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1. The Moderate Alcohol and Cardiovascular Health Trial (MACH15): Design and methods for a randomized trial of moderate alcohol consumption and cardiometabolic risk

Author: Joline W. J. Beulens, Kenneth J. Mukamal, Lars O. Dragsted, Donna Spiegelman, Diederick E. Grobbee, Howard J. Edenberg, Margaret M. Murray, Janelle W. Coughlin, Sally N. Adebamowo, Lawrence J. Appel, Eric B. Rimm, Jane N. Eriksen, Jeff D. Williamson, Ilse C. Schrieks, Polyna Khudyakov, Vilma Irazola, Ramon Estruch, Pablo Gulayin, Clement Adebamowo, John H. Krystal, T.L. Wilkens, Laura C. Lovato, Mariana Lazo, ACS - Diabetes & metabolism, Epidemiology and Data Science, APH - Health Behaviors & Chronic Diseases, and ACS - Heart failure & arrhythmias
Subjects: Male, Research design, Time Factors, Epidemiology, Health Behavior, CARDIOVASCULAR DISEASES, RANDOMIZED CONTROLLED TRIAL, Alcohol, 030204 cardiovascular system & hematology, Global Health, Cardiovascular System, RESEARCH DESIGN, law.invention, GERIATRIC, chemistry.chemical_compound, 0302 clinical medicine, Randomized controlled trial, law, Faculty of Science, 030212 general & internal medicine, Metabolic Syndrome, Cardiometabolic risk, Middle Aged, DIABETES MELLITUS TYPE 2, Cardiovascular Diseases, purl.org/becyt/ford/3 [https], Female, Cardiology and Cardiovascular Medicine, Alcohol consumption, Adult, medicine.medical_specialty, Alcohol Drinking, Cardiovascular health, Risk Assessment, Article, purl.org/becyt/ford/3.3 [https], 03 medical and health sciences, Internal medicine, Diabetes mellitus, ETHANOL, medicine, Humans, Aged, Ethanol, business.industry, medicine.disease, Coronary heart disease, chemistry, Feasibility Studies, Morbidity, business, Follow-Up Studies
Abstract: Background: Observational studies have documented lower risks of coronary heart disease and diabetes among moderate alcohol consumers relative to abstainers, but only a randomized clinical trial can provide conclusive evidence for or against these associations. Aim: The purpose of this study was to describe the rationale and design of the Moderate Alcohol and Cardiovascular Health Trial, aimed to assess the cardiometabolic effects of one alcoholic drink daily over an average of six years among adults 50 years or older. Methods: This multicenter, parallel-arm randomized trial was designed to compare the effects of one standard serving (∼11–15 g) daily of a preferred alcoholic beverage to abstention. The trial aimed to enroll 7800 people at high risk of cardiovascular disease. The primary composite endpoint comprised time to the first occurrence of non-fatal myocardial infarction, non-fatal ischemic stroke, hospitalized angina, coronary/carotid revascularization, or total mortality. The trial was designed to provide >80% power to detect a 15% reduction in the risk of the primary outcome. Secondary outcomes included diabetes. Adverse effects of special interest included injuries, congestive heart failure, alcohol use disorders, and cancer. Results: We describe the design, governance, masking issues, and data handling. In three months of field center activity until termination by the funder, the trial randomized 32 participants, successfully screened another 70, and identified ∼400 additional interested individuals. Conclusions: We describe a feasible design for a long-term randomized trial of moderate alcohol consumption. Such a study will provide the highest level of evidence for the effects of moderate alcohol consumption on cardiovascular disease and diabetes, and will directly inform clinical and public health guidelines. Fil: Spiegelman, Donna. Harvard University. Harvard School of Public Health; Estados Unidos Fil: Lovato, Laura C.. Universidad de Barcelona; España Fil: Khudyakov, Polyna. Harvard University. Harvard School of Public Health; Estados Unidos. Universidad de Barcelona; España Fil: Wilkens, Trine L.. Universidad de Copenhagen; Dinamarca Fil: Adebamowo, Clement A.. University of Maryland; Estados Unidos Fil: Adebamowo, Sally N.. University of Maryland; Estados Unidos Fil: Appel, Lawrence J.. No especifíca; Fil: Beulens, Joline W.J.. No especifíca; Fil: Coughlin, Janelle W.. No especifíca; Fil: Dragsted, Lars Ove. Universidad de Copenhagen; Dinamarca Fil: Edenberg, Howard J. No especifíca; Fil: Eriksen, Jane N.. Universidad de Copenhagen; Dinamarca Fil: Estruch, Ramon. Universidad de Barcelona; España Fil: Grobbee, Diederick E.. No especifíca; Fil: Gulayin, Pablo Elías. No especifíca; Fil: Irazola, Vilma. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Centro de Investigaciones en Epidemiología y Salud Pública. Instituto de Efectividad Clínica y Sanitaria. Centro de Investigaciones en Epidemiología y Salud Pública; Argentina Fil: Krystal, John H.. University of Yale. School of Medicine; Estados Unidos Fil: Lazo, Mariana. No especifíca; Fil: Murray, Margaret M.. University of Yale. School of Medicine; Estados Unidos Fil: Rimm, Eric B.. Harvard University. Harvard School of Public Health; Estados Unidos Fil: Schrieks, Ilse C.. Universidad de Barcelona; España Fil: Williamson, Jeff D.. No especifíca; Fil: Mukamal, Kenneth J.. Harvard Medical School; Estados Unidos
Published: 2020
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2. Creative Approaches to Global Cancer Research and Control

Author: Maria T. Bourlon, Clement Adebamowo, Anne F. Rositch, Christopher A. Loffredo, and Paul C. Pearlman
Subjects: Cancer Research, Knowledge management, business.industry, Extramural, Research, Editorials, MEDLINE, Creativity, Text mining, Oncology, Neoplasms, Humans, business, Psychology, Control (linguistics)
Published: 2020
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3. Modeling spatial access to cervical cancer screening services in Ondo State, Nigeria

Author: Kathleen Stewart, Stephen Ayodele Adewole, Olusegun Adeyemo, Clement Adebamowo, Zhiyue Xia, and Moying Li
Subjects: General Computer Science, Health geography, Population, Uterine Cervical Neoplasms, Nigeria, lcsh:Computer applications to medicine. Medical informatics, Health Services Accessibility, 03 medical and health sciences, 0302 clinical medicine, Spatial accessibility, Catchment Area, Health, Health care, medicine, Humans, 030212 general & internal medicine, Socioeconomics, education, Early Detection of Cancer, Distance decay, Cervical cancer, education.field_of_study, business.industry, Research, Low-and middle-income countries, Public Health, Environmental and Occupational Health, Cancer screening services, medicine.disease, General Business, Management and Accounting, Geography, 030220 oncology & carcinogenesis, Public transport, Health care planning, Geocoding, lcsh:R858-859.7, Female, Catchment area, business
Abstract: Background Women in low- and middle-income countries (LMIC) remain at high risk of developing cervical cancer and have limited access to screening programs. The limits include geographical barriers related to road network characteristics and travel behaviors but these have neither been well studied in LMIC nor have methods to overcome them been incorporated into cervical cancer screening delivery programs. Methods To identify and evaluate spatial barriers to cervical cancer prevention services in Ondo State, Nigeria, we applied a Multi-Mode Enhanced Two-Step Floating Catchment Area model to create a spatial access index for cervical cancer screening services in Ondo City and the surrounding region. The model used inputs that included the distance between service locations and population centers, local population density, quantity of healthcare infrastructures, modes of transportation, and the travel time budgets of clients. Two different travel modes, taxi and mini bus, represented common modes of transit. Geocoded client residential locations were compared to spatial access results to identify patterns of spatial access and estimate where gaps in access existed. Results Ondo City was estimated to have the highest access in the region, while the largest city, Akure, was estimated to be in only the middle tier of access. While 73.5% of clients of the hospital in Ondo City resided in the two highest access zones, 21.5% of clients were from locations estimated to be in the lowest access catchment, and a further 2.25% resided outside these limits. Some areas that were relatively close to cervical cancer screening centers had lower access values due to poor road network coverage and fewer options for public transportation. Conclusions Variations in spatial access were revealed based on client residential patterns, travel time differences, distance decay assumptions, and travel mode choices. Assessing access to cervical cancer screening better identifies potentially underserved locations in rural Nigeria that can inform plans for cervical cancer screening including new or improved infrastructure, effective resource allocation, introduction of service options for areas with lower access, and design of public transportation networks.
Published: 2020
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4. Is the HERV-K HML-2 Xq21.33, an endogenous retrovirus mutated by gene conversion of chromosome X in a subset of African populations, associated with human breast cancer?

Author: Sofia D. Merajver, Javed Siddiqui, Michael H. Dosik, Lisa A. Newman, Galya Bigman, Ganesh S. Palapattu, Rafael Contreras-Galindo, Clement Adebamowo, Mark H. Kaplan, Arul M. Chinnaiyan, Evelyn Jiagge, and Sally N. Adebamowo
Subjects: Oncology, Cancer Research, medicine.medical_specialty, Epidemiology, Single-nucleotide polymorphism, lcsh:RC254-282, Virus, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, 0302 clinical medicine, Breast cancer, Internal medicine, Genetic variation, medicine, SNP, lcsh:RC109-216, HERV-K HML-2, X chromosome, 030304 developmental biology, 0303 health sciences, business.industry, Cancer, Provirus, medicine.disease, Xq21.33, lcsh:Neoplasms. Tumors. Oncology. Including cancer and carcinogens, 3. Good health, HERV-K, Infectious Diseases, Endogenous viruses, 030220 oncology & carcinogenesis, Gene conversion, business, Research Article
Abstract: The human endogenous retroviruses HERV-K HML-2 have been considered a possible cause of human breast cancer (BrC). A HERV-K HML-2 fully intact provirus Xq21.33 was recently identified in some West African people. We used PCR technology to search for the Xq21.33 provirus in DNA from Nigerian women with BrC and controls. to see if Xq21.33 plays any role in predisposing to BrC. This provirus was detected in 27 of 216 (12.5%) women with BrC and in 22 of 219 (10.0%) controls. These results were not statistically significant. The prevalence of provirus in premenopausal control women 44 years or younger [18/157 (11.46%)} vs women with BrC [12/117 (10.26%)] showed no statistical difference. The prevalence of virus in postmenopausal control women > 45 yrs. was 7.4% (4/54) vs 15.31% (15/98) in postmenopausal women with BrC. These changes were not statistically significant at p value of nv regions of the virus which differed by 2–3 SNPs did not alter the protein sequence of the virus. SNP at 5730 and 8529 were seen in all persons with provirus, while 54% had an additional SNP at 7596.Two Nigerian women and 2 Ghanaian women had additional unusual SNPs. Homozygosity was seen in (5/27) BrC and (2/22) control women. The genetic variation and homozygosity patterns suggested that there was gene conversion of this X chromosome associated virus. The suggestive finding in this preliminary data of possible increased prevalence of Xq21.33 provirus in post-menopausal Nigerian women with BrC should be clarified by a more statistically powered study sample to see if postmenopausal African and/or African American women carriers of Xq21.33 might show increased risk of BrC. The implication of finding such a link would be the development of antiretroviral drugs that might aid in preventing BrC in Xq21.33+ women.
Published: 2020
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5. Heterogeneity in head and neck Cancer incidence among black populations from Africa, the Caribbean and the USA: Analysis of Cancer registry data by the AC3

