cancer risk: a HUGE systematic review and meta-analysis. Breast Cancer Res Treat 2016; 155:313-35. [PMID: 26728143 DOI: 10.1007/s10549-015-3670-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 12/25/2015] [Indexed: 10/22/2022]
Abstract
Extensive epidemiological studies have demonstrated that there are associations between variants in intron 2 of FGFR2 and the breast cancer risk in various populations; however, the relationships are not yet conclusively established. To comprehensively review the epidemiological studies showing associations between the variants of FGFR2 and the breast cancer risk, and to establish correlations via a meta-analysis. The PubMed and MEDLINE databases were searched for eligible studies. The associations between the variants and breast cancer risk were evaluated using a random-effects model. The heterogeneity among the studies and the potential publication bias were also evaluated. Fifty-three studies with a total of 121,740 cases and 198,549 controls have examined the associations between 23 variants in intron 2 of FGFR2 and the breast cancer risk. The relationships for the 10 most frequently evaluated variants-rs1078806, rs11200014, rs1219648, rs2420946, rs2981578, rs2981579, rs2981582, rs3135718, rs10736303, and rs3750817-were synthesized based on a meta-analysis. Interestingly, we found that all 10 variants were significantly associated with the risk of breast cancer. In studies stratified by ethnicity, we found that the associations were more notable in Caucasians and Asians compared to Africans. Similar pooled results were found in population-based and hospital-based case-control studies and in studies with small and large sample sizes. FGFR2 is a breast cancer susceptibility gene, and various variants of FGFR2 are significantly associated with the breast cancer risk. However, the biological mechanisms underlying the associations need to be elucidated in future studies.
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32
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Association of three SNPs in TOX3 and breast cancer risk: Evidence from 97275 cases and 128686 controls. Sci Rep 2015; 5:12773. [PMID: 26239137 PMCID: PMC4523945 DOI: 10.1038/srep12773] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 07/09/2015] [Indexed: 11/21/2022] Open
Abstract
The associations of SNPs in TOX3 gene with breast cancer risk were investigated by some Genome-wide association studies and epidemiological studies, but the study results were contradictory. To derive a more precise estimate of the associations, we conducted a meta-analysis. ORs with 95% CI were used to assess the strength of association between TOX3 polymorphisms and breast cancer risk in fixed or random effect model. A total of 37 publications with 97275 cases and 128686 controls were identified. We observed that the rs3803662 C > T, rs12443621 A > G and rs8051542 C > T were all correlated with increased risk of breast cancer. In the stratified analyses by ethnicity, significantly elevated risk was detected for all genetic models of the three SNPs in Caucasians. In Asian populations, there were significant associations of rs3803662 and rs8051542 with breast cancer risk. Whereas there was no evidence for statistical significant association between the three SNPs and breast cancer risk in Africans. Additionally, we observed different associations of rs3803662 with breast cancer risk based on different ER subtype and BRCA1/BRCA2 mutation carriers. In conclusion, the meta-analysis suggested that three SNPs in TOX3 were significantly associated with breast cancer risk in different populations.
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Siegert S, Wolf A, Cooper DN, Krawczak M, Nothnagel M. Mutations Causing Complex Disease May under Certain Circumstances Be Protective in an Epidemiological Sense. PLoS One 2015; 10:e0132150. [PMID: 26161957 PMCID: PMC4498598 DOI: 10.1371/journal.pone.0132150] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 06/10/2015] [Indexed: 01/19/2023] Open
Abstract
Guided by the practice of classical epidemiology, research into the genetic basis of complex disease has usually taken for granted the dictum that causative mutations are invariably over-represented among clinically affected as compared to unaffected individuals. However, we show that this supposition is not true and that a mutation contributing to the etiology of a complex disease can, under certain circumstances, be depleted among patients. Populations with defined disease prevalence were repeatedly simulated under a Wright-Fisher model, assuming various types of population history and genotype-phenotype relationship. For each simulation, the resulting mutation-specific population frequencies and odds ratios (ORs) were evaluated. In addition, the relationship between mutation frequency and OR was studied using real data from the NIH GWAS catalogue of reported phenotype associations of single-nucleotide polymorphisms (SNPs). While rare diseases (prevalence <1%) were found to be consistently caused by rare mutations with ORs>1, up to 20% of mutations causing a pandemic disease (prevalence 10-20%) had ORs<1, and their population frequency ranged from 0% to 100%. Moreover, simulation-based ORs exhibited a wide distribution, irrespective of mutation frequency. In conclusion, a substantial proportion of mutations causing common complex diseases may appear 'protective' in genetic epidemiological studies and hence would normally tend to be excluded, albeit erroneously, from further study. This apparently paradoxical result is explicable in terms of mutual confounding of the respective genotype-phenotype relationships due to a negative correlation between causal mutations induced by their common gene genealogy. As would be predicted by our findings, a significant negative correlation became apparent in published genome-wide association studies between the OR of genetic variants associated with a particular disease and the prevalence of that disease.
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Affiliation(s)
- Sabine Siegert
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
- Institute of Epidemiology, Christian-Albrechts University, Kiel, Germany
| | - Andreas Wolf
- Institute of Medical Informatics and Statistics, Christian-Albrechts University, Kiel, Germany
| | - David N. Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Michael Krawczak
- Institute of Medical Informatics and Statistics, Christian-Albrechts University, Kiel, Germany
| | - Michael Nothnagel
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
- Institute of Medical Informatics and Statistics, Christian-Albrechts University, Kiel, Germany
- * E-mail:
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Keller BM, McCarthy AM, Chen J, Armstrong K, Conant EF, Domchek SM, Kontos D. Associations between breast density and a panel of single nucleotide polymorphisms linked to breast cancer risk: a cohort study with digital mammography. BMC Cancer 2015; 15:143. [PMID: 25881232 PMCID: PMC4365961 DOI: 10.1186/s12885-015-1159-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 03/04/2015] [Indexed: 12/16/2022] Open
Abstract
Background Breast density and single-nucleotide polymorphisms (SNPs) have both been associated with breast cancer risk. To determine the extent to which these two breast cancer risk factors are associated, we investigate the association between a panel of validated SNPs related to breast cancer and quantitative measures of mammographic density in a cohort of Caucasian and African-American women. Methods In this IRB-approved, HIPAA-compliant study, we analyzed a screening population of 639 women (250 African American and 389 Caucasian) who were tested with a validated panel assay of 12 SNPs previously associated to breast cancer risk. Each woman underwent digital mammography as part of routine screening and all were interpreted as negative. Both absolute and percent estimates of area and volumetric density were quantified on a per-woman basis using validated software. Associations between the number of risk alleles in each SNP and the density measures were assessed through a race-stratified linear regression analysis, adjusted for age, BMI, and Gail lifetime risk. Results The majority of SNPs were not found to be associated with any measure of breast density. SNP rs3817198 (in LSP1) was significantly associated with both absolute area (p = 0.004) and volumetric (p = 0.019) breast density in Caucasian women. In African-American women, SNPs rs3803662 (in TNRC9/TOX3) and rs4973768 (in NEK10) were significantly associated with absolute (p = 0.042) and percent (p = 0.028) volume density respectively. Conclusions The majority of SNPs investigated in our study were not found to be significantly associated with breast density, even when accounting for age, BMI, and Gail risk, suggesting that these two different risk factors contain potentially independent information regarding a woman’s risk to develop breast cancer. Additionally, the few statistically significant associations between breast density and SNPs were different for Caucasian versus African American women. Larger prospective studies are warranted to validate our findings and determine potential implications for breast cancer risk assessment. Electronic supplementary material The online version of this article (doi:10.1186/s12885-015-1159-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Brad M Keller
- Department of Radiology, University of Pennsylvania Perelman School of Medicine, 3600 Market St. Ste 360, Philadelphia, PA, 19104, USA.