Author: Danièle Luce, Michael Odutola, Ann Korir, Kufre Iseh, Paulo S. Pinheiro, Nguundja Uamburu, TN Gibson, Simon G. Anderson, Jacqueline Deloumeaux, Clement Adebamowo, Ima-Obong A. Ekanem, Adeola Akintola, Baffour Awuah, Nasiru Raheem, Jessica Peruvien, Samuel Gathere, Evans Kiptanui, Andrew Gachii, Veronica Roach, Natasha Sobers, Kellie Alleyne-Mike, Festus Igbinoba, Adana Llanos, Aviane Auguste, Camille Ragin, Stanie Gaete, Nkese Felix, Kimlin Tam Ashing, Fred K. Awittor, Uwemedimbuk Ekanem, Sharon R Harrison, Emmanuel Ezeome, Maira du Plessis, Bernard Bhakkan, Robert Hage, Theresa Otu, Dawn McNaughton, Heather-Dawn Lawson-Myers, Abidemi Omonisi, CHU Pointe-à-Pitre/Abymes [Guadeloupe], University of Maryland System, The University of the West Indies, Columbia University [New York], Institut de recherche en santé, environnement et travail (Irset), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de la Santé et de la Recherche Médicale (INSERM)-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Université d'Angers (UA), École des Hautes Études en Santé Publique [EHESP] (EHESP), University of New South Wales [Sydney] (UNSW), Fox Chase Cancer Center, National Cancer Institute United States Department of Health and Human ServicesNational Institutes of Health (NIH) - USANIH National Cancer Institute (NCI) [R13 CA249974, R01 CA238061, P20 CA210294, CA006927], TUFCCC/HC Regional Comprehensive Cancer Health Disparity Partnership [U54 CA221704], French National Cancer Institute (Institut National du Cancer, INCa) Institut National du Cancer (INCA) France, French National Public health Agency (Sante Publique France), Kenya Medical Research Institute (KEMRI), University of Miami, University of Maryland [Baltimore], Federal Ministry of Health [Abuja, Nigeria], City of Hope Comprehensive Cancer Center [Duarte], Komfo Anokye Teaching Hospital, University of Calabar (UNICAL), University of Uyo, University of Nigeria (UNN), Université d'Angers (UA)-Université de Rennes (UR)-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Ekiti State University, and University of Abuja
Subjects: Male, Cancer Research, Kenya, HPV, Epidemiology, [SDV]Life Sciences [q-bio], Population, Alcohol drinking, Article, 03 medical and health sciences, 0302 clinical medicine, Black Populations, Medicine, Humans, 030212 general & internal medicine, Registries, education, Head and neck cancer, Population-based cancer registry, USA, Caribbean, education.field_of_study, business.industry, Incidence (epidemiology), Incidence, Cancer, Nasopharyngeal Neoplasms, Blacks, medicine.disease, Tobacco smoking, United States, 3. Good health, Cancer registry, Oncology, Caribbean Region, Head and Neck Neoplasms, 030220 oncology & carcinogenesis, Africa, Etiology, Female, business, Demography
Abstract: International audience; Background: Africa and the Caribbean are projected to have greater increases in Head and neck cancer (HNC) burden in comparison to North America and Europe. The knowledge needed to reinforce prevention in these populations is limited. We compared for the first time, incidence rates of HNC in black populations from African, the Caribbean and USA. Methods: Annual age-standardized incidence rates (IR) and 95% confidence intervals (95%CI) per 100,000 were calculated for 2013-2015 using population-based cancer registry data for 14,911 HNC cases from the Caribbean (Barbados, Guadeloupe, Trinidad and Tobago, N = 443), Africa (Kenya, Nigeria, N = 772) and the United States (SEER, Florida, N = 13,696). We compared rates by sub-sites and sex among countries using data from registries with high quality and completeness. Results: In 2013-2015, compared to other countries, HNC incidence was highest among SEER states (IR: 18.2, 95%CI = 17.6-18.8) among men, and highest in Kenya (IR: 7.5, 95%CI = 6.3-8.7) among women. Nasopharyngeal cancer IR was higher in Kenya for men (IR: 3.1, 95%CI = 2.5-3.7) and women (IR: 1.5, 95% CI = 1.0-1.9). Female oral cavity cancer was also notably higher in Kenya (IR = 3.9, 95%CI = 3.0-4.9). Blacks from SEER states had higher incidence of laryngeal cancer (IR: 5.5, 95%CI = 5.2-5.8) compared to other countries and even Florida blacks (IR: 4.4, 95%CI = 3.9-5.0). Conclusion: We found heterogeneity in IRs for HNC among these diverse black populations; notably, Kenya which had distinctively higher incidence of nasopharyngeal and female oral cavity cancer. Targeted etiological investigations are warranted considering the low consumption of tobacco and alcohol among Kenyan women. Overall, our findings suggest that behavioral and environmental factors are more important determinants of HNC than race.
Published: 2021
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6. Prevalence of Vaginal HPV Infection Among Adolescent Girls in Jos, North-Central Nigeria

Author: Ayo Famooto, Sally N. Adebamowo, Daniel Z. Egah, Nanma T. Cosmas, Lohya Nimzing, and Clement Adebamowo
Subjects: business.industry, North central, HPV infection, Medicine, business, medicine.disease, Demography
Abstract: Purpose: Knowledge of the prevalence of HPV infection among adolescents is essential to determining the best age for introduction of HPV vaccine, monitoring vaccine efficacy and giving insight into determinants of persistent high-risk HPV infection, a necessary cause of cervical cancer. Yet, there’s been limited studies in low-and-middle-income countries.Methods: In this cross-sectional study, we randomly selected 205 girls, aged 9–20 years, from 10 schools. We obtained informed consent and assent, collected data and trained participants who self-collected vaginal samples using swab stick. We genotyped HPV using SPF10-DEIA/LiPA25 and analyzed data using Stata 14®.Results: The mean (SD) age of the girls was 14.9 (2.3) years. We found HPV in 13.2% of vaginal swabs. The earliest age at which anyHPV and hrHPV infections were detected was 10 and 12 years respectively. The prevalence of any HPV peaked at 16 and 17 years, hrHPV at 16 years, lrHPV at 17 and 18 years and multiple hrHPV 18 years of age. The prevalence of hrHPV infection was 1.5% among the 9–12 years age group, 2.9% among 13–16 years and 3.4% among 17–20 years old. The commonest hrHPV types detected were 52 (3.9%), 18 (1.5%) and 51 (2.4%). The most common lrHPV types was 6 (2.9%).Conclusion: The prevalence of HPV infection in these urbanized young girls in Nigeria is high and commences after 9 years of age. HPV vaccination in this population should start at 9 years of age or younger to prevent establishment of persistent HPV infection.
Published: 2021
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7. Type 2 diabetes complications and comorbidity in Sub-Saharan Africans

Author: Georgia M. Dunston, Johnnie Oli, Thomas Johnson, Ayo P. Doumatey, Clement Adebamowo, Albert G.B. Amoah, Charles N. Rotimi, Francis S. Collins, Guanjie Chen, Joseph Acheampong, Jie Zhou, Kenneth Ekoru, Amy R. Bentley, Godfrey Okafor, Williams Balogun, Benjamin A. Eghan, Olufemi Fasanmade, Jokotade Adeleye, Kofi Agyenim-Boateng, Adebowale Adeyemo, and Daniel Shriner
Subjects: medicine.medical_specialty, Complications, Epidemiology, Co-morbidity, Type 2 diabetes, 01 natural sciences, 03 medical and health sciences, 0302 clinical medicine, Diabetes mellitus, Internal medicine, 0502 economics and business, Health care, Global health, medicine, 030212 general & internal medicine, 050207 economics, 0101 mathematics, 2. Zero hunger, lcsh:R5-920, 050208 finance, business.industry, Public health, 05 social sciences, 010102 general mathematics, General Medicine, Diabetic retinopathy, Institutional review board, 16. Peace & justice, medicine.disease, Obesity, Comorbidity, 3. Good health, Type 2 Diabetes, Sub-Sahara Africa, Emergency medicine, lcsh:Medicine (General), business, Body mass index, Research Paper
Abstract: Background: Context-specific evidence of the spectrum of type 2 diabetes (T2D) burden is essential for setting priorities and designing interventions to reduce associated morbidity and mortality. However, there are currently limited data on the burden of T2D complications and comorbidity in sub-Saharan Africa (SSA). Here, we aimed to estimate the burden and risk factors for T2D complications and comorbidity in a large sample of sub-Saharan Africans. Methods: Using a standardized protocol, we documented and estimated the burden of T2D complications and comorbidities in 2,784 diabetes participants enrolled from tertiary health centers from Nigeria, Ghana and Kenya. T2D complications and comorbidities evaluated by study physicians and clinic staffs included cardiometabolic, ocular, neurological and renal characteristics. Using the same protocol, we contextualized the burden of these complications and comorbidities by evaluating them in a sample of 3,209 individuals without diabetes enrolled from the catchment communities where the cases originated. Logistic regression models were used to identify risk factors and to adjust estimates of risk. Results: The mean age of T2D participants was 56 (SD 11) years with a median duration of diabetes of 5 (interquartile range 2-10) years. The notable complications/comorbidities observed in this sample of T2D participants included hypertension (71%; 95% CI 69-73), obesity 27% (25-29) and hyperlipidemia 34% (32-36). Diabetic retinopathy was found in 15% (13-17) and cataracts in 32% (30-35). About 13% (12-15) had impaired renal function as assessed by eGFR, representing 1 in 8 participants. Erectile dysfunction was a complication in 35% (32-38) of men. Age, duration of T2D and body mass index were significant risk factors for most complications/comorbidities. Population-attributable fraction ranged between 6 and 64 percent for most comorbidities. Conclusion: We observed a substantial burden of diabetes complications and comorbidity in this sample of T2D participants from SSA. Given the reported association of these complications with increased burden of T2D morbidity and mortality we call for public health strategies that prioritise early detection, the maintenance of healthy blood pressure, weight and lipid levels, as well as strengthen health care system capacities to provide treatment and care for neurological and ophthalmological complications of diabetes. Funding Statement: The study was supported in part by the Intramural Research Program of the National Institutes of Health in the Center for Research on Genomics and Global Health (CRGGH). The CRGGH is supported by the National Human Genome Research Institute (NHGRI), the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), the Center for Information Technology, and the Office of the Director at the National Institutes of Health (1ZIAHG200362). Support for participant recruitment and initial genetic studies of the AADM study was provided by NIH grant No. 3T37TW00041-03S2 from the Office of Research on Minority Health. Declaration of Interests: The authors declare no competing interests. Ethics Approval Statement: The study received ethical approval from the Institutional Review Board at each study site, Howard University and the United States National Institutes of Health.
Published: 2019

8. Human Papillomavirus Vaccine Acceptability and Campaign Message Preferences Among African American Parents: a Qualitative Study

Author: Min Qi Wang, Yan Qin, Shana O. Ntiri, Yuki Lama, Xiaoli Nan, Clement Adebamowo, and Cheryl L. Knott
Subjects: Parents, medicine.medical_specialty, Health Knowledge, Attitudes, Practice, Health campaigns, Adolescent, Word of mouth, Human papillomavirus vaccine, Article, 03 medical and health sciences, 0302 clinical medicine, medicine, Humans, Social media, 030212 general & internal medicine, Papillomavirus Vaccines, Child, Government, Cancer prevention, business.industry, Papillomavirus Infections, Public Health, Environmental and Occupational Health, Patient Acceptance of Health Care, Focus group, Vaccination, Black or African American, Oncology, 030220 oncology & carcinogenesis, Family medicine, Female, business, Inclusion (education), African American health, Qualitative research
Abstract: Human papillomavirus (HPV) vaccination can prevent numerous cancers, yet uptake remains low for adolescents. Given disproportionate burden of cancers among African Americans, it is important to identify factors that influence HPV vaccination decisions among African American parents, specifically the role and preferences of vaccine campaign messages. The objectives of this study were to (1) identify the predictors of parents’ decisions to get their children vaccinated against HPV, (2) assess parents’ evaluation of current HPV vaccination campaign messages, and (3) uncover message strategies or themes parents consider to be effective and motivating to vaccinate their children against HPV. Focus groups were conducted with African American mothers and fathers (n = 18) in person. Several themes emerged regarding HPV vaccine acceptability including the desire to be informed, the unfamiliarity of vaccination, and mistrust toward government, pharmaceutical companies, and healthcare providers. Parental review of existing campaign messages highlighted the importance of clarifying risks and benefits of vaccination, including cancer prevention, and the preference for straightforward language. When brainstorming strategies to craft effective messages, parents highlighted need for the inclusion of diverse groups across race, gender, and age. Additionally, parents recommended clear language on side effects, eligibility, and additional resources for further information. Our findings highlight concerns and potential strategies to promote HPV vaccination tailored to African American parents and their children. Targeted interventions to increase vaccination need to consider the importance of building trust and representation in health promotional materials. Considerations for how messages were shared were also discussed such as physical locations, word of mouth, and social media.
Published: 2021

9. Vaginal microbiota diversity and paucity of Lactobacillus species are associated with persistent hrHPV infection in HIV negative but not in HIV positive women

Author: Sally N. Adebamowo, Eileen Dareng, Ayotunde Famooto, Paul D.P. Pharoah, Jacques Ravel, Bing Ma, Clement Adebamowo, and Apollo - University of Cambridge Repository
Subjects: 0301 basic medicine, Epidemiology, Human immunodeficiency virus (HIV), lcsh:Medicine, HIV Infections, Logistic regression, medicine.disease_cause, Cohort Studies, 0302 clinical medicine, Risk Factors, Lactobacillus, RNA, Ribosomal, 16S, Medicine, 030212 general & internal medicine, Lactobacillus species, lcsh:Science, Generalized estimating equation, Multidisciplinary, Molecular medicine, biology, Microbiota, Biodiversity, Middle Aged, Vagina, Female, Infection, Cancer microenvironment, Adult, medicine.medical_specialty, Persistently infected, Nigeria, Predictive markers, Models, Biological, Article, 03 medical and health sciences, Internal medicine, HIV Seronegativity, Humans, Human papillomavirus, Oncogenesis, business.industry, lcsh:R, Papillomavirus Infections, biology.organism_classification, 030104 developmental biology, Case-Control Studies, Cervical cancer, lcsh:Q, Hiv status, business
Abstract: Funder: Maryland Department of Health and Mental Hygiene; doi: http://dx.doi.org/10.13039/100006671, The vaginal microbiota is thought to play a role in modulating risk of high-risk human papillomavirus (hrHPV) infection. We examined the relationship between the vaginal microbiota and persistent hrHPV infection in HIV-negative and HIV-positive women. We used 16S-rRNA sequencing to characterize the vaginal microbiota of two serial samples taken six months apart from 211 Nigerian women (67%, 142/211 HIV-positive and 33%, 69/211 HIV-negative) and evaluated the association between the vaginal microbiota and persistent hrHPV infection using generalized estimating equation logistic regression models and linear discriminant analysis effect size (LEfSe) algorithm to identify phylotypic biomarkers of persistent hrHPV infection. The high diversity microbiota, Community State Type IV-B, was the most prevalent in both HIV-negative (38% at baseline, 30% at the follow-up visit) and HIV-positive (27% at baseline, 35% at the follow-up visit) women. The relationship between the vaginal microbiota and persistent hrHPV was modified by HIV status. In HIV-negative women, women with Lactobacillus dominant microbiota had lower odds (OR: 0.35, 95% CI 0.14-0.89, p = 0.03) of persistent hrHPV compared to women with Lactobacillus deficient microbiota. While among HIV-positive women, the odds of being persistently infected with hrHPV was higher in women with Lactobacillus dominant microbiota (OR: 1.25, 95% CI 0.73-2.14 p = 0.41). This difference in effect estimates by HIV was statistically significant (p = 0.02). A high diversity vaginal microbial community with paucity of Lactobacillus species was associated with persistent hrHPV infection in HIV-negative women but not in HIV-positive women.
Published: 2020

10. Leisure-Time Physical Activity is Associated with reduced Risk of Breast Cancer and Triple Negative Breast Cancer in Nigerian Women

Author: Iliya Karniliyus Salu, Benjamin Achusi, Clement Adebamowo, Olawale A Badejo, Elima Jedy-Agba, Monday Yilkudi, Ayo Famooto, Elijah Miner, King-David Terna Yawe, Ikechukwu Anosike, Emmanuel Ezeome, Sally N. Adebamowo, Galya Bigman, and Oluwole Olaomi
Subjects: Oncology, medicine.medical_specialty, Reduced risk, Breast cancer, business.industry, Internal medicine, Leisure time, medicine, Physical activity, medicine.disease, business, Triple-negative breast cancer
Abstract: Background: Physical activity (PA) is associated with reduced risk of breast cancer and its various subtypes but this association is less well described in African women, particularly in women with triple-negative breast cancer that is more common in Sub-Saharan Africa. In this study, we examined the associations between leisure-time physical activity (LTPA) and breast cancer in total and by subtypes in Nigerian women.Methods: We studied 472 newly diagnosed primary invasive breast cancer patients age-matched (±5years) with 472 controls from the Nigerian Integrative Epidemiology of Breast Cancer (NIBBLE) Study enrolled from January 2014 to July 2016. We derived the average amount of time spent on LTPA per week over the past year using a modified Nurses’ Health Study-II physical activity questionnaire. We calculated the total metabolic equivalents (METs) for each reported LTPA per hour/week (i.e. walking, cycling, and dancing) and compared odds of breast cancer among participants who attained the World Health Organization (WHO) physical activity(PA) recommendations of at least 150 minutes of moderate-intensity or/and 75 minutes of vigorous-intensity aerobic activity/week with those who did not. In addition, we evaluated these by categories of LTPA in quartiles of METs. We used conditional and unconditional logistic regression models to estimate the adjusted Odds Ratio (OR) of LTPA for overall breast cancer and by molecular subtypes. Results: The mean age (SD) of cases, 44.4 (10.0) years, was similar to that of controls, 43.5 (9.5) after matching. The OR for breast cancer among women who attained the WHO PA recommendations compared with those who did not was 0.64 (95% CI: 0.45-0.90). LTPA was associated with 51% reduced odds of hormone receptor-positive and 65% reduced odds of triple-negative breast cancer. We observed a significant dose-response relationship where women with high levels of LTPA had lower odds of overall breast cancer, triple-negative and hormone receptor-positive breast cancer. Conclusions: Increasing LTPA in African women may play a significant role in reducing the incidence of breast cancer, particularly of the more aggressive subtype as triple-negative, which is more prevalent in Sub-Saharan Africa.
Published: 2020
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11. Breast cancer treatment: A phased approach to implementation

Author: Alexandru Eniu, Benjamin O. Anderson, Cynthia Villarreal-Garza, Gertrude Nakigudde, Clement Adebamowo, Manoj Menon, Riccardo Masetti, Catherine Duggan, Anne Ng’ang’a, Luiz Henrique Gebrim, Miriam Mutebi, Nagi S. El Saghir, Karla Unger-Saldaña, Nixon Niyonzima, Shahla Masood, Anne F. Rositch, Peter Bird, Gaurav Agarwal, Rebecca DeBoer, Julie R. Gralow, Zipporah Ali, Jean Marc Bourque, and Allison Dvaladze
Subjects: Cancer Research, Delayed Diagnosis, Palliative care, dissemination and implementation science, Settore MED/18 - CHIRURGIA GENERALE, supportive and palliative care, Decentralization, 0302 clinical medicine, Multidisciplinary approach, low- and middle-income countries (LMICs), 030212 general & internal medicine, cancer center of excellence, media_common, treatment, phased implementation, Combined Modality Therapy, Health equity, Checklist, Oncology, 030220 oncology & carcinogenesis, multidisciplinary evaluation, Workforce, Female, Brazil, early diagnosis, media_common.quotation_subject, Breast Neoplasms, underserved communities, Time-to-Treatment, 03 medical and health sciences, Breast cancer, breast cancer, centralized care, Excellence, medicine, Humans, Operations management, health disparities, Romania, business.industry, Developed Countries, Health Plan Implementation, medicine.disease, decentralized care, resource-stratification, Kenya, Interdisciplinary Communication, business, Situation analysis
Abstract: Optimal treatment outcomes for breast cancer are dependent on a timely diagnosis followed by an organized, multidisciplinary approach to care. However, in many low- and middle-income countries, effective care management pathways can be difficult to follow because of financial constraints, a lack of resources, an insufficiently trained workforce, and/or poor infrastructure. On the basis of prior work by the Breast Health Global Initiative, this article proposes a phased implementation strategy for developing sustainable approaches to enhancing patient care in limited-resource settings by creating roadmaps that are individualized and adapted to the baseline environment. This strategy proposes that, after a situational analysis, implementation phases begin with bolstering palliative care capacity, especially in settings where a late-stage diagnosis is common. This is followed by strengthening the patient pathway, with consideration given to a dynamic balance between centralization of services into centers of excellence to achieve better quality and decentralization of services to increase patient access. The use of resource checklists ensures that comprehensive therapy or palliative care can be delivered safely and effectively. Episodic or continuous monitoring with established process and quality metrics facilitates ongoing assessment, which should drive continual process improvements. A series of case studies provides a snapshot of country experiences with enhancing patient care, including the implementation of national cancer control plans in Kenya, palliative care in Romania, the introduction of a 1-stop clinic for diagnosis in Brazil, the surgical management of breast cancer in India, and the establishment of a women's cancer center in Ghana.
Published: 2020

12. Age, HIV status, and research context determined attrition in a longitudinal cohort in Nigeria

Author: Sally N. Adebamowo, Richard Offiong, Yinka Olaniyan, Elonna M. Obiefuna, Michael Odutola, Paul D.P. Pharoah, Olabimpe R. Eseyin, Eileen Dareng, and Clement Adebamowo
Subjects: Adult, 0301 basic medicine, Epidemiology, Research context, Nigeria, HIV Infections, Logistic regression, Article, 03 medical and health sciences, 0302 clinical medicine, Drop out, Humans, Mass Screening, Medicine, Attrition, Longitudinal Studies, Prospective Studies, 030212 general & internal medicine, Longitudinal cohort, Prospective cohort study, Qualitative Research, business.industry, Age Factors, Focus Groups, Middle Aged, medicine.disease, 030112 virology, Focus group, Confidence interval, Research Design, Patient Compliance, Female, Lost to Follow-Up, business, Demography
Abstract: OBJECTIVE: We explored determinants of attrition a longitudinal cohort study in Nigeria. STUDY DESIGN AND SETTING: We enroled 1,020 women into a prospective study. Of these, 973 were eligible to return for follow-up. We investigated the determinants of attrition among eligible women using a sequential mixed methods design. We used logistic regression models to compare the baseline characteristics of responders and non-responders. At the end of the parent study, we conducted 4 focus group discussions and 8 key informant interviews with non-responders RESULTS. Of the 973 women included in the quantitative analysis, 26% were non-responders. From quantitative analysis, older women were less likely to drop out than younger women (reference: women ≤30 years; OR 0.46; 95%CI 0.30 – 0.70, p
Published: 2018
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13. Development of a Breast Cancer Risk Prediction Model for Women in Nigeria

Author: Olufunmilayo I. Olopade, Millicent Olubunmi Obajimi, Oluwasola A. Olayiwola, Adewunmi Adeoye, Dezheng Huo, Clement Adebamowo, Shengfeng Wang, Temidayo O. Ogundiran, Oladosu Ojengbede, Stella Odedina, Imaria Agwai, Imran O. Morhason-Bello, Adenike Temitayo Adenijiâ€‘Sofoluwe, and Adeyinka Ademola
Subjects: Breast Cancer Early Detection, medicine.medical_specialty, Epidemiology, Population, Nigeria, Breast Neoplasms, Logistic regression, Article, 03 medical and health sciences, Breast cancer screening, 0302 clinical medicine, Breast cancer, Risk Factors, Humans, Medicine, 030212 general & internal medicine, education, education.field_of_study, Models, Statistical, medicine.diagnostic_test, business.industry, Obstetrics, medicine.disease, Confidence interval, Oncology, Case-Control Studies, 030220 oncology & carcinogenesis, Women's Health, Female, business, Risk assessment, Breast feeding
Abstract: Background: Risk prediction models have been widely used to identify women at higher risk of breast cancer. We aimed to develop a model for absolute breast cancer risk prediction for Nigerian women. Methods: A total of 1,811 breast cancer cases and 2,225 controls from the Nigerian Breast Cancer Study (NBCS, 1998–2015) were included. Subjects were randomly divided into the training and validation sets. Incorporating local incidence rates, multivariable logistic regressions were used to develop the model. Results: The NBCS model included age, age at menarche, parity, duration of breastfeeding, family history of breast cancer, height, body mass index, benign breast diseases, and alcohol consumption. The model developed in the training set performed well in the validation set. The discriminating accuracy of the NBCS model [area under ROC curve (AUC) = 0.703, 95% confidence interval (CI), 0.687–0.719] was better than the Black Women's Health Study (BWHS) model (AUC = 0.605; 95% CI, 0.586–0.624), Gail model for white population (AUC = 0.551; 95% CI, 0.531–0.571), and Gail model for black population (AUC = 0.545; 95% CI, 0.525–0.565). Compared with the BWHS and two Gail models, the net reclassification improvement of the NBCS model were 8.26%, 13.45%, and 14.19%, respectively. Conclusions: We have developed a breast cancer risk prediction model specific to women in Nigeria, which provides a promising and indispensable tool to identify women in need of breast cancer early detection in Sub-Saharan Africa populations. Impact: Our model is the first breast cancer risk prediction model in Africa. It can be used to identify women at high risk for breast cancer screening. Cancer Epidemiol Biomarkers Prev; 27(6); 636–43. ©2018 AACR.
Published: 2018
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14. Machine Learning Detects Pan-cancer Ras Pathway Activation in The Cancer Genome Atlas