| | - Anne Marie McCarthy
- Department of Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA.
| | - Jinbo Chen
- Department of Biostatistics and Epidemiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA.
| | - Katrina Armstrong
- Department of Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA.
| | - Emily F Conant
- Department of Radiology, University of Pennsylvania Perelman School of Medicine, 3600 Market St. Ste 360, Philadelphia, PA, 19104, USA.
| | - Susan M Domchek
- Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA.
| | - Despina Kontos
- Department of Radiology, University of Pennsylvania Perelman School of Medicine, 3600 Market St. Ste 360, Philadelphia, PA, 19104, USA.
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Sighoko D, Ogundiran T, Ademola A, Adebamowo C, Chen L, Odedina S, Anetor I, Ndom P, Gakwaya A, Ojengbede O, Huo D, Olopade OI. Breast cancer risk after full-term pregnancies among African women from Nigeria, Cameroon, and Uganda. Cancer 2015; 121:2237-43. [PMID: 25781581 PMCID: PMC4573769 DOI: 10.1002/cncr.29305] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Revised: 12/22/2014] [Accepted: 12/23/2014] [Indexed: 12/22/2022]
Abstract
BACKGROUND The breast cancer (BC) risk profiles of African women differ significantly from those of women of European ancestry. African women are younger at the age of onset and tend to have high parity. The purpose of this study was to examine the relationship between full‐term pregnancy (FTP) and the risk of BC. METHODS A case‐control study was conducted among 1995 women with invasive BC and 2631 controls in Nigeria, Cameroon, and Uganda. Odds ratios (ORs) for individual ages at FTP according to the time since delivery were calculated and adjusted for confounders. A fitted spline model was used to assess the impact of the number of pregnancies on BC risk. RESULTS In comparison with a nulliparous woman, a parous woman with her first FTP at 20 years showed an OR of 0.76 (95% confidence interval [CI], 0.57‐0.99) for developing BC in the following 5 years. Ten years later, this risk was 0.76 (95% CI, 0.58‐0.99) and 0.76 (95% CI, 0.58‐0.98) for women aged 25 and 30 years, respectively. Similarly, a parous woman with 1 pregnancy had an OR of 0.69 (95% CI, 0.49‐0.96), whereas the OR was 0.66 (95% CI, 0.48‐0.91) with 2 or 5 pregnancies and 0.67 (95% CI, 0.47‐0.94) with 6 pregnancies in comparison with nulliparous women. CONCLUSIONS In contrast to studies in women of European ancestry, this study showed no transient increase in the risk of developing BC after FTP among African women. Further studies are needed to examine the impact of reproductive factors on early‐onset BC in African women. Cancer 2015;121:2237–2243. © 2015 American Cancer Society. There is no transient increase in breast cancer risk after a full‐term pregnancy among African women. The protection conferred by pregnancy occurs immediately after the first full‐term pregnancy regardless of the age at that pregnancy and the number of pregnancies.
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Affiliation(s)
- Dominique Sighoko
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, University of Chicago, Chicago, Illinois
| | - Temidayo Ogundiran
- Department of Surgery, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Adeyinka Ademola
- Department of Surgery, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Clement Adebamowo
- Department of Epidemiology and Preventive Medicine, Institute of Human Virology and Greenebaum Cancer Center, University of Maryland, Baltimore, Maryland.,Institute of Human Virology, Abuja, Nigeria
| | - Lin Chen
- Department of Public Health Sciences, University of Chicago, Chicago, Illinois
| | - Stella Odedina
- Center for Population and Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Imaria Anetor
- Center for Population and Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Paul Ndom
- Yaounde General Hospital, Yaounde, Cameroon
| | | | - Oladosu Ojengbede
- Center for Population and Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Dezheng Huo
- Department of Public Health Sciences, University of Chicago, Chicago, Illinois
| | - Olufunmilayo I Olopade
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, University of Chicago, Chicago, Illinois
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McCarthy AM, Keller B, Kontos D, Boghossian L, McGuire E, Bristol M, Chen J, Domchek S, Armstrong K. The use of the Gail model, body mass index and SNPs to predict breast cancer among women with abnormal (BI-RADS 4) mammograms. Breast Cancer Res 2015; 17:1. [PMID: 25567532 PMCID: PMC4311477 DOI: 10.1186/s13058-014-0509-4] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 12/18/2014] [Indexed: 11/10/2022] Open
Abstract
Introduction Mammography screening results in a significant number of false-positives. The use of pretest breast cancer risk factors to guide follow-up of abnormal mammograms could improve the positive predictive value of screening. We evaluated the use of the Gail model, body mass index (BMI), and genetic markers to predict cancer diagnosis among women with abnormal mammograms. We also examined the extent to which pretest risk factors could reclassify women without cancer below the biopsy threshold. Methods We recruited a prospective cohort of women referred for biopsy with abnormal (BI-RADS 4) mammograms according to the American College of Radiology’s Breast Imaging-Reporting and Data System (BI-RADS). Breast cancer risk factors were assessed prior to biopsy. A validated panel of 12 single-nucleotide polymorphisms (SNPs) associated with breast cancer were measured. Logistic regression was used to assess the association of Gail risk factors, BMI and SNPs with cancer diagnosis (invasive or ductal carcinoma in situ). Model discrimination was assessed using the area under the receiver operating characteristic curve, and calibration was assessed using the Hosmer-Lemeshow goodness-of-fit test. The distribution of predicted probabilities of a cancer diagnosis were compared for women with or without breast cancer. Results In the multivariate model, age (odds ratio (OR) = 1.05; 95% confidence interval (CI), 1.03 to 1.08; P < 0.001), SNP panel relative risk (OR = 2.30; 95% CI, 1.06 to 4.99, P = 0.035) and BMI (≥30 kg/m2 versus <25 kg/m2; OR = 2.20; 95% CI, 1.05 to 4.58; P = 0.036) were significantly associated with breast cancer diagnosis. Older women were more likely than younger women to be diagnosed with breast cancer. The SNP panel relative risk remained strongly associated with breast cancer diagnosis after multivariable adjustment. Higher BMI was also strongly associated with increased odds of a breast cancer diagnosis. Obese women (OR = 2.20; 95% CI, 1.05 to 4.58; P = 0.036) had more than twice the odds of cancer diagnosis compared to women with a BMI <25 kg/m2. The SNP panel appeared to have predictive ability among both white and black women. Conclusions Breast cancer risk factors, including BMI and genetic markers, are predictive of cancer diagnosis among women with BI-RADS 4 mammograms. Using pretest risk factors to guide follow-up of abnormal mammograms could reduce the burden of false-positive mammograms. Electronic supplementary material The online version of this article (doi:10.1186/s13058-014-0509-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anne Marie McCarthy
- Department of Medicine, Massachusetts General Hospital, 50 Staniford Street, 940F, Boston, MA, 02114, USA.
| | - Brad Keller
- Department of Radiology, University of Pennsylvania, Philadelphia, PA, USA.
| | - Despina Kontos
- Department of Radiology, University of Pennsylvania, Philadelphia, PA, USA.
| | - Leigh Boghossian
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA.
| | - Erin McGuire
- Department of General Internal Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Mirar Bristol
- Department of Medicine, Massachusetts General Hospital, 50 Staniford Street, 940F, Boston, MA, 02114, USA.
| | - Jinbo Chen
- Department of Clinical Epidemiology and Biostatistics, University of Pennsylvania, Philadelphia, PA, USA.
| | - Susan Domchek
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA.
| | - Katrina Armstrong
- Department of Medicine, Massachusetts General Hospital, 50 Staniford Street, 940F, Boston, MA, 02114, USA.
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A study on genetic variants of Fibroblast growth factor receptor 2 (FGFR2) and the risk of breast cancer from North India. PLoS One 2014; 9:e110426. [PMID: 25333473 PMCID: PMC4204868 DOI: 10.1371/journal.pone.0110426] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 09/04/2014] [Indexed: 12/29/2022] Open
Abstract
Genome-Wide Association Studies (GWAS) have identified Fibroblast growth factor receptor 2 (FGFR2) as a candidate gene for breast cancer with single nucleotide polymorphisms (SNPs) located in intron 2 region as the susceptibility loci strongly associated with the risk. However, replicate studies have often failed to extrapolate the association to diverse ethnic regions. This hints towards the existing heterogeneity among different populations, arising due to differential linkage disequilibrium (LD) structures and frequencies of SNPs within the associated regions of the genome. It is therefore important to revisit the previously linked candidates in varied population groups to unravel the extent of heterogeneity. In an attempt to investigate the role of FGFR2 polymorphisms in susceptibility to the risk of breast cancer among North Indian women, we genotyped rs2981582, rs1219648, rs2981578 and rs7895676 polymorphisms in 368 breast cancer patients and 484 healthy controls by Polymerase chain reaction-Restriction fragment length polymorphism (PCR-RFLP) assay. We observed a statistically significant association with breast cancer risk for all the four genetic variants (P<0.05). In per-allele model for rs2981582, rs1219648, rs7895676 and in dominant model for rs2981578, association remained significant after bonferroni correction (P<0.0125). On performing stratified analysis, significant correlations with various clinicopathological as well as environmental and lifestyle characteristics were observed. It was evident that rs1219648 and rs2981578 interacted with exogenous hormone use and advanced clinical stage III (after Bonferroni correction, P<0.000694), respectively. Furthermore, combined analysis on these four loci revealed that compared to women with 0–1 risk loci, those with 2–4 risk loci had increased risk (OR = 1.645, 95%CI = 1.152–2.347, P = 0.006). In haplotype analysis, for rs2981578, rs2981582 and rs1219648, risk haplotype (GTG) was associated with a significantly increased risk compared to the common (ACA) haplotype (OR = 1.365, 95% CI = 1.086–1.717, P = 0.008). Our results suggest that intron 2 SNPs of FGFR2 may contribute to genetic susceptibility of breast cancer in North India population.
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Association of genetic variants at TOX3, 2q35 and 8q24 with the risk of familial and early-onset breast cancer in a South-American population. Mol Biol Rep 2014; 41:3715-22. [PMID: 24532140 DOI: 10.1007/s11033-014-3236-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 02/06/2014] [Indexed: 10/25/2022]
Abstract
Recent Genome-Wide Association Studies have identified several single nucleotide polymorphisms (SNPs) associated with breast cancer (BC) among women of Asian, European, and African-American ancestry. Nevertheless, the contribution of these variants in the South American population is unknown. Furthermore, there is little information about the effect of these risk alleles in women with early BC diagnosis. In the present study, we evaluated the association between rs3803662 (TOX3, also known as TNRC9), rs13387042 (2q35), and rs13281615 (8q24) with BC risk in 344 Chilean BRCA1/2-negative BC cases and in 801 controls. Two SNPs, rs3803662 and rs13387042, were significantly associated with increased BC risk in familial BC and in non-familial early-onset BC. The risk of BC increased in a dose-dependent manner with the number of risk alleles (P-trend < 0.0001 and 0.0091, respectively). The odds ratios for BC in familial BC and in early-onset non-familial BC were 3.76 (95%CI 1.02-13.84, P = 0.046) and 8.0 (95%CI 2.20-29.04, P = 0.002), respectively, for the maximum versus minimum number of risk alleles. These results indicate an additive effect of the TOX3 rs3803662 and 2q35 rs13387042 alleles for BC risk. We also evaluated the interaction between rs3803662 and rs13387042 SNPs. We observed an additive interaction only in non-familial early-onset BC cases (AP = 0.72 (0.28-1.16), P = 0.001). No significant association was observed for rs13281615 (8q24) with BC risk in women from the Chilean population. The strongly increased risk associated with the combination of low-penetrance risk alleles supports the polygenic inheritance model of BC.