Author: Gregory P. Way, Francisco Sanchez-Vega, Konnor La, Joshua Armenia, Walid K. Chatila, Augustin Luna, Chris Sander, Andrew D. Cherniack, Marco Mina, Giovanni Ciriello, Nikolaus Schultz, Yolanda Sanchez, Casey S. Greene, Samantha J. Caesar-Johnson, John A. Demchok, Ina Felau, Melpomeni Kasapi, Martin L. Ferguson, Carolyn M. Hutter, Heidi J. Sofia, Roy Tarnuzzer, Zhining Wang, Liming Yang, Jean C. Zenklusen, Jiashan (Julia) Zhang, Sudha Chudamani, Jia Liu, Laxmi Lolla, Rashi Naresh, Todd Pihl, Qiang Sun, Yunhu Wan, Ye Wu, Juok Cho, Timothy DeFreitas, Scott Frazer, Nils Gehlenborg, Gad Getz, David I. Heiman, Jaegil Kim, Michael S. Lawrence, Pei Lin, Sam Meier, Michael S. Noble, Gordon Saksena, Doug Voet, Hailei Zhang, Brady Bernard, Nyasha Chambwe, Varsha Dhankani, Theo Knijnenburg, Roger Kramer, Kalle Leinonen, Yuexin Liu, Michael Miller, Sheila Reynolds, Ilya Shmulevich, Vesteinn Thorsson, Wei Zhang, Rehan Akbani, Bradley M. Broom, Apurva M. Hegde, Zhenlin Ju, Rupa S. Kanchi, Anil Korkut, Jun Li, Han Liang, Shiyun Ling, Wenbin Liu, Yiling Lu, Gordon B. Mills, Kwok-Shing Ng, Arvind Rao, Michael Ryan, Jing Wang, John N. Weinstein, Jiexin Zhang, Adam Abeshouse, Debyani Chakravarty, Ino de Bruijn, Jianjiong Gao, Benjamin E. Gross, Zachary J. Heins, Ritika Kundra, Marc Ladanyi, Moriah G. Nissan, Angelica Ochoa, Sarah M. Phillips, Ed Reznik, Robert Sheridan, S. Onur Sumer, Yichao Sun, Barry S. Taylor, Jioajiao Wang, Hongxin Zhang, Pavana Anur, Myron Peto, Paul Spellman, Christopher Benz, Joshua M. Stuart, Christopher K. Wong, Christina Yau, D. Neil Hayes, Joel S. Parker, Matthew D. Wilkerson, Adrian Ally, Miruna Balasundaram, Reanne Bowlby, Denise Brooks, Rebecca Carlsen, Eric Chuah, Noreen Dhalla, Robert Holt, Steven J.M. Jones, Katayoon Kasaian, Darlene Lee, Yussanne Ma, Marco A. Marra, Michael Mayo, Richard A. Moore, Andrew J. Mungall, Karen Mungall, A. Gordon Robertson, Sara Sadeghi, Jacqueline E. Schein, Payal Sipahimalani, Angela Tam, Nina Thiessen, Kane Tse, Tina Wong, Ashton C. Berger, Rameen Beroukhim, Carrie Cibulskis, Stacey B. Gabriel, Galen F. Gao, Gavin Ha, Matthew Meyerson, Steven E. Schumacher, Juliann Shih, Melanie H. Kucherlapati, Raju S. Kucherlapati, Stephen Baylin, Leslie Cope, Ludmila Danilova, Moiz S. Bootwalla, Phillip H. Lai, Dennis T. Maglinte, David J. Van Den Berg, Daniel J. Weisenberger, J. Todd Auman, Saianand Balu, Tom Bodenheimer, Cheng Fan, Katherine A. Hoadley, Alan P. Hoyle, Stuart R. Jefferys, Corbin D. Jones, Shaowu Meng, Piotr A. Mieczkowski, Lisle E. Mose, Amy H. Perou, Charles M. Perou, Jeffrey Roach, Yan Shi, Janae V. Simons, Tara Skelly, Matthew G. Soloway, Donghui Tan, Umadevi Veluvolu, Huihui Fan, Toshinori Hinoue, Peter W. Laird, Hui Shen, Wanding Zhou, Michelle Bellair, Kyle Chang, Kyle Covington, Chad J. Creighton, Huyen Dinh, HarshaVardhan Doddapaneni, Lawrence A. Donehower, Jennifer Drummond, Richard A. Gibbs, Robert Glenn, Walker Hale, Yi Han, Jianhong Hu, Viktoriya Korchina, Sandra Lee, Lora Lewis, Wei Li, Xiuping Liu, Margaret Morgan, Donna Morton, Donna Muzny, Jireh Santibanez, Margi Sheth, Eve Shinbrot, Linghua Wang, Min Wang, David A. Wheeler, Liu Xi, Fengmei Zhao, Julian Hess, Elizabeth L. Appelbaum, Matthew Bailey, Matthew G. Cordes, Li Ding, Catrina C. Fronick, Lucinda A. Fulton, Robert S. Fulton, Cyriac Kandoth, Elaine R. Mardis, Michael D. McLellan, Christopher A. Miller, Heather K. Schmidt, Richard K. Wilson, Daniel Crain, Erin Curley, Johanna Gardner, Kevin Lau, David Mallery, Scott Morris, Joseph Paulauskis, Robert Penny, Candace Shelton, Troy Shelton, Mark Sherman, Eric Thompson, Peggy Yena, Jay Bowen, Julie M. Gastier-Foster, Mark Gerken, Kristen M. Leraas, Tara M. Lichtenberg, Nilsa C. Ramirez, Lisa Wise, Erik Zmuda, Niall Corcoran, Tony Costello, Christopher Hovens, Andre L. Carvalho, Ana C. de Carvalho, José H. Fregnani, Adhemar Longatto-Filho, Rui M. Reis, Cristovam Scapulatempo-Neto, Henrique C.S. Silveira, Daniel O. Vidal, Andrew Burnette, Jennifer Eschbacher, Beth Hermes, Ardene Noss, Rosy Singh, Matthew L. Anderson, Patricia D. Castro, Michael Ittmann, David Huntsman, Bernard Kohl, Xuan Le, Richard Thorp, Chris Andry, Elizabeth R. Duffy, Vladimir Lyadov, Oxana Paklina, Galiya Setdikova, Alexey Shabunin, Mikhail Tavobilov, Christopher McPherson, Ronald Warnick, Ross Berkowitz, Daniel Cramer, Colleen Feltmate, Neil Horowitz, Adam Kibel, Michael Muto, Chandrajit P. Raut, Andrei Malykh, Jill S. Barnholtz-Sloan, Wendi Barrett, Karen Devine, Jordonna Fulop, Quinn T. Ostrom, Kristen Shimmel, Yingli Wolinsky, Andrew E. Sloan, Agostino De Rose, Felice Giuliante, Marc Goodman, Beth Y. Karlan, Curt H. Hagedorn, John Eckman, Jodi Harr, Jerome Myers, Kelinda Tucker, Leigh Anne Zach, Brenda Deyarmin, Hai Hu, Leonid Kvecher, Caroline Larson, Richard J. Mural, Stella Somiari, Ales Vicha, Tomas Zelinka, Joseph Bennett, Mary Iacocca, Brenda Rabeno, Patricia Swanson, Mathieu Latour, Louis Lacombe, Bernard Têtu, Alain Bergeron, Mary McGraw, Susan M. Staugaitis, John Chabot, Hanina Hibshoosh, Antonia Sepulveda, Tao Su, Timothy Wang, Olga Potapova, Olga Voronina, Laurence Desjardins, Odette Mariani, Sergio Roman-Roman, Xavier Sastre, Marc-Henri Stern, Feixiong Cheng, Sabina Signoretti, Andrew Berchuck, Darell Bigner, Eric Lipp, Jeffrey Marks, Shannon McCall, Roger McLendon, Angeles Secord, Alexis Sharp, Madhusmita Behera, Daniel J. Brat, Amy Chen, Keith Delman, Seth Force, Fadlo Khuri, Kelly Magliocca, Shishir Maithel, Jeffrey J. Olson, Taofeek Owonikoko, Alan Pickens, Suresh Ramalingam, Dong M. Shin, Gabriel Sica, Erwin G. Van Meir, Hongzheng Zhang, Wil Eijckenboom, Ad Gillis, Esther Korpershoek, Leendert Looijenga, Wolter Oosterhuis, Hans Stoop, Kim E. van Kessel, Ellen C. Zwarthoff, Chiara Calatozzolo, Lucia Cuppini, Stefania Cuzzubbo, Francesco DiMeco, Gaetano Finocchiaro, Luca Mattei, Alessandro Perin, Bianca Pollo, Chu Chen, John Houck, Pawadee Lohavanichbutr, Arndt Hartmann, Christine Stoehr, Robert Stoehr, Helge Taubert, Sven Wach, Bernd Wullich, Witold Kycler, Dawid Murawa, Maciej Wiznerowicz, Ki Chung, W. Jeffrey Edenfield, Julie Martin, Eric Baudin, Glenn Bubley, Raphael Bueno, Assunta De Rienzo, William G. Richards, Steven Kalkanis, Tom Mikkelsen, Houtan Noushmehr, Lisa Scarpace, Nicolas Girard, Marta Aymerich, Elias Campo, Eva Giné, Armando López Guillermo, Nguyen Van Bang, Phan Thi Hanh, Bui Duc Phu, Yufang Tang, Howard Colman, Kimberley Evason, Peter R. Dottino, John A. Martignetti, Hani Gabra, Hartmut Juhl, Teniola Akeredolu, Serghei Stepa, Dave Hoon, Keunsoo Ahn, Koo Jeong Kang, Felix Beuschlein, Anne Breggia, Michael Birrer, Debra Bell, Mitesh Borad, Alan H. Bryce, Erik Castle, Vishal Chandan, John Cheville, John A. Copland, Michael Farnell, Thomas Flotte, Nasra Giama, Thai Ho, Michael Kendrick, Jean-Pierre Kocher, Karla Kopp, Catherine Moser, David Nagorney, Daniel O’Brien, Brian Patrick O’Neill, Tushar Patel, Gloria Petersen, Florencia Que, Michael Rivera, Lewis Roberts, Robert Smallridge, Thomas Smyrk, Melissa Stanton, R. Houston Thompson, Michael Torbenson, Ju Dong Yang, Lizhi Zhang, Fadi Brimo, Jaffer A. Ajani, Ana Maria Angulo Gonzalez, Carmen Behrens, Jolanta Bondaruk, Russell Broaddus, Bogdan Czerniak, Bita Esmaeli, Junya Fujimoto, Jeffrey Gershenwald, Charles Guo, Alexander J. Lazar, Christopher Logothetis, Funda Meric-Bernstam, Cesar Moran, Lois Ramondetta, David Rice, Anil Sood, Pheroze Tamboli, Timothy Thompson, Patricia Troncoso, Anne Tsao, Ignacio Wistuba, Candace Carter, Lauren Haydu, Peter Hersey, Valerie Jakrot, Hojabr Kakavand, Richard Kefford, Kenneth Lee, Georgina Long, Graham Mann, Michael Quinn, Robyn Saw, Richard Scolyer, Kerwin Shannon, Andrew Spillane, Jonathan Stretch, Maria Synott, John Thompson, James Wilmott, Hikmat Al-Ahmadie, Timothy A. Chan, Ronald Ghossein, Anuradha Gopalan, Douglas A. Levine, Victor Reuter, Samuel Singer, Bhuvanesh Singh, Nguyen Viet Tien, Thomas Broudy, Cyrus Mirsaidi, Praveen Nair, Paul Drwiega, Judy Miller, Jennifer Smith, Howard Zaren, Joong-Won Park, Nguyen Phi Hung, Electron Kebebew, W. Marston Linehan, Adam R. Metwalli, Karel Pacak, Peter A. Pinto, Mark Schiffman, Laura S. Schmidt, Cathy D. Vocke, Nicolas Wentzensen, Robert Worrell, Hannah Yang, Marc Moncrieff, Chandra Goparaju, Jonathan Melamed, Harvey Pass, Natalia Botnariuc, Irina Caraman, Mircea Cernat, Inga Chemencedji, Adrian Clipca, Serghei Doruc, Ghenadie Gorincioi, Sergiu Mura, Maria Pirtac, Irina Stancul, Diana Tcaciuc, Monique Albert, Iakovina Alexopoulou, Angel Arnaout, John Bartlett, Jay Engel, Sebastien Gilbert, Jeremy Parfitt, Harman Sekhon, George Thomas, Doris M. Rassl, Robert C. Rintoul, Carlo Bifulco, Raina Tamakawa, Walter Urba, Nicholas Hayward, Henri Timmers, Anna Antenucci, Francesco Facciolo, Gianluca Grazi, Mirella Marino, Roberta Merola, Ronald de Krijger, Anne-Paule Gimenez-Roqueplo, Alain Piché, Simone Chevalier, Ginette McKercher, Kivanc Birsoy, Gene Barnett, Cathy Brewer, Carol Farver, Theresa Naska, Nathan A. Pennell, Daniel Raymond, Cathy Schilero, Kathy Smolenski, Felicia Williams, Carl Morrison, Jeffrey A. Borgia, Michael J. Liptay, Mark Pool, Christopher W. Seder, Kerstin Junker, Larsson Omberg, Mikhail Dinkin, George Manikhas, Domenico Alvaro, Maria Consiglia Bragazzi, Vincenzo Cardinale, Guido Carpino, Eugenio Gaudio, David Chesla, Sandra Cottingham, Michael Dubina, Fedor Moiseenko, Renumathy Dhanasekaran, Karl-Friedrich Becker, Klaus-Peter Janssen, Julia Slotta-Huspenina, Mohamed H. Abdel-Rahman, Dina Aziz, Sue Bell, Colleen M. Cebulla, Amy Davis, Rebecca Duell, J. Bradley Elder, Joe Hilty, Bahavna Kumar, James Lang, Norman L. Lehman, Randy Mandt, Phuong Nguyen, Robert Pilarski, Karan Rai, Lynn Schoenfield, Kelly Senecal, Paul Wakely, Paul Hansen, Ronald Lechan, James Powers, Arthur Tischler, William E. Grizzle, Katherine C. Sexton, Alison Kastl, Joel Henderson, Sima Porten, Jens Waldmann, Martin Fassnacht, Sylvia L. Asa, Dirk Schadendorf, Marta Couce, Markus Graefen, Hartwig Huland, Guido Sauter, Thorsten Schlomm, Ronald Simon, Pierre Tennstedt, Oluwole Olabode, Mark Nelson, Oliver Bathe, Peter R. Carroll, June M. Chan, Philip Disaia, Pat Glenn, Robin K. Kelley, Charles N. Landen, Joanna Phillips, Michael Prados, Jeffry Simko, Karen Smith-McCune, Scott VandenBerg, Kevin Roggin, Ashley Fehrenbach, Ady Kendler, Suzanne Sifri, Ruth Steele, Antonio Jimeno, Francis Carey, Ian Forgie, Massimo Mannelli, Michael Carney, Brenda Hernandez, Benito Campos, Christel Herold-Mende, Christin Jungk, Andreas Unterberg, Andreas von Deimling, Aaron Bossler, Joseph Galbraith, Laura Jacobus, Michael Knudson, Tina Knutson, Deqin Ma, Mohammed Milhem, Rita Sigmund, Andrew K. Godwin, Rashna Madan, Howard G. Rosenthal, Clement Adebamowo, Sally N. Adebamowo, Alex Boussioutas, David Beer, Thomas Giordano, Anne-Marie Mes-Masson, Fred Saad, Therese Bocklage, Lisa Landrum, Robert Mannel, Kathleen Moore, Katherine Moxley, Russel Postier, Joan Walker, Rosemary Zuna, Michael Feldman, Federico Valdivieso, Rajiv Dhir, James Luketich, Edna M. Mora Pinero, Mario Quintero-Aguilo, Carlos Gilberto Carlotti, Jose Sebastião Dos Santos, Rafael Kemp, Ajith Sankarankuty, Daniela Tirapelli, James Catto, Kathy Agnew, Elizabeth Swisher, Jenette Creaney, Bruce Robinson, Carl Simon Shelley, Eryn M. Godwin, Sara Kendall, Cassaundra Shipman, Carol Bradford, Thomas Carey, Andrea Haddad, Jeffey Moyer, Lisa Peterson, Mark Prince, Laura Rozek, Gregory Wolf, Rayleen Bowman, Kwun M. Fong, Ian Yang, Robert Korst, W. Kimryn Rathmell, J. Leigh Fantacone-Campbell, Jeffrey A. Hooke, Albert J. Kovatich, Craig D. Shriver, John DiPersio, Bettina Drake, Ramaswamy Govindan, Sharon Heath, Timothy Ley, Brian Van Tine, Peter Westervelt, Mark A. Rubin, Jung Il Lee, Natália D. Aredes, Armaz Mariamidze, Cancer Genome Atlas Research