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O'Brien KM, Cole SR, Poole C, Bensen JT, Herring AH, Engel LS, Millikan RC. Replication of breast cancer susceptibility loci in whites and African Americans using a Bayesian approach. Am J Epidemiol 2014; 179:382-94. [PMID: 24218030 DOI: 10.1093/aje/kwt258] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Genome-wide association studies (GWAS) and candidate gene analyses have led to the discovery of several dozen genetic polymorphisms associated with breast cancer susceptibility, many of which are considered well-established risk factors for the disease. Despite attempts to replicate these same variant-disease associations in African Americans, the evaluable populations are often too small to produce precise or consistent results. We estimated the associations between 83 previously identified single nucleotide polymorphisms (SNPs) and breast cancer among Carolina Breast Cancer Study (1993-2001) participants using maximum likelihood, Bayesian, and hierarchical methods. The selected SNPs were previous GWAS hits (n = 22), near-hits (n = 19), otherwise well-established risk loci (n = 5), or located in the same genes as selected variants (n = 37). We successfully replicated 18 GWAS-identified SNPs in whites (n = 2,352) and 10 in African Americans (n = 1,447). SNPs in the fibroblast growth factor receptor 2 gene (FGFR2) and the TOC high mobility group box family member 3 gene (TOX3) were strongly associated with breast cancer in both races. SNPs in the mitochondrial ribosomal protein S30 gene (MRPS30), mitogen-activated protein kinase kinase kinase 1 gene (MAP3K1), zinc finger, MIZ-type containing 1 gene (ZMIZ1), and H19, imprinted maternally expressed transcript gene (H19) were associated with breast cancer in whites, and SNPs in the estrogen receptor 1 gene (ESR1) and H19 gene were associated with breast cancer in African Americans. We provide precise and well-informed race-stratified odds ratios for key breast cancer-related SNPs. Our results demonstrate the utility of Bayesian methods in genetic epidemiology and provide support for their application in small, etiologically driven investigations.
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Maxwell KN, Nathanson KL. Common breast cancer risk variants in the post-COGS era: a comprehensive review. Breast Cancer Res 2013; 15:212. [PMID: 24359602 PMCID: PMC3978855 DOI: 10.1186/bcr3591] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Breast cancer has a strong heritable component, with approximately 15% of cases exhibiting a family history of the disease. Mutations in genes such as BRCA1, BRCA2 and TP53 lead to autosomal dominant inherited cancer susceptibility and confer a high lifetime risk of breast cancers. Identification of mutations in these genes through clinical genetic testing enables patients to undergo screening and prevention strategies, some of which provide overall survival benefit. In addition, a number of mutant alleles have been identified in genes such as CHEK2, PALB2, ATM and BRIP1, which often display incomplete penetrance and confer moderate lifetime risks of breast cancer. Studies are underway to determine how to use the identification of mutations in these genes to guide clinical practice. Altogether, however, mutations in high and moderate penetrance genes probably account for approximately 25% of familial breast cancer risk; the remainder may be due to mutations in as yet unidentified genes or lower penetrance variants. Common low penetrance alleles, which have been mainly identified through genome-wide association studies (GWAS), are generally present at 10 to 50% population frequencies and confer less than 1.5-fold increases in breast cancer risk. A number of single nucleotide polymorphisms (SNPs) have been identified and risk associations extensively replicated in populations of European ancestry, the number of which has substantially increased as a result of GWAS performed by the Collaborative Oncological Gene–environment Study consortium. It is now estimated that 28% of familial breast cancer risk is explained by common breast cancer susceptibility loci. In some cases, SNP associations may be specific to different subsets of women with breast cancer, as defined by ethnicity or estrogen receptor status. Although not yet clinically established, it is hoped that identification of common risk variants may eventually allow identification of women at higher risk of breast cancer and enable implementation of breast cancer screening, prevention or treatment strategies that provide clinical benefit.
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A collaborative study of the etiology of breast cancer subtypes in African American women: the AMBER consortium. Cancer Causes Control 2013; 25:309-19. [PMID: 24343304 DOI: 10.1007/s10552-013-0332-8] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Accepted: 12/06/2013] [Indexed: 12/16/2022]
Abstract
PURPOSE Breast cancer is a heterogeneous disease, with at least five intrinsic subtypes defined by molecular characteristics. Tumors that express the estrogen receptor (ER+) have better outcomes than ER- tumors, due in part to the success of hormonal therapies that target ER+ tumors. The incidence of ER- breast cancer, and the subset of ER- cancers that are basal-like, is about twice as high among African American (AA) women as among US women of European descent (EA). This disparity appears to explain, in part, the disproportionately high mortality from breast cancer that occurs in AA women. Epidemiologic research on breast cancer in AA women lags behind research in EA women. Here, we review differences in the etiology of breast cancer subtypes among AA women and describe a new consortium of ongoing studies of breast cancer in AA women. METHODS We combined samples and data from four large epidemiologic studies of breast cancer in AA women, two cohort and two case-control, creating the African American Breast Cancer Epidemiology and Risk consortium. Tumor tissue is obtained and stored in tissue microarrays, with assays of molecular markers carried out at a pathology core. Genotyping, carried out centrally, includes a whole exome SNP array and over 180,000 custom SNPs for fine-mapping of genome-wide association studies loci and candidate pathways. RESULTS To date, questionnaire data from 5,739 breast cancer cases and 14,273 controls have been harmonized. Genotyping of the first 3,200 cases and 3,700 controls is underway, with a total of 6,000 each expected by the end of the study period. CONCLUSIONS The new consortium will likely have sufficient statistical power to assess potential risk factors, both genetic and non-genetic, in relation to specific subtypes of breast cancer in AA women.
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Wang X, Zhang L, Chen Z, Ma Y, Zhao Y, Rewuti A, Zhang F, Fu D, Han Y. Association between 5p12 genomic markers and breast cancer susceptibility: evidence from 19 case-control studies. PLoS One 2013; 8:e73611. [PMID: 24039999 PMCID: PMC3765311 DOI: 10.1371/journal.pone.0073611] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2013] [Accepted: 07/20/2013] [Indexed: 11/19/2022] Open
Abstract
Background The association between polymorphisms on 5p12 and breast cancer (BC) has been widely evaluated since it was first identified through genome-wide association approach; however, the studies have yielded contradictory results. We sought to investigate this inconsistency by performing a comprehensive meta-analysis on two wildly studied polymorphisms (rs10941679 and rs4415084) on 5p12. Methods Databases including Pubmed, EMBASE, Web of Science, EBSCO, and Cochrane Library databases were searched to find relevant studies. Odds ratios (ORs) with 95% confidence intervals (CIs) were used to assess the strength of association. The random-effects model was applied, addressing heterogeneity and publication bias. Results A total of 19 articles involving 100,083 cases and 163,894 controls were included. An overall random-effects per-allele OR of 1.09 (95% CI: 1.06–1.12; P = 4.5×10−8) and 1.09 (95% CI: 1.05–1.12; P = 4.2×10−7) was found for the rs10941679 and rs4415084 polymorphism respectively. Significant results were found in Asians and Caucasians when stratified by ethnicity; whereas no significant associations were found among Africans/African-Americans. Similar results were also observed using dominant or recessive genetic models. In addition, we find both rs4415084 and rs10941679 conferred significantly greater risks of ER-positive breast cancer than of ER-negative tumors. Conclusions Our findings demonstrated that rs10941679-G allele and rs4415084-T allele might be risk-conferring factors for the development of breast cancer, especially in Caucasians and East-Asians.
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Affiliation(s)
- Xiaofeng Wang
- Department of Orthopedics Surgery, Zhongshan Hospital, Fudan University, Shanghai, People's Republic of China
| | - Liang Zhang
- Department of Orthopedics Surgery, Zhongshan Hospital, Fudan University, Shanghai, People's Republic of China
| | - Zixian Chen
- Department of Orthopedics Surgery, Zhongshan Hospital, Fudan University, Shanghai, People's Republic of China
| | - Yushui Ma
- Department of Orthopedics Surgery, Zhongshan Hospital, Fudan University, Shanghai, People's Republic of China
| | - Yuan Zhao
- Department of Gastroenterology, Zhongshan Hospital, Fudan University, Shanghai, People's Republic of China
| | - Abudouaini Rewuti
- Department of Orthopedics Surgery, Zhongshan Hospital, Fudan University, Shanghai, People's Republic of China
| | - Feng Zhang
- Department of Orthopedics Surgery, Zhongshan Hospital, Fudan University, Shanghai, People's Republic of China
| | - Da Fu
- Department of Orthopedics Surgery, Zhongshan Hospital, Fudan University, Shanghai, People's Republic of China
- * E-mail: (DF); (YSH)
| | - Yusong Han
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, People's Republic of China
- * E-mail: (DF); (YSH)
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Yu Y, Chen Z, Wang H, Zhang Y. Quantitative assessment of common genetic variants on chromosome 5p12 and hormone receptor status with breast cancer risk. PLoS One 2013; 8:e72154. [PMID: 23977236 PMCID: PMC3747047 DOI: 10.1371/journal.pone.0072154] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2013] [Accepted: 07/06/2013] [Indexed: 12/14/2022] Open
Abstract
Several genome-wide association studies on breast cancer (BC) have reported similar findings of a new susceptibility locus, 5p12. After that, a number of studies reported that the rs10941679, rs4415084, and rs981782 polymorphism in chromosome 5p12 has been implicated in BC risk. However, the studies have yielded contradictory results. To derive a more precise estimation of the relationship, a meta-analysis of 131,983 BC cases and 200,314 controls from 24 published case-control studies was performed. Overall, significantly elevated BC risk was associated with rs10941679, rs4415084, and rs981782 risk allele when all studies were pooled into the meta-analysis. In the subgroup analysis by ethnicity, significantly increased risks were found for the rs10941679 and rs4415084 polymorphism among Caucasians and East Asians, while no significant associations were observed for the two polymorphisms in African and other ethnic populations. For 5p12-rs981782, significant associations were only detected among Caucasians. In addition, we found that rs10941679 and rs4415084 on 5p12 confer risk, exclusively for estrogen receptor (ER)-positive tumors with per-allele OR of 1.16 (95% CI: 1.11-1.21; P<10(-5)) and of 1.14 (95% CI: 1.09-1.19; P<10(-5)) respectively. Ethnicity was identified as a potential source of between-study heterogeneity. In conclusion, this meta-analysis demonstrated that common variations are a risk factor associated with increased BC susceptibility, but these associations vary in different ethnic populations.
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Affiliation(s)
- Yanmin Yu
- Department of Breast Surgery, Huangpu Central Hospital of Shanghai, Shanghai, People’s Republic of China
| | - Zenggan Chen
- Department of Orthopedics, Zhongshan Hospital, Fudan University, Shanghai, People’s Republic of China
| | - Hong Wang
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, People’s Republic of China
- * E-mail: (HW); (YZ)
| | - Yan Zhang
- Department of Radiology, Huangpu Central Hospital of Shanghai, Shanghai, People’s Republic of China
- * E-mail: (HW); (YZ)
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Huang T, Hong J, Lin W, Yang Q, Ni K, Wu Q, Sun J. Assessing interactions between common genetic variant on 2q35 and hormone receptor status with breast cancer risk: evidence based on 26 studies. PLoS One 2013; 8:e69056. [PMID: 23976942 PMCID: PMC3745398 DOI: 10.1371/journal.pone.0069056] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2013] [Accepted: 06/04/2013] [Indexed: 01/17/2023] Open
Abstract
Genome-wide association studies have identified 2q35-rs13387042 as a new breast cancer (BC) susceptibility locus in populations of European descent. Since then, the relationship between 2q35-rs13387042 and breast cancer has been reported in various ethnic groups; however, these studies have yielded inconsistent results. To investigate this inconsistency, we performed a meta-analysis of 26 studies involving a total of 101,529 cases and 167,363 controls for 2q35-rs13387042 polymorphism to evaluate its effect on genetic susceptibility for breast cancer. An overall random effects odds ratio of 1.14 (95% CI: 1.11-1.16, P<10⁻⁵) was found for rs13387042-A variant. Significant results were also observed using dominant (OR = 1.14, 95% CI: 1.12-1.17, P<10⁻⁵), recessive (OR = 1.17, 95% CI: 1.13-1.21, P<10⁻⁵) and co-dominant genetic model (heterozygous: OR = 1.15, 95% CI: 1.12-1.19, P<10⁻⁵; homozygous: OR = 1.20, 95% CI: 1.15-1.24, P<10⁻⁵). There was strong evidence of heterogeneity, which largely disappeared after stratification by ethnicity. Significant associations were found in East Asians, and White populations when stratified by ethnicity; while no significant associations were observed in Africans and other ethnic populations. An association was observed for both ER-positive (OR = 1.17, 95% 1.15-1.19; P<10⁻⁵) and ER-negative disease (OR = 1.08, 95% CI: 1.04-1.13; P<10⁻⁴) and both progesterone receptor (PR)-positive (OR = 1.18, 95% CI: 1.15-1.21; P<10⁻⁵) and PR-negative disease (OR = 1.10, 95% CI: 1.05-1.15; P<10⁻⁴). In conclusion, this meta-analysis demonstrated that the A allele of 2q35-rs13387042 is a risk factor associated with increased breast cancer susceptibility.