Network, Caesar-Johnson, S.J., Demchok, J.A., Felau, I., Kasapi, M., Ferguson, M.L., Hutter, C.M., Sofia, H.J., Tarnuzzer, R., Wang, Z., Yang, L., Zenklusen, J.C., Zhang, J.J., Chudamani, S., Liu, J., Lolla, L., Naresh, R., Pihl, T., Sun, Q., Wan, Y., Wu, Y., Cho, J., DeFreitas, T., Frazer, S., Gehlenborg, N., Getz, G., Heiman, D.I., Kim, J., Lawrence, M.S., Lin, P., Meier, S., Noble, M.S., Saksena, G., Voet, D., Zhang, H., Bernard, B., Chambwe, N., Dhankani, V., Knijnenburg, T., Kramer, R., Leinonen, K., Liu, Y., Miller, M., Reynolds, S., Shmulevich, I., Thorsson, V., Zhang, W., Akbani, R., Broom, B.M., Hegde, A.M., Ju, Z., Kanchi, R.S., Korkut, A., Li, J., Liang, H., Ling, S., Liu, W., Lu, Y., Mills, G.B., Ng, K.S., Rao, A., Ryan, M., Wang, J., Weinstein, J.N., Zhang, J., Abeshouse, A., Armenia, J., Chakravarty, D., Chatila, W.K., de Bruijn, I., Gao, J., Gross, B.E., Heins, Z.J., Kundra, R., La, K., Ladanyi, M., Luna, A., Nissan, M.G., Ochoa, A., Phillips, S.M., Reznik, E., Sanchez-Vega, F., Sander, C., Schultz, N., Sheridan, R., Sumer, S.O., Sun, Y., Taylor, B.S., Anur, P., Peto, M., Spellman, P., Benz, C., Stuart, J.M., Wong, C.K., Yau, C., Hayes, D.N., Parker, J.S., Wilkerson, M.D., Ally, A., Balasundaram, M., Bowlby, R., Brooks, D., Carlsen, R., Chuah, E., Dhalla, N., Holt, R., Jones, SJM, Kasaian, K., Lee, D., Ma, Y., Marra, M.A., Mayo, M., Moore, R.A., Mungall, A.J., Mungall, K., Robertson, A.G., Sadeghi, S., Schein, J.E., Sipahimalani, P., Tam, A., Thiessen, N., Tse, K., Wong, T., Berger, A.C., Beroukhim, R., Cherniack, A.D., Cibulskis, C., Gabriel, S.B., Gao, G.F., Ha, G., Meyerson, M., Schumacher, S.E., Shih, J., Kucherlapati, M.H., Kucherlapati, R.S., Baylin, S., Cope, L., Danilova, L., Bootwalla, M.S., Lai, P.H., Maglinte, D.T., Van Den Berg, D.J., Weisenberger, D.J., Auman, J.T., Balu, S., Bodenheimer, T., Fan, C., Hoadley, K.A., Hoyle, A.P., Jefferys, S.R., Jones, C.D., Meng, S., Mieczkowski, P.A., Mose, L.E., Perou, A.H., Perou, C.M., Roach, J., Shi, Y., Simons, J.V., Skelly, T., Soloway, M.G., Tan, D., Veluvolu, U., Fan, H., Hinoue, T., Laird, P.W., Shen, H., Zhou, W., Bellair, M., Chang, K., Covington, K., Creighton, C.J., Dinh, H., Doddapaneni, H., Donehower, L.A., Drummond, J., Gibbs, R.A., Glenn, R., Hale, W., Han, Y., Hu, J., Korchina, V., Lee, S., Lewis, L., Li, W., Liu, X., Morgan, M., Morton, D., Muzny, D., Santibanez, J., Sheth, M., Shinbrot, E., Wang, L., Wang, M., Wheeler, D.A., Xi, L., Zhao, F., Hess, J., Appelbaum, E.L., Bailey, M., Cordes, M.G., Ding, L., Fronick, C.C., Fulton, L.A., Fulton, R.S., Kandoth, C., Mardis, E.R., McLellan, M.D., Miller, C.A., Schmidt, H.K., Wilson, R.K., Crain, D., Curley, E., Gardner, J., Lau, K., Mallery, D., Morris, S., Paulauskis, J., Penny, R., Shelton, C., Shelton, T., Sherman, M., Thompson, E., Yena, P., Bowen, J., Gastier-Foster, J.M., Gerken, M., Leraas, K.M., Lichtenberg, T.M., Ramirez, N.C., Wise, L., Zmuda, E., Corcoran, N., Costello, T., Hovens, C., Carvalho, A.L., de Carvalho, A.C., Fregnani, J.H., Longatto-Filho, A., Reis, R.M., Scapulatempo-Neto, C., Silveira, HCS, Vidal, D.O., Burnette, A., Eschbacher, J., Hermes, B., Noss, A., Singh, R., Anderson, M.L., Castro, P.D., Ittmann, M., Huntsman, D., Kohl, B., Le, X., Thorp, R., Andry, C., Duffy, E.R., Lyadov, V., Paklina, O., Setdikova, G., Shabunin, A., Tavobilov, M., McPherson, C., Warnick, R., Berkowitz, R., Cramer, D., Feltmate, C., Horowitz, N., Kibel, A., Muto, M., Raut, C.P., Malykh, A., Barnholtz-Sloan, J.S., Barrett, W., Devine, K., Fulop, J., Ostrom, Q.T., Shimmel, K., Wolinsky, Y., Sloan, A.E., De Rose, A., Giuliante, F., Goodman, M., Karlan, B.Y., Hagedorn, C.H., Eckman, J., Harr, J., Myers, J., Tucker, K., Zach, L.A., Deyarmin, B., Hu, H., Kvecher, L., Larson, C., Mural, R.J., Somiari, S., Vicha, A., Zelinka, T., Bennett, J., Iacocca, M., Rabeno, B., Swanson, P., Latour, M., Lacombe, L., Têtu, B., Bergeron, A., McGraw, M., Staugaitis, S.M., Chabot, J., Hibshoosh, H., Sepulveda, A., Su, T., Wang, T., Potapova, O., Voronina, O., Desjardins, L., Mariani, O., Roman-Roman, S., Sastre, X., Stern, M.H., Cheng, F., Signoretti, S., Berchuck, A., Bigner, D., Lipp, E., Marks, J., McCall, S., McLendon, R., Secord, A., Sharp, A., Behera, M., Brat, D.J., Chen, A., Delman, K., Force, S., Khuri, F., Magliocca, K., Maithel, S., Olson, J.J., Owonikoko, T., Pickens, A., Ramalingam, S., Shin, D.M., Sica, G., Van Meir, E.G., Eijckenboom, W., Gillis, A., Korpershoek, E., Looijenga, L., Oosterhuis, W., Stoop, H., van Kessel, K.E., Zwarthoff, E.C., Calatozzolo, C., Cuppini, L., Cuzzubbo, S., DiMeco, F., Finocchiaro, G., Mattei, L., Perin, A., Pollo, B., Chen, C., Houck, J., Lohavanichbutr, P., Hartmann, A., Stoehr, C., Stoehr, R., Taubert, H., Wach, S., Wullich, B., Kycler, W., Murawa, D., Wiznerowicz, M., Chung, K., Edenfield, W.J., Martin, J., Baudin, E., Bubley, G., Bueno, R., De Rienzo, A., Richards, W.G., Kalkanis, S., Mikkelsen, T., Noushmehr, H., Scarpace, L., Girard, N., Aymerich, M., Campo, E., Giné, E., Guillermo, A.L., Van Bang, N., Hanh, P.T., Phu, B.D., Tang, Y., Colman, H., Evason, K., Dottino, P.R., Martignetti, J.A., Gabra, H., Juhl, H., Akeredolu, T., Stepa, S., Hoon, D., Ahn, K., Kang, K.J., Beuschlein, F., Breggia, A., Birrer, M., Bell, D., Borad, M., Bryce, A.H., Castle, E., Chandan, V., Cheville, J., Copland, J.A., Farnell, M., Flotte, T., Giama, N., Ho, T., Kendrick, M., Kocher, J.P., Kopp, K., Moser, C., Nagorney, D., O'Brien, D., O'Neill, B.P., Patel, T., Petersen, G., Que, F., Rivera, M., Roberts, L., Smallridge, R., Smyrk, T., Stanton, M., Thompson, R.H., Torbenson, M., Yang, J.D., Zhang, L., Brimo, F., Ajani, J.A., Gonzalez, AMA, Behrens, C., Bondaruk, J., Broaddus, R., Czerniak, B., Esmaeli, B., Fujimoto, J., Gershenwald, J., Guo, C., Lazar, A.J., Logothetis, C., Meric-Bernstam, F., Moran, C., Ramondetta, L., Rice, D., Sood, A., Tamboli, P., Thompson, T., Troncoso, P., Tsao, A., Wistuba, I., Carter, C., Haydu, L., Hersey, P., Jakrot, V., Kakavand, H., Kefford, R., Lee, K., Long, G., Mann, G., Quinn, M., Saw, R., Scolyer, R., Shannon, K., Spillane, A., Stretch, J., Synott, M., Thompson, J., Wilmott, J., Al-Ahmadie, H., Chan, T.A., Ghossein, R., Gopalan, A., Levine, D.A., Reuter, V., Singer, S., Singh, B., Tien, N.V., Broudy, T., Mirsaidi, C., Nair, P., Drwiega, P., Miller, J., Smith, J., Zaren, H., Park, J.W., Hung, N.P., Kebebew, E., Linehan, W.M., Metwalli, A.R., Pacak, K., Pinto, P.A., Schiffman, M., Schmidt, L.S., Vocke, C.D., Wentzensen, N., Worrell, R., Yang, H., Moncrieff, M., Goparaju, C., Melamed, J., Pass, H., Botnariuc, N., Caraman, I., Cernat, M., Chemencedji, I., Clipca, A., Doruc, S., Gorincioi, G., Mura, S., Pirtac, M., Stancul, I., Tcaciuc, D., Albert, M., Alexopoulou, I., Arnaout, A., Bartlett, J., Engel, J., Gilbert, S., Parfitt, J., Sekhon, H., Thomas, G., Rassl, D.M., Rintoul, R.C., Bifulco, C., Tamakawa, R., Urba, W., Hayward, N., Timmers, H., Antenucci, A., Facciolo, F., Grazi, G., Marino, M., Merola, R., de Krijger, R., Gimenez-Roqueplo, A.P., Piché, A., Chevalier, S., McKercher, G., Birsoy, K., Barnett, G., Brewer, C., Farver, C., Naska, T., Pennell, N.A., Raymond, D., Schilero, C., Smolenski, K., Williams, F., Morrison, C., Borgia, J.A., Liptay, M.J., Pool, M., Seder, C.W., Junker, K., Omberg, L., Dinkin, M., Manikhas, G., Alvaro, D., Bragazzi, M.C., Cardinale, V., Carpino, G., Gaudio, E., Chesla, D., Cottingham, S., Dubina, M., Moiseenko, F., Dhanasekaran, R., Becker, K.F., Janssen, K.P., Slotta-Huspenina, J., Abdel-Rahman, M.H., Aziz, D., Bell, S., Cebulla, C.M., Davis, A., Duell, R., Elder, J.B., Hilty, J., Kumar, B., Lang, J., Lehman, N.L., Mandt, R., Nguyen, P., Pilarski, R., Rai, K., Schoenfield, L., Senecal, K., Wakely, P., Hansen, P., Lechan, R., Powers, J., Tischler, A., Grizzle, W.E., Sexton, K.C., Kastl, A., Henderson, J., Porten, S., Waldmann, J., Fassnacht, M., Asa, S.L., Schadendorf, D., Couce, M., Graefen, M., Huland, H., Sauter, G., Schlomm, T., Simon, R., Tennstedt, P., Olabode, O., Nelson, M., Bathe, O., Carroll, P.R., Chan, J.M., Disaia, P., Glenn, P., Kelley, R.K., Landen, C.N., Phillips, J., Prados, M., Simko, J., Smith-McCune, K., VandenBerg, S., Roggin, K., Fehrenbach, A., Kendler, A., Sifri, S., Steele, R., Jimeno, A., Carey, F., Forgie, I., Mannelli, M., Carney, M., Hernandez, B., Campos, B., Herold-Mende, C., Jungk, C., Unterberg, A., von Deimling, A., Bossler, A., Galbraith, J., Jacobus, L., Knudson, M., Knutson, T., Ma, D., Milhem, M., Sigmund, R., Godwin, A.K., Madan, R., Rosenthal, H.G., Adebamowo, C., Adebamowo, S.N., Boussioutas, A., Beer, D., Giordano, T., Mes-Masson, A.M., Saad, F., Bocklage, T., Landrum, L., Mannel, R., Moore, K., Moxley, K., Postier, R., Walker, J., Zuna, R., Feldman, M., Valdivieso, F., Dhir, R., Luketich, J., Pinero, EMM, Quintero-Aguilo, M., Carlotti, C.G., Dos Santos, J.S., Kemp, R., Sankarankuty, A., Tirapelli, D., Catto, J., Agnew, K., Swisher, E., Creaney, J., Robinson, B., Shelley, C.S., Godwin, E.M., Kendall, S., Shipman, C., Bradford, C., Carey, T., Haddad, A., Moyer, J., Peterson, L., Prince, M., Rozek, L., Wolf, G., Bowman, R., Fong, K.M., Yang, I., Korst, R., Rathmell, W.K., Fantacone-Campbell, J.L., Hooke, J.A., Kovatich, A.J., Shriver, C.D., DiPersio, J., Drake, B., Govindan, R., Heath, S., Ley, T., Van Tine, B., Westervelt, P., Rubin, M.A., Lee, J.I., Aredes, N.D., Mariamidze, A., SAIC-F-Frederick, Inc, and Leidos Biomedical Research, Inc.
Subjects: 0301 basic medicine, Neuroblastoma RAS viral oncogene homolog, Genetics and Molecular Biology (all), PATHOGENESIS, pan-cancer, PROTEIN, Cancer Genome Atlas Research Network, medicine.disease_cause, computer.software_genre, Genome, Biochemistry, Transcriptome, Gene expression, HRAS, KRAS, NF1, NRAS, Ras, TCGA, drug sensitivity, machine learning, Neoplasms, PRECISION ONCOLOGY, lcsh:QH301-705.5, Regulation of gene expression, PREVIOUSLY TREATED PATIENTS, 3. Good health, Gene Expression Regulation, Neoplastic, PHASE-II, Life Sciences & Biomedicine, Signal Transduction, Biology, Machine learning, General Biochemistry, Genetics and Molecular Biology, Article, BRAF, 03 medical and health sciences, Cell Line, Tumor, medicine, Biochemistry, Genetics and Molecular Biology (all), Humans, Gene, SIGNATURES, Science & Technology, business.industry, Genome, Human, MUTATIONS, EXPRESSÃO GÊNICA, Cell Biology, SELUMETINIB, GENE, 030104 developmental biology, lcsh:Biology (General), Selumetinib, ras Proteins, Artificial intelligence, business, computer
Abstract: SUMMARY Precision oncology uses genomic evidence to match patients with treatment but often fails to identify all patients who may respond. The transcriptome of these “hidden responders” may reveal responsive molecular states. We describe and evaluate a machine-learning approach to classify aberrant pathway activity in tumors, which may aid in hidden responder identification. The algorithm integrates RNA-seq, copy number, and mutations from 33 different cancer types across The Cancer Genome Atlas (TCGA) PanCanAtlas project to predict aberrant molecular states in tumors. Applied to the Ras pathway, the method detects Ras activation across cancer types and identifies phenocopying variants. The model, trained on human tumors, can predict response to MEK inhibitors in wild-type Ras cell lines. We also present data that suggest that multiple hits in the Ras pathway confer increased Ras activity. The transcriptome is underused in precision oncology and, combined with machine learning, can aid in the identification of hidden responders., In Brief Way et al. develop a machine-learning approach using PanCanAtlas data to detect Ras activation in cancer. Integrating mutation, copy number, and expression data, the authors show that their method detects Ras-activating variants in tumors and sensitivity to MEK inhibitors in cell lines.
Published: 2018