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Affiliation(s)
- Tao Huang
- Department of General Surgery, Shanghai Eighth People's Hospital, Shanghai, People's Republic of China
| | - Jun Hong
- Department of General Surgery, Shanghai Putuo District Center Hospital, Shanghai, People's Republic of China
| | - Wanlong Lin
- Department of Oncology, Shanghai Zhabei District Shibei Hospital, Shanghai, People's Republic of China
| | - Qungqing Yang
- Department of General Surgery, Shanghai Zhabei District Shibei Hospital, Shanghai, People's Republic of China
| | - Keliang Ni
- Department of General Surgery, Shanghai Zhabei District Shibei Hospital, Shanghai, People's Republic of China
| | - Qingyu Wu
- Department of General Surgery, Shanghai Zhabei District Shibei Hospital, Shanghai, People's Republic of China
- * E-mail: (QYW); (JS)
| | - Jie Sun
- Department of General Surgery, Shanghai Zhabei District Shibei Hospital, Shanghai, People's Republic of China
- * E-mail: (QYW); (JS)
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Assessing interactions between the association of common genetic variant at 1p11 (rs11249433) and hormone receptor status with breast cancer risk. PLoS One 2013; 8:e72487. [PMID: 23977306 PMCID: PMC3745461 DOI: 10.1371/journal.pone.0072487] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Accepted: 07/10/2013] [Indexed: 02/07/2023] Open
Abstract
Background The association between rs11249433 polymorphism on 1p11 and breast cancer (BC) has been widely evaluated since it was first identified through genome-wide association approach. However, the results have been inconclusive. To investigate this inconsistency, we performed a meta-analysis of all available studies dealing with the relationship between the 1p11-rs11249433 polymorphism and BC. Methods Databases including Pubmed, SCOPUS, ISI web of knowledge, Embase and Cochrane databases were searched to find relevant studies. Odds ratios (ORs) with 95% confidence intervals (CIs) were used to assess the strength of association. The random-effects model was applied, addressing heterogeneity and publication bias. Results A total of 15 articles involving 90,291 cases and 137,525 controls were included. In a combined analysis, the summary per-allele odds ratio (OR) for BC of 1p11-rs11249433 polymorphism was 1.09 (95% CI: 1.06–1.12; P<10−5). Significant associations were also observed under dominant and recessive genetic models. In the subgroup analysis by ethnicity, significantly increased risks were found in Caucasians; whereas no significant associations were found among Asians and Africans. In addition, our data indicate that 1p11-rs11249433 polymorphism is involved in BC susceptibility and confer its effect primarily in estrogen receptor-positive and progesterone receptor-positive tumors. Conclusions In conclusion, this meta-analysis demonstrated that the G allele of 1p11-rs11249433 is a risk factor associated with increased breast cancer susceptibility, but these associations vary in different ethnic populations.
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Wu S, Cai J, Wang H, Zhang H, Yang W. Association between 1p11-rs11249433 polymorphism and breast cancer susceptibility: evidence from 15 case-control studies. PLoS One 2013; 8:e72526. [PMID: 23977314 PMCID: PMC3744559 DOI: 10.1371/journal.pone.0072526] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Accepted: 07/15/2013] [Indexed: 01/10/2023] Open
Abstract
Genome-wide association studies have identified SNP rs11249433 at chromosome 1p11 as a new breast cancer (BC) susceptibility locus in populations of European descent. Since then, the relationship between 1p11- rs11249433 and breast cancer has been reported in various ethnic groups; however, these studies have yielded inconsistent results. To investigate this inconsistency, we performed a meta-analysis of 15 studies involving a total of 90,154 cases and 137,238 controls for 1p11-rs11249433 polymorphism to evaluate its effect on genetic susceptibility for breast cancer. An overall random effects odds ratio of 1.09 (95% CI: 1.06-1.12, P<10-5) was found for rs11249433-G variant. Significant results were also observed for heterozygous (OR=1.09, 95% CI: 1.05-1.12, P<10-5) and homozygote (OR=1.14, 95% CI: 1.08-1.21, P<10-5). There was strong evidence of heterogeneity, which largely disappeared after stratification by ethnicity. After stratified by ethnicity, significant associations were found among Caucasians. However, no significant associations were detected among East Asian and African populations. In addition, we found that rs11249433 polymorphism on 1p11 confer risk, exclusively for ER-positive tumors with per-allele OR of 1.13 (95% CI: 1.08-1.18; P <10-5) compared to ER-negative tumors of 1.01 (95% CI: 0.98-1.04; P=0.49). Similar results were also observed when stratified by PR status. Our findings demonstrated that rs11249433-G allele is a risk-conferring factor for the development of breast cancer, especially in Caucasians.
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Affiliation(s)
- Sheng Wu
- Department of General Surgery, Zhongshan Hospital, Qingpu Branch, Fudan University, Shanghai, People’s Republic of China
| | - Jungang Cai
- Department of General Surgery, Zhongshan Hospital, Qingpu Branch, Fudan University, Shanghai, People’s Republic of China
| | - Hong Wang
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, People’s Republic of China
- * E-mail: (HW); (HWZ)
| | - Hongwei Zhang
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, People’s Republic of China
- * E-mail: (HW); (HWZ)
| | - Weige Yang
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, People’s Republic of China
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Gu C, Zhou L, Yu J. Quantitative assessment of 2q35-rs13387042 polymorphism and hormone receptor status with breast cancer risk. PLoS One 2013; 8:e66979. [PMID: 23894282 PMCID: PMC3718795 DOI: 10.1371/journal.pone.0066979] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 05/15/2013] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The association between rs13387042 polymorphism on 2q35 and breast cancer (BC) has been widely evaluated since it was first identified through genome-wide association approach. However, the results have been inconclusive. To investigate this inconsistency, we performed a meta-analysis of all available studies dealing with the relationship between the 2q35-rs13387042 polymorphism and BC. METHODS Databases including MEDLINE, PubMed, EMBASE, ISI web of science and CNKI (China National Knowledge Infrastructure) were searched to find relevant studies. Odds ratios (ORs) with 95% confidence intervals (CIs) were used to assess the strength of association. The random-effects model was applied, addressing heterogeneity and publication bias. RESULTS A total of 24 articles involving 99,772 cases and 164,985 controls were included. In a combined analysis, the summary per-allele odds ratio (OR) for BC of 2q35-rs13387042 polymorphism was 1.13 (95% CI: 1.11-1.16; P<10(-5)). Significant associations were also detected under co-dominant, dominant and recessive genetic models. In the subgroup analysis by ethnicity, significantly increased risks were found in Asians, Caucasians and Hispanic whites for the polymorphism in all comparisons; whereas no significant associations were found among Africans. In addition, we find 2q35-rs13387042 polymorphism conferred significantly risks for both ER-positive and ER-negative tumors. Furthermore, significant associations were also detected both in PR-positive and PR-negative cancer. CONCLUSIONS Our findings demonstrated that rs13387042-A allele is a risk-conferring factors for the development of BC, especially in Asians, Caucasians and Hispanic whites.
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Affiliation(s)
- Chao Gu
- Department of General Surgery, Jinshan Hospital, Fudan University, Shanghai, People's Republic of China
| | - Liang Zhou
- Department of General Surgery, Jinshan Hospital, Fudan University, Shanghai, People's Republic of China
| | - Jianping Yu
- Department of General Surgery, Jinshan Hospital, Fudan University, Shanghai, People's Republic of China
- * E-mail:
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Shi J, Sung H, Zhang B, Lu W, Choi JY, Xiang YB, Kim MK, Iwasaki M, Long J, Ji BT, Park SK, Zheng Y, Tsugane S, Yoo KY, Wang W, Noh DY, Han W, Kim SW, Lee MH, Lee JW, Lee JY, Shen CY, Matsuo K, Ahn SH, Gao YT, Shu XO, Cai Q, Kang D, Zheng W. New breast cancer risk variant discovered at 10q25 in East Asian women. Cancer Epidemiol Biomarkers Prev 2013; 22:1297-303. [PMID: 23677579 PMCID: PMC3720126 DOI: 10.1158/1055-9965.epi-12-1393] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Recently, 41 new genetic susceptibility loci for breast cancer risk were identified in a genome-wide association study (GWAS) conducted in European descendants. Most of these risk variants have not been directly replicated in Asian populations. METHODS We evaluated nine of those nonreplication loci in East Asians to identify new risk variants for breast cancer in these regions. First, we analyzed single-nucleotide polymorphisms (SNP) in these regions using data from two GWAS conducted among Chinese and Korean women, including 5,083 cases and 4,376 controls (stage 1). In each region, we selected an SNP showing the strongest association with breast cancer risk for replication in an independent set of 7,294 cases and 9,404 controls of East Asian descents (stage 2). Logistic regression models were used to calculate adjusted ORs and 95% confidence intervals (CI) as a measure of the association of breast cancer risk and genetic variants. RESULTS Two SNPs were replicated in stage 2 at P < 0.05: rs1419026 at 6q14 [per allele OR, 1.07; 95% confidence interval (CI), 1.03-1.12; P = 3.0 × 10(-4)] and rs941827 at 10q25 (OR, 0.92, 95% CI, 0.89-0.96; P = 5.3 × 10(-5)). The association with rs941827 remained highly statistically significant after adjusting for the risk variant identified initially in women of European ancestry (OR, 0.88; 95% CI, 0.82-0.97; P = 5.3 × 10(-5)). CONCLUSION We identified a new breast cancer risk variant at 10q25 in East Asian women. IMPACT Results from this study improve the understanding of the genetic basis for breast cancer.
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Affiliation(s)
- Jiajun Shi
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Hyuna Sung
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea
| | - Ben Zhang
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Wei Lu
- Shanghai Center for Disease Control and Prevention, Shanghai, China
| | - Ji-Yeob Choi
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Yong-Bing Xiang
- Department of Epidemiology, Shanghai Cancer Institute, Shanghai, China
| | - Mi Kyung Kim
- Cancer Epidemiology Division, Breast Cancer Center, National Cancer Center, Korea
- Department of Surgery, College of Medicine, University of Ulsan, Asan Medical Center, Korea
| | - Motoki Iwasaki
- Epidemiology and Prevention Division, Research Center for Cancer Prevention and Screening, National Cancer Center, Tokyo, Japan
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Bu-Tian Ji
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Department of Health and Human Services, Bethesda, Maryland, USA
| | - Sue K. Park
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Ying Zheng
- Shanghai Center for Disease Control and Prevention, Shanghai, China
| | - Shoichiro Tsugane
- Epidemiology and Prevention Division, Research Center for Cancer Prevention and Screening, National Cancer Center, Tokyo, Japan
| | - Keun-Young Yoo
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Wenjing Wang
- Shanghai Center for Disease Control and Prevention, Shanghai, China
| | - Dong-Young Noh
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
- Department of Surgery, Seoul National University College of Medicine, Seoul, Korea
| | - Wonshik Han
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
- Department of Surgery, Seoul National University College of Medicine, Seoul, Korea
| | - Sung-Won Kim
- Department of Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea
| | - Min Hyuk Lee
- Department of Surgery, Soonchunhynag University Hospital, Korea
| | - Jong Won Lee