15. Prevalence and risk factor for injury in sub-Saharan Africa: a multicountry study

Author: Francis Bajunirwe, David Guwatudde, Marina Njelekela, IkeOluwapo O. Ajayi, Carien Laurence, Faraja S. Chiwanga, Hans-Olov Adami, Michelle D. Holmes, Shona Dalal, Joan Nankya-Mutyoba, Clement Adebamowo, David Hemenway, Todd G. Reid, Robert Kalyesubula, and Megan B. Diamond
Subjects: Adult, Male, medicine.medical_specialty, Alcohol Drinking, Cross-sectional study, Pilot Projects, Violence, Logistic regression, Odds, Young Adult, 03 medical and health sciences, 0302 clinical medicine, Risk Factors, Environmental health, Epidemiology, Prevalence, medicine, Humans, 030212 general & internal medicine, Risk factor, Africa South of the Sahara, business.industry, 030503 health policy & services, Incidence (epidemiology), Public Health, Environmental and Occupational Health, Middle Aged, medicine.disease, Accidents, Cohort, Educational Status, Wounds and Injuries, Population study, Female, Public Health, Medical emergency, 0305 other medical science, business, Follow-Up Studies
Abstract: IntroductionInjury-related morbidity is a neglected health concern in many low-income and middle-income countries. Most injury data in Africa have been collected from hospital-based studies, and few studies have occurred across multiple countries. Using data from a novel cohort, we examined the prevalence and incidence of serious injuries and associated risk factors across five sites in sub-Saharan Africa (SSA).MethodsA common baseline and follow-up survey was administered to participants. The study population included 1316 persons at baseline and 904 persons at follow-up. Frequencies were calculated, and logistic regression models were used to assess risk factors for injury.ResultsA total of 233 (17.7%) persons reported a serious injury at baseline and 60 (6.6%) reported a serious injury 6 months later at follow-up. Sixty-nine per cent of participants responded to the follow-up questionnaire. At baseline and follow-up, the most common cause of serious injury at urban sites was transport related, followed by poison/overdose. In rural Uganda, sharp instruments injuries were most common, followed by transport-related injuries. Living at an urban site was associated with an increased odds for serious injury compared with those at the rural site (OR: 1.83, 95% CI 1.15 to 2.90). Participants who consumed above a moderate amount of alcohol were at a higher risk of serious injury compared with those who did not consume alcohol (OR: 1.86, 95% CI 1.02 to 3.41). High level of education was an important risk factor for injury.ConclusionAt baseline and follow-up, common causes of serious injury were transport related, sharp instrument and poison/overdose. Alcohol consumption, urban location and education are important risk factors for injury. It is feasible to collect longitudinal injury data using a standardised questionnaire across multiples sites in SSA. Longitudinal data collection should be leveraged to obtain robust data on risk factors for injury in SSA.
Published: 2017
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16. Serum Metabolomic Profiles Identify ER-Positive Early Breast Cancer Patients at Increased Risk of Disease Recurrence in a Multicenter Population

Author: Angelo Di Leo, Clement Adebamowo, Emanuela Risi, Claudio Luchinat, Christopher D. Hart, Gemma Leonora Uy, Richard R. Love, Alessia Vignoli, Syed Mozammel Hossain, Ta Van To, Leonardo Tenori, and Laura Biganzoli
Subjects: 0301 basic medicine, Oncology, Cancer Research, medicine.medical_specialty, Receptor, ErbB-2, medicine.medical_treatment, Population, Estrogen receptor, Breast Neoplasms, Disease, Article, 03 medical and health sciences, 0302 clinical medicine, Breast cancer, Risk Factors, Internal medicine, Biomarkers, Tumor, medicine, Humans, Metabolomics, Neoplasm Metastasis, education, Nuclear Magnetic Resonance, Biomolecular, education.field_of_study, business.industry, Cancer, Prognosis, medicine.disease, metabolomics, breast cancer, NMR, relapse prediction, Metastatic breast cancer, respiratory tract diseases, Surgery, 030104 developmental biology, Receptors, Estrogen, 030220 oncology & carcinogenesis, Cohort, Metabolome, Female, Neoplasm Recurrence, Local, business, Adjuvant
Abstract: Purpose: Detecting signals of micrometastatic disease in patients with early breast cancer (EBC) could improve risk stratification and allow better tailoring of adjuvant therapies. We previously showed that postoperative serum metabolomic profiles were predictive of relapse in a single-center cohort of estrogen receptor (ER)–negative EBC patients. Here, we investigated this further using preoperative serum samples from ER-positive, premenopausal women with EBC who were enrolled in an international phase III trial. Experimental Design: Proton nuclear magnetic resonance (NMR) spectroscopy of 590 EBC samples (319 with relapse or ≥6 years clinical follow-up) and 109 metastatic breast cancer (MBC) samples was performed. A Random Forest (RF) classification model was built using a training set of 85 EBC and all MBC samples. The model was then applied to a test set of 234 EBC samples, and a risk of recurrence score was generated on the basis of the likelihood of the sample being misclassified as metastatic. Results: In the training set, the RF model separated EBC from MBC with a discrimination accuracy of 84.9%. In the test set, the RF recurrence risk score correlated with relapse, with an AUC of 0.747 in ROC analysis. Accuracy was maximized at 71.3% (sensitivity, 70.8%; specificity, 71.4%). The model performed independently of age, tumor size, grade, HER2 status and nodal status, and also of Adjuvant! Online risk of relapse score. Conclusions: In a multicenter group of EBC patients, we developed a model based on preoperative serum metabolomic profiles that was prognostic for disease recurrence, independent of traditional clinicopathologic risk factors. Clin Cancer Res; 23(6); 1422–31. ©2017 AACR.
Published: 2017
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17. Genome-wide analysis identifies an african-specific variant in SEMA4D associated with body mass index

Author: Albert G.B. Amoah, Thomas Johnson, Jennifer L. Baker, Joseph Acheampong, Ayo P. Doumatey, Johnnie Oli, Clement Adebamowo, Guanjie Chen, Charles N. Rotimi, Fasil Tekola-Ayele, Jie Zhou, Amy R. Bentley, Lin Lei, Godfrey Okafor, Benjamin A. Eghan, Olufemi Fasanmade, Daniel Shriner, Kofi Agyenim-Boateng, Adebowale Adeyemo, and Sally N. Adebamowo
Subjects: 0301 basic medicine, Genetics, medicine.medical_specialty, Nutrition and Dietetics, business.industry, Endocrinology, Diabetes and Metabolism, Medicine (miscellaneous), 030209 endocrinology & metabolism, Genome-wide association study, Locus (genetics), medicine.disease, Obesity, Minor allele frequency, 03 medical and health sciences, 030104 developmental biology, 0302 clinical medicine, Endocrinology, Internal medicine, Genotype, medicine, Allele, business, Body mass index, Allele frequency
Abstract: Objective The prevalence of obesity varies between ethnic groups. No genome-wide association study (GWAS) for body mass index (BMI) has been conducted in continental Africans. Methods We performed a GWAS for BMI in 1,570 West Africans (WA). Replication was conducted in independent samples of WA (n = 1,411) and African Americans (AA) (n = 9,020). Results We identified a novel genome-wide significant African-specific locus for BMI (SEMA4D, rs80068415; minor allele frequency = 0.008, P = 2.10 × 10−8). This finding was replicated in independent samples of WA (P = 0.013) and AA (P = 0.017). Individuals with obesity had higher serum SEMA4D levels compared to those without obesity (P
Published: 2017
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18. Leisure Time Physical Activity Is Associated with Substantial Reduction in Risk of Breast Cancer and Breast Cancer Subtypes in Nigerian Women (P16-007-19)

Author: Iliya Karniliyus Salu, Emmanuel Ezeome, Clement Adebamowo, Galya Bigman, Owale Badejo, Elima Jedy-Agba, and Sally Adebamowo
Subjects: Oncology, medicine.medical_specialty, Nutrition and Dietetics, business.industry, media_common.quotation_subject, Leisure time, Physical activity, Medicine (miscellaneous), Estrogen receptor, Fertility, Nutrition Education and Behavioral Science, medicine.disease, Breast cancer, Internal medicine, medicine, Aerobic exercise, Nurses' Health Study, business, human activities, Triple-negative breast cancer, Food Science, media_common
Abstract: OBJECTIVES: To examine the association between leisure-time physical activity (LTPA) and breast cancer in Nigerian women. The hypothesis was that LTPA decreased breast cancer cases in Nigerian women. To examine the association between LTPA and estrogen receptor positive (ER+), triple negative breast cancer (TNBC+), Luminal A breast cancer in Nigerian women. The hypothesis was that LTPA decreased breast cancer subtypes in Nigerian women. METHODS: We enrolled 739 newly diagnosed primary invasive breast cancer and 739 age-matched controls in Nigeria from 01/2014 to 07/2016. This analysis is restricted to the 40% of cases for whom we have complete ER, TNBC, and Luminal-A data and their matched controls. We derived the average amount of time per week spent on LTPA over the past year using a modified Nurses’ Health Study II PA questionnaire. LTPA was calculated from the total metabolic equivalent (METs) assigned for each reported physical activity hour/week (i.e., walking, cycling, and dancing). We examined LTPA by comparing participants who attained the WHO physical activity recommendations of at least 150 minutes of moderate-intensity or/and 75 minutes of vigorous-intensity aerobic activity weekly with those who did not. We used conditional logistic regression to estimate the adjusted Odds Ratio (OR) of LTPA and overall as well as subtypes of breast cancer. RESULTS: The mean (SD) age of cases was 41.6 (9.1) and controls 43.9 (11.8) years. Women who attained the WHO physical activity recommendations had 43% decreased the risk of breast cancer (OR = 0.57, 95% CI:0.42–0.77) compared with those who did not, after controlling for demographic, anthropometric and fertility-related factors. LTPA was also associated with reduced risk of breast cancer subtypes by 41% for ER+, 59% for TNBC+and 59% for Luminal A. CONCLUSIONS: Physical activity is associated with reduced risk of breast cancer overall and by subtypes in Nigerian women. FUNDING SOURCES: Training Program in Nigeria for Non-Communicable Diseases Research (TRAPING NCD) grant number FIC/NIH D43TW009106 from the Fogarty International Centre. The content is solely the responsibility of the authors and does not necessarily represent the official views of the Fogarty International Centre or the National Institutes of Health.
Published: 2019

19. Epidemiologic and viral predictors of antiretroviral drug resistance among persons living with HIV in a large treatment program in Nigeria