- Department of Surgery, University of Ulsan College of Medicine and Asan Medical Center, Seoul, Korea
| | - Jong-Young Lee
- Center for Genome Science, Korea National Institute of Health, Osong Health Technology Administration Complex, Chungcheongbuk-do, Korea
| | - Chen-Yang Shen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
- College of Public Health, China Medical University, Taichung, Taiwan
| | - Keitaro Matsuo
- Division of Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Sei-Hyun Ahn
- Cancer Epidemiology Division, Breast Cancer Center, National Cancer Center, Korea
- Department of Surgery, College of Medicine, University of Ulsan, Asan Medical Center, Korea
| | - Yu-Tang Gao
- Department of Epidemiology, Shanghai Cancer Institute, Shanghai, China
| | - Xiao Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Daehee Kang
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
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Wu X, Xu QQ, Guo L, Yu CT, Xiong YY, Wei ZY, Huo R, Li ST, Shen L, Niu JM, Liu L, Lin Y, He L, Qin SY. Quantitative assessment of the association between rs2046210 at 6q25.1 and breast cancer risk. PLoS One 2013; 8:e65206. [PMID: 23785413 PMCID: PMC3681980 DOI: 10.1371/journal.pone.0065206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Accepted: 04/23/2013] [Indexed: 11/18/2022] Open
Abstract
Genome-wide association studies (GWAS) have identified several genetic susceptibility loci for breast cancer (BC). One of them, conducted among Chinese women, found an association of rs2046210 at 6q25.1 with the risk of BC recently. Since then, numerous association studies have been carried out to investigate the relationship between this polymorphism and BC risk in various populations. However, these have yielded contradictory results. We therefore performed a meta-analysis to clarify this inconsistency. Overall, a total of 235003 subjects based on 13 studies were included in our study. Significantly increased BC risk was detected in the pooled analysis [allele contrast: OR = 1.13, 95%CI = 1.10-1.17, P(Z) <10(-5), P(Q) <10(-4); dominant model: OR = 1.21, 95%CI = 1.14-1.27, P(Z) <10(-5), P(Q) <10(-4); recessive model: OR = 1.18, 95%CI = 1.12-1.24, P(Z) <10(-5), P(Q) = 0.04]. In addition, our data revealed that rs2046210 conferred greater risk in estrogen receptor (ER)-negative tumors [OR = 1.27, 95%CI = 1.15-1.40, P(Z) <10(-5), P(Q) <10(-4)] than in ER-positive ones [OR = 1.18, 95%CI = 1.09-1.28, P(Z) <10(-4), P(Q) = 0.0003]. When stratified by ethnicity, significant associations were found in Caucasian and Asian populations, but not detected among Africans. There was evidence of heterogeneity (P<0.05), however, the heterogeneity largely disappeared after stratification by ethnicity. The present meta-analysis demonstrated that the rs2046210 polymorphism may be associated with increased BC susceptibility, but this association varies in different ethnicities.
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Affiliation(s)
- Xi Wu
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, P.R. China
- Shanghai Institutes of Genome Pilot and Human Health, Shanghai, China
| | - Qing-Qing Xu
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, P.R. China
- Shanghai Institutes of Genome Pilot and Human Health, Shanghai, China
| | - Liang Guo
- The Fourth Hospital of Jinan City, Taishan Medical College, Jinan, China
| | - Chuan-Ting Yu
- Clinical Laboratory, Yantaishan Hospital, Yantai, China
| | - Yu-Yu Xiong
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, P.R. China
- Shanghai Institutes of Genome Pilot and Human Health, Shanghai, China
| | - Zhi-Yun Wei
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, P.R. China
- Shanghai Institutes of Genome Pilot and Human Health, Shanghai, China
| | - Ran Huo
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, P.R. China
- Shanghai Institutes of Genome Pilot and Human Health, Shanghai, China
| | - Sheng-Tian Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Lu Shen
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, P.R. China
- Shanghai Institutes of Genome Pilot and Human Health, Shanghai, China
| | | | - Lu Liu
- Laiwu Hospital, Shandong, China
| | - Yi Lin
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, P.R. China
- School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Lin He
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, P.R. China
- Shanghai Institutes of Genome Pilot and Human Health, Shanghai, China
- Institutes of Biomedical Sciences, Fudan University, Shanghai, China
- * E-mail: (SYQ); (LH)
| | - Sheng-Ying Qin
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, P.R. China
- Shanghai Institutes of Genome Pilot and Human Health, Shanghai, China
- * E-mail: (SYQ); (LH)
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Zheng W, Zhang B, Cai Q, Sung H, Michailidou K, Shi J, Choi JY, Long J, Dennis J, Humphreys MK, Wang Q, Lu W, Gao YT, Li C, Cai H, Park SK, Yoo KY, Noh DY, Han W, Dunning AM, Benitez J, Vincent D, Bacot F, Tessier D, Kim SW, Lee MH, Lee JW, Lee JY, Xiang YB, Zheng Y, Wang W, Ji BT, Matsuo K, Ito H, Iwata H, Tanaka H, Wu AH, Tseng CC, Van Den Berg D, Stram DO, Teo SH, Yip CH, Kang IN, Wong TY, Shen CY, Yu JC, Huang CS, Hou MF, Hartman M, Miao H, Lee SC, Putti TC, Muir K, Lophatananon A, Stewart-Brown S, Siriwanarangsan P, Sangrajrang S, Shen H, Chen K, Wu PE, Ren Z, Haiman CA, Sueta A, Kim MK, Khoo US, Iwasaki M, Pharoah PDP, Wen W, Hall P, Shu XO, Easton DF, Kang D. Common genetic determinants of breast-cancer risk in East Asian women: a collaborative study of 23 637 breast cancer cases and 25 579 controls. Hum Mol Genet 2013; 22:2539-50. [PMID: 23535825 PMCID: PMC3658167 DOI: 10.1093/hmg/ddt089] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Revised: 11/30/2012] [Accepted: 02/18/2013] [Indexed: 11/13/2022] Open
Abstract
In a consortium including 23 637 breast cancer patients and 25 579 controls of East Asian ancestry, we investigated 70 single-nucleotide polymorphisms (SNPs) in 67 independent breast cancer susceptibility loci recently identified by genome-wide association studies (GWASs) conducted primarily in European-ancestry populations. SNPs in 31 loci showed an association with breast cancer risk at P < 0.05 in a direction consistent with that reported previously. Twenty-one of them remained statistically significant after adjusting for multiple comparisons with the Bonferroni-corrected significance level of <0.0015. Eight of the 70 SNPs showed a significantly different association with breast cancer risk by estrogen receptor (ER) status at P < 0.05. With the exception of rs2046210 at 6q25.1, the seven other SNPs showed a stronger association with ER-positive than ER-negative cancer. This study replicated all five genetic risk variants initially identified in Asians and provided evidence for associations of breast cancer risk in the East Asian population with nearly half of the genetic risk variants initially reported in GWASs conducted in European descendants. Taken together, these common genetic risk variants explain ~10% of excess familial risk of breast cancer in Asian populations.
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Affiliation(s)
- Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA.
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