Author: Patricia A. Agaba, Prosper Okonkwo, Manhattan Charurat, Bolanle Banigbe, John Idoko, Patrick Dakum, Ernest Ekong, William A. Blattner, James Okuma, Nicaise Ndembi, and Clement Adebamowo
Subjects: 0301 basic medicine, Cart, lcsh:Immunologic diseases. Allergy, Adult, Male, medicine.medical_specialty, Adolescent, Anti-HIV Agents, Psychological intervention, Nigeria, HIV Infections, Drug resistance, Logistic regression, 03 medical and health sciences, Young Adult, 0302 clinical medicine, Virology, Internal medicine, Drug Resistance, Viral, medicine, Electronic Health Records, Humans, Pharmacology (medical), 030212 general & internal medicine, Treatment Failure, Low Middle Income Countries (LMICs), business.industry, Predictors, Research, Odds ratio, Viral Load, 030112 virology, Resource-limited settings, Confidence interval, CD4 Lymphocyte Count, Antiretroviral therapy, Expanded access, Case-Control Studies, HIV-1, Molecular Medicine, Health Resources, Female, business, lcsh:RC581-607, HIV drug resistance testing, Viral load, Acquired drug resistance
Abstract: Background Expanded access to combination antiretroviral therapy (cART) throughout sub-Saharan Africa over the last decade has remarkably improved the prognosis of persons living with HIV (PLWH). However, some PLWH experience virologic rebound after a period of viral suppression, usually followed by selection of drug resistant virus. Determining factors associated with drug resistance can inform patient management and healthcare policies, particularly in resource-limited settings where drug resistance testing is not routine. Methods A case–control study was conducted using data captured from an electronic medical record in a large treatment program in Nigeria. Cases PLWH receiving cART who developed acquired drug resistance (ADR) and controls were those without ADR between 2004 and 2011. Each case was matched to up to 2 controls by sex, age, and education. Logistic regression was used estimate odds ratios (ORs) and 95% confidence intervals (CIs) for factors associated with ADR. Results We evaluated 159 cases with ADR and 299 controls without ADR. In a multivariate model, factors associated with ADR included older age (OR = 2.35 [age 30–40 years 95% CI 1.29, 4.27], age 41 + years OR = 2.31 [95% CI 1.11, 4.84], compared to age 17–30), higher education level (secondary OR 2.14 [95% CI 1.1.11–4.13]), compared to primary and tertiary), non-adherence to care (OR = 2.48 [95% CI 1.50–4.00]), longer treatment duration (OR = 1.80 [95% CI 1.37–2.35]), lower CD4 count((OR = 0.95 [95% CI 0.95–0.97]) and higher viral load (OR = 1.97 [95% CI 1.44–2.54]). Conclusions Understanding these predictors may guide programs in developing interventions to identify patients at risk of developing ADR and implementing prevention strategies.
Published: 2019

20. Prevalence and incidence of genital warts and cervical Human Papillomavirus infections in Nigerian women

Author: Michael Odutola, Richard Offiong, Yinka Olaniyan, Eileen Dareng, Clement Adebamowo, Sally N. Adebamowo, Paul D.P. Pharoah, Ayotunde Famooto, Oluwatoyosi Olawande, Apollo - University of Cambridge Repository, and Pharoah, Paul [0000-0001-8494-732X]
Subjects: Adult, 0301 basic medicine, HPV, medicine.medical_specialty, Epidemiology, 030106 microbiology, Population, Prevalence, Genital tract infection, Nigeria, HIV Infections, Cervix Uteri, lcsh:Infectious and parasitic diseases, Genital warts, Cohort Studies, 03 medical and health sciences, 0302 clinical medicine, Risk Factors, HIV Seronegativity, medicine, Humans, lcsh:RC109-216, Prospective Studies, 030212 general & internal medicine, education, Prospective cohort study, Cervix, education.field_of_study, Human papillomavirus 11, business.industry, Obstetrics, Incidence, Incidence (epidemiology), Papillomavirus Infections, HIV, virus diseases, medicine.disease, 3. Good health, Sexual Partners, Infectious Diseases, medicine.anatomical_structure, Condylomata Acuminata, Female, business, Research Article, Cohort study
Abstract: Background Genital warts are important causes of morbidity and their prevalence and incidence can be used to evaluate the impact of HPV vaccination in a population. Methods We enrolled 1020 women in a prospective cohort study in Nigeria and followed them for a mean (SD) of 9 (4) months. Nurses conducted pelvic examinations and collected ectocervical samples for HPV testing. We used exact logistic regression models to identify risk factors for genital warts. Results The mean age of study participants was 38 years, 56% (535/962) were HIV-negative and 44% (427/962) were HIV-positive. Prevalence of genital warts at enrolment was 1% (4/535) among HIV-negative women, and 5% (23/427) among HIV-positive women. Of 614 women (307 HIV negative and 307 HIV positive women) for whom we could compute genital wart incidence, it was 515 (95% CI:13–2872) per 100,000 person-years in HIV-negative and 1370 (95% CI:283–4033) per 100,000 person-years in HIV-positive women. HIV was associated with higher risk of prevalent genital warts (OR:7.14, 95% CI:2.41–28.7, p
Published: 2019

21. Prevalence and Risk Factors for Type 2 Diabetes Complications and Comorbidity in Sub-Saharan Africans

Author: Daniel Shriner, Francis Collins, Godfrey Okafor, Olufemi Fasanmade, Thomas Johnson, Kenneth Ekoru, Amy R. Bentley, Joseph Acheampong, Williams Balogun, Guanjie Chen, Albert G.B. Amoah, Benjamin A. Eghan, Clement Adebamowo, Kofi Agyenim-Boateng, Jokotade Adeleye, Adebowale Adeyemo, Johnnie Oli, Georgia M. Dunston, Charles N. Rotimi, Jie Zhou, and Ayo P. Doumatey
Subjects: medicine.medical_specialty, business.industry, Type 2 diabetes, Institutional review board, medicine.disease, Obesity, Comorbidity, Family medicine, Epidemiology, Health care, medicine, Global health, business, Body mass index
Abstract: Background: Context-specific evidence of the spectrum of type 2 diabetes (T2D) burden is essential for setting priorities and designing interventions to reduce T2D morbidity and mortality. However, there are currently limited data on the burden of T2D complications and comorbidity in sub-Saharan Africa (SSA). Using a study of ~6,000 participants, we aimed to estimate the burden and risk factors for T2D complications and comorbidity in sub-Saharan Africans. Methods: Participants (2784 T2D, 3209 controls) were African men and women aged 18 years or older, enrolled from major academic medical centres and surrounding communities in Ghana, Nigeria and Kenya. T2D was defined according to the American Diabetes Association criteria. T2D complications and comorbidities evaluated included cardiometabolic, ocular, neurological and renal characteristics. Logistic regression models were used to identify risk factors and to adjust estimates of risk and prevalence for covariates. Results: T2D participants had a mean age of 56 [SD 11] years and a median duration of T2D of 5 (interquartile range 2-10) years. Among the T2D participants, notable associated complications/comorbidities included hypertension with a prevalence of 71% (95% CI 69-73), obesity 27% (25-29) and hyperlipidemia 34% (32-36). Diabetic retinopathy was found in 15% (13-17) and cataracts in 32% (30-35). About 13% (12-15) had impaired renal function as assessed by eGFR, representing 1 in 8 participants. Erectile dysfunction was a complication in 35% (32-38) of men. Age, duration of T2D and body mass index were significant risk factors for most complications/comorbidities. There was significant heterogeneity between sites in prevalence of most complications/comorbidities after adjusting for covariates. Population-attributable fraction ranged between 6 and 64 percent for most comorbidities. Conclusion: The burden of T2D complications and comorbidity is substantial among sub-Saharan Africans. Interventions to reduce T2D morbidity and mortality in SSA need to prioritise early detection, the maintenance of healthy blood pressure, weight and lipid levels, as well as strengthen health care system capacities to provide treatment and care for neurological and ophthalmological complications of T2D. Funding Statement: The study was supported in part by the Intramural Research Program of the National Institutes of Health in the Center for Research on Genomics and Global Health (CRGGH). The CRGGH is supported by the National Human Genome Research Institute (NHGRI), the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), the Center for Information Technology, and the Office of the Director at the National Institutes of Health (1ZIAHG200362). Support for participant recruitment and initial genetic studies of the AADM study was provided by NIH grant No. 3T37TW00041-03S2 from the Office of Research on Minority Health. Declaration of Interests: The authors declare no competing interests. Ethics Approval Statement: The study received ethical approval from the Institutional Review Board at each study site, Howard University and the United States National Institutes of Health.
Published: 2019
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22. Systematic review of family studies of heritable breast cancer in Africa

Author: Sally N. Adebamowo, Clement Adebamowo, and Amina Dhahri
Subjects: Cancer Research, Family studies, Breast cancer, Oncology, business.industry, Mortality rate, Incidence (epidemiology), Medicine, business, medicine.disease, Demography
Abstract: e22508 Background: The incidence of breast cancer (BC) in Africa (40.4 per 100,000) is 49% that of Europe and North America (81.9 per 100,000) but the mortality rate is 42% higher (19.4 versus 13.7 per 100,000). The high mortality is due to lack of screening. However, more targeted screening based on genomic risks are also missed because of stigmatization, poor family history, and limited information on BC susceptibility gene mutations. Internationally based family members are influencing cultural attitudes to BC in Africa leading to reduced stigmatization, increased better family history and uptake of genomic screening. Family-based studies of BC in Africa would provide useful information on prevalence of mutations that can inform genomic screening panels. We conducted systemic review of all family-based studies of BC in Africa to document state of the art, identify barriers and facilitators of this research method and methods of advancing the science. Methods: Using a comprehensive research strategy, we reviewed articles indexed in PubMed and African Journals Online (AJOL) to identify studies of familial BC in Africa. Specifically, we searched for family-based, study design papers on BC in each country in Africa using the following keywords: breast cancer, family-studies, hereditary, genetic, gene, mutations, and Africa. We excluded case-control, and registry studies, and clinical trials. We extracted relevant information from each study using standardized criteria: number of first- and second-degree relatives affected by BC, mutations, genetic variations, and polymorphisms. Results: A total of 12 out of 727 studies met our inclusion criteria. 80% of these studies were published after the year 2010. There were 9 publications from North Africa evaluating 191 families in total. One study reported novel breast cancer candidate genes: MMS19, DNAH3, POLK and KATB6 and nine publications investigated the mutation spectrum of BRCA genes. One publication from West Africa and one publication from Southern Africa included 1 and 219 families, respectively. All the studies done in these two regions reported targeted genomic screening for only BRCA genes. No study was done in Central and East Africa. Conclusions: There is paucity of family-based studies of breast cancer in Africa. Given the high level of heterogeneity in African genomes, these types of studies may be needed to identify high penetrance, germline mutations to better understand hereditary BC risk and ultimately develop a multigene panel testing to for diagnosis of heritable BC in this population.
Published: 2021
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23. Stage at diagnosis of breast cancer in sub-Saharan Africa: a systematic review and meta-analysis

Author: Valerie McCormack, Elima Jedy-Agba, Clement Adebamowo, and Isabel dos-Santos-Silva
Subjects: medicine.medical_specialty, MEDLINE, Black People, Breast Neoplasms, Disease, 03 medical and health sciences, 0302 clinical medicine, Breast cancer, Epidemiology, Humans, Medicine, 030212 general & internal medicine, Stage (cooking), Africa South of the Sahara, Neoplasm Staging, Gynecology, business.industry, Incidence, Incidence (epidemiology), Mortality rate, 1. No poverty, General Medicine, medicine.disease, 3. Good health, 030220 oncology & carcinogenesis, Meta-analysis, Women's Health, business, Demography
Abstract: BACKGROUND: The incidence of breast cancer in sub-Saharan Africa is relatively low, but as survival from the disease in the region is poor, mortality rates are as high as in high-income countries. Stage at diagnosis is a major contributing factor to poor survival from breast cancer. We aimed to do a systematic review and meta-analysis on stage at diagnosis of breast cancer in sub-Saharan Africa to examine trends over time, and investigate sources of variations across the region. METHODS: We searched MEDLINE, Embase, Web of Knowledge, and Africa-Wide Information to identify studies on breast cancer stage at diagnosis in sub-Saharan African women published before Jan 1, 2014, and in any language. Random-effects meta-analyses were done to investigate between-study heterogeneity in percentage of late-stage breast cancer (stage III/IV), and meta-regression analyses to identify potential sources of variation. Percentages of women with late-stage breast cancer at diagnosis in sub-Saharan Africa were compared with similar estimates for black and white women in the USA from the Surveillance, Epidemiology, and End Results database. FINDINGS: 83 studies were included, which consisted of 26 788 women from 17 sub-Saharan African countries. There was wide between-study heterogeneity in the percentage of late-stage disease at diagnosis (median 74·7%, range 30·3-100%, I2=93·3%, p
Published: 2016
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24. Urban–rural and geographic differences in overweight and obesity in four sub-Saharan African adult populations: a multi-country cross-sectional study

Author: Francis Bajunirwe, Shona Dalal, Megan B. Diamond, Donna Spiegelman, Clement Adebamowo, Douglas W. Dockery, Marina Njelekela, David Hemenway, David Guwatudde, Faraja S. Chiwanga, Joan Nankya-Mutyoba, Jimmy Volmink, Hans-Olov Adami, Carien Laurence, Robert Kalyesubula, IkeOluwapo O. Ajayi, Michelle D. Holmes, and Todd G. Reid
Subjects: Male, Rural Population, Urban Population, Cross-sectional study, Overweight, Tanzania, Body Mass Index, South Africa, 0302 clinical medicine, Residence Characteristics, Risk Factors, Surveys and Questionnaires, Prevalence, Medicine, Uganda, 030212 general & internal medicine, risk factors for over-nutrition, biology, Traditional medicine, Sub-Saharan Africa, lcsh:Public aspects of medicine, Middle Aged, Marital status, Female, medicine.symptom, Research Article, Adult, medicine.medical_specialty, Nigeria, 030209 endocrinology & metabolism, 03 medical and health sciences, parasitic diseases, Humans, Obesity, business.industry, Public health, Public Health, Environmental and Occupational Health, lcsh:RA1-1270, biology.organism_classification, medicine.disease, Cross-Sectional Studies, Logistic Models, Prevalence of obesity and overweight, Biostatistics, business, Body mass index, Demography
Abstract: Background Overweight and obesity are on the rise in developing countries including sub-Saharan Africa. We undertook a four-country survey to show the collective burden of these health conditions as they occur currently in sub-Saharan Africa and to determine the differences between urban and rural populations and other socio-economic factors. Methods Participants were nurses in two hospitals in Nigeria (200), school teachers in South Africa (489) and Tanzania (229), and village residents in one peri-urban (297) and one rural location in Uganda (200) who completed a standardised questionnaire. Their height and weight were measured and body mass index calculated. Factor analysis procedure (Principal component) was used to generate a wealth index. Univariate and multivariate analyses with binary logistic regression models were conducted to examine the associations between potential correlates and the prevalence of overweight and obesity with 95 % confidence intervals. Results The prevalence of overweight and obese (combined) was 46 %, 48 %, 68 %, 75 % and 85 % in rural Uganda, peri-urban Uganda, Nigeria, Tanzania and South Africa (SA), respectively. Rural Uganda, Peri- urban Uganda, Nigeria, Tanzania and SA had obesity prevalence of 10 %, 14 %, 31 %, 40 % and 54 %, respectively (p =25 kg/m2 in Nigeria [Age > =45 - AOR = 9.11; 95 % CI: 1.72, 48.16] and SA [AOR = 6.22; 95 % CI: 2.75, 14.07], while marital status was predictor of BMI > =25 kg/m2 only in peri-urban Uganda. [Married - AOR = 4.49; 95 % CI: 1.74, 11.57]. Those in Nigeria [AOR = 2.56; 95 % CI: 1.45, 4.53], SA [AOR = 4.97; 95 % CI: 3.18, 7.78], and Tanzania [AOR = 2.68; 95 % CI: 1.60, 4.49] were more likely to have BMI > =25 kg/m2 compared with the rural and peri-urban sites. Conclusion The high prevalence of overweight and obesity in these sub-Saharan African countries and the differentials in prevalence and risk factors further highlights the need for urgent focused intervention to stem this trend, especially among women, professionals and urban dwellers.
Published: 2016
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25. Global Health Equity: Cancer Care Outcome Disparities in High-, Middle-, and Low-Income Countries

Author: Clement Adebamowo, Fredrick Chite Asirwa, Jonas A. De Souza, Gilberto Lopes, and Bijou Hunt
Subjects: Cancer Research, Economic growth, Equity (economics), Health Equity, Task force, business.industry, MEDLINE, Developing country, Health Status Disparities, Institute of medicine, Global Health, Health equity, 03 medical and health sciences, 0302 clinical medicine, Socioeconomic Factors, Oncology, Neoplasms, 030220 oncology & carcinogenesis, Expanded access, Global health, Humans, Medicine, 030212 general & internal medicine, business, Review Articles
Abstract: Breakthroughs in our global fight against cancer have been achieved. However, this progress has been unequal. In low- and middle-income countries and for specific populations in high-income settings, many of these advancements are but an aspiration and hope for the future. This review will focus on health disparities in cancer within and across countries, drawing from examples in Kenya, Brazil, and the United States. Placed in context with these examples, the authors also draw basic recommendations from several initiatives and groups that are working on the issue of global cancer disparities, including the US Institute of Medicine, the Global Task Force on Expanded Access to Cancer Care and Control in Developing Countries, and the Union for International Cancer Control. From increasing initiatives in basic resources in low-income countries to rapid learning systems in high-income countries, the authors argue that beyond ethics and equity issues, it makes economic sense to invest in global cancer control, especially in low- and middle-income countries.
Published: 2016
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26. Matched Case-Control Study of Beans Intakes and Breast Cancer Risk in Urbanized Nigerian Women

Author: Sally N. Adebamowo, Clement Adebamowo, and Galya Bigman
Subjects: Oncology, medicine.medical_specialty, Diet and Cancer, Nutrition and Dietetics, business.industry, Case-control study, food and beverages, Medicine (miscellaneous), Fetal Restitution, Breast Cancer Epidemiology, medicine.disease, Menopause, Waist–hip ratio, Breast cancer, Internal medicine, Medicine, Microbiome, business, Breast feeding, Food Science
Abstract: OBJECTIVES: To examine the association between dietary intake of beans and breast cancer in Nigerian women. METHODS: Overall 630 newly diagnosed patients with primary invasive breast cancer were age-matched (±5 years) with 630 controls from the Nigerian Integrative Epidemiology of Breast Cancer (NIBBLE) Study from 01/2014 to 07/2016. Dietary intakes were collected using a food frequency questionnaire (FFQ) to derive daily intake of beans. The daily bean intakes included intakes of beans alone, bean porridge, bean cake (akara), bean pudding (moinmoin), beans and corn (adalu) and bean soup (gbegiri). We categorized the daily bean intake into low, medium and high equally based on the distribution. Additional covariates included occupation, education, wealth index, contraceptive use, menopause status, number of pregnancies, breastfeeding, Body Mass Index, Waist to Hip Ratio and physical activity. Conditional logistic regression models were utilized to estimate the crude and adjusted Odds Ratio (OR) of total beans intake per day and breast cancer. RESULTS: The mean (SD) age of the cases was 42.5 (10.1) and controls was 41.5 (9.2) years. Among controls, almost 36% consume a high intake of total bean compared to 30% among cases, whereas among the cases 37.3% consumed the low intake of total bean compared to 31.6% among controls. In the multivariable, we found a significant association between total beans intakes and breast cancer (OR = 0.85; 95% CI: 0.74–0.97, p-value = 0.02). Comparing the highest category (approximately two portions or more a day) with the lowest category (less than one portion a day), the adjusted OR was 0.72 (95% CI: 0.52–0.98, p-value for trend = 0.04). CONCLUSIONS: We found a significant association between high intakes of beans and reduce risks for breast cancer. Future studies are needed to evaluate the causality of this relationship and the specific component of beans that is responsible for this reduction. FUNDING SOURCES: National Human Genome Research Institute of the National Institutes of Health's African Collaborative Center for Microbiome and Genomics Research grant, Award Number U54HG006947; the Fogarty International Center of the National Institutes of Health's Training Program in Nigeria for Non-communicable Diseases Research (TRAPING NCD), Award Number D43TW009106, the Maryland Department of Health's Cigarette Restitution Fund Program.
Published: 2020
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27. American Society of Clinical Oncology's Global Oncology Leadership Task Force: Findings and Actions

Author: Gary H. Lyman, Sandra L. Wong, Gabriel N. Hortobagyi, Doug Pyle, Peter Paul Yu, Lawrence N. Shulman, Clement Adebamowo, Lowell E. Schnipper, David R. Gandara, Julie M. Vose, Eduardo Cazap, and Nagi S. El Saghir
Subjects: Oncology, Cancer Research, medicine.medical_specialty, Quality management, education, Advisory Committees, MEDLINE, Medical Oncology, lcsh:RC254-282, 03 medical and health sciences, Special Article, 0302 clinical medicine, Internal medicine, medicine, Humans, 030212 general & internal medicine, Societies, Medical, Quality of Health Care, Clinical Oncology, business.industry, Task force, Professional development, South America, lcsh:Neoplasms. Tumors. Oncology. Including cancer and carcinogens, Focus group, Quality Improvement, Leadership, Cancer incidence, Work (electrical), 030220 oncology & carcinogenesis, business, Delivery of Health Care
Abstract: In response to rising cancer incidence and mortality rates in low- and middle-income countries and the increasingly global profile of ASCO’s membership, the ASCO Board of Directors appointed the Global Oncology Leadership Task Force (Task Force) to provide recommendations on ASCO’s engagement in global oncology. To accomplish its work, the Task Force convened meetings of global oncology experts, conducted focus group discussions with member groups, did site visits to South America and India, and met regularly to analyze the findings and develop recommendations. Task Force findings included global concerns, such as access to care, and specific concerns of middle- and low-resource settings. The need to strengthen health systems and the importance of alliances with a range of international cancer stakeholders were emphasized. Task Force recommendations to the ASCO Board of Directors were based on a three-part global oncology strategy of professional development, improvement of access to quality care, and acceleration of global oncology research. Specific areas of focus within each of these strategic pillars are provided along with an update on areas of ASCO activity as these recommendations are implemented.
Published: 2018

28. Inherited Breast Cancer in Nigerian Women

Author: Ming K. Lee, Jing Zhang, Chinedum P. Babalola, Adeyinka Ademola, Gabriela E. S. Felix, Yonglan Zheng, Olufunmilayo I. Olopade, Mary Claire King, Toshio F. Yoshimatsu, Imaria Anetor, Adewumi O. Adeoye, Oladosu Ojengbede, Stella Odedina, Adeyinka G. Falusi, Shengfeng Wang, Abayomi Odetunde, Suleyman Gulsuner, Temidayo O. Ogundiran, Dezheng Huo, Tom Walsh, Silvia Casadei, A O Oluwasola, and Clement Adebamowo
Subjects: 0301 basic medicine, Oncology, Adult, Cancer Research, medicine.medical_specialty, Nigeria, Breast Neoplasms, Disease, Inherited Predisposition, 03 medical and health sciences, 0302 clinical medicine, Breast cancer, Internal medicine, Breast Cancer, medicine, Humans, Genetic Predisposition to Disease, Genetic Testing, Family history, Stage (cooking), skin and connective tissue diseases, Genetic testing, medicine.diagnostic_test, Population Health, business.industry, Cancer, ORIGINAL REPORTS, Middle Aged, medicine.disease, 3. Good health, 030104 developmental biology, Hormone receptor, 030220 oncology & carcinogenesis, Mutation, Female, business, Fanconi Anemia Complementation Group N Protein
Abstract: Purpose Among Nigerian women, breast cancer is diagnosed at later stages, is more frequently triple-negative disease, and is far more frequently fatal than in Europe or the United States. We evaluated the contribution of an inherited predisposition to breast cancer in this population. Patients and Methods Cases were 1,136 women with invasive breast cancer (mean age at diagnosis, 47.5 ± 11.5 years) ascertained in Ibadan, Nigeria. Patients were selected regardless of age at diagnosis, family history, or prior genetic testing. Controls were 997 women without cancer (mean age at interview, 47.0 ± 12.4 years) from the same communities. BROCA panel sequencing was used to identify loss-of-function mutations in known and candidate breast cancer genes. Results Of 577 patients with information on tumor stage, 86.1% (497) were diagnosed at stage III (241) or IV (256). Of 290 patients with information on tumor hormone receptor status and human epidermal growth factor receptor 2, 45.9% (133) had triple-negative breast cancer. Among all cases, 14.7% (167 of 1,136) carried a loss-of-function mutation in a breast cancer gene: 7.0% in BRCA1, 4.1% in BRCA2, 1.0% in PALB2, 0.4% in TP53, and 2.1% in any of 10 other genes. Odds ratios were 23.4 (95% CI, 7.4 to 73.9) for BRCA1 and 10.3 (95% CI, 3.7 to 28.5) for BRCA2. Risks were also significantly associated with PALB2 (11 cases, zero controls; P = .002) and TP53 (five cases, zero controls; P = .036). Compared with other patients, BRCA1 mutation carriers were younger ( P < .001) and more likely to have triple-negative breast cancer ( P = .028). Conclusion Among Nigerian women, one in eight cases of invasive breast cancer is a result of inherited mutations in BRCA1, BRCA2, PALB2, or TP53, and breast cancer risks associated with these genes are extremely high. Given limited resources, prevention and early detection services should be especially focused on these highest-risk women.
Published: 2018

29. Neurodevelopmental Outcomes of Twins Compared With Singleton Children: A Systematic Review

Author: Oluwole Adeyemi Babatunde, Ikeoluwa Ajayi, Sally N. Adebamowo, and Clement Adebamowo
Subjects: Male, Twins, Developing country, Article, law.invention, 03 medical and health sciences, 0302 clinical medicine, Child Development, Randomized controlled trial, law, 030225 pediatrics, Cognitive development, Medicine, Humans, 030212 general & internal medicine, Genetics (clinical), Randomized Controlled Trials as Topic, business.industry, Singleton, Obstetrics and Gynecology, Infant, Cognition, Cross-Sectional Studies, Sample size determination, Neurodevelopmental Disorders, Child, Preschool, Pediatrics, Perinatology and Child Health, Female, business, Medline database, Developed country, Clinical psychology, Follow-Up Studies
Abstract: More than 200 million children aged
Published: 2018

30. Consumption of processed food dietary patterns in four African populations

Author: Walter C. Willett, Francis Bajunirwe, Clement Adebamowo, Todd G. Reid, Shona Dalal, Carien Laurence, Teresa T. Fung, IkeOluwapo O. Ajayi, David Guwatudde, Hans-Olov Adami, Megan B. Diamond, Faraja S. Chiwanga, Jimmy Volmink, Marina Njelekela, Joan Nankya-Mutyoba, Michelle D. Holmes, Vikash Sewram, and Sally N. Adebamowo
Subjects: 0301 basic medicine, Adult, Male, medicine.medical_specialty, Longitudinal study, Medicine (miscellaneous), Overweight, 03 medical and health sciences, Environmental health, Medicine, Humans, Refined grains, Africa South of the Sahara, 030109 nutrition & dietetics, Nutrition and Dietetics, biology, business.industry, Public health, Public Health, Environmental and Occupational Health, Feeding Behavior, Middle Aged, biology.organism_classification, medicine.disease, Obesity, Research Papers, Diet, Tanzania, Cross-Sectional Studies, Cohort, Food processing, Fast Foods, Female, medicine.symptom, business
Abstract: ObjectiveTo identify predominant dietary patterns in four African populations and examine their association with obesity.DesignCross-sectional study.Setting/SubjectsWe used data from the Africa/Harvard School of Public Health Partnership for Cohort Research and Training (PaCT) pilot study established to investigate the feasibility of a multi-country longitudinal study of non-communicable chronic disease in sub-Saharan Africa. We applied principal component analysis to dietary intake data collected from an FFQ developed for PaCT to ascertain dietary patterns in Tanzania, South Africa, and peri-urban and rural Uganda. The sample consisted of 444 women and 294 men.ResultsWe identified two dietary patterns: the Mixed Diet pattern characterized by high intakes of unprocessed foods such as vegetables and fresh fish, but also cold cuts and refined grains; and the Processed Diet pattern characterized by high intakes of salad dressing, cold cuts and sweets. Women in the highest tertile of the Processed Diet pattern score were 3·00 times more likely to be overweight (95 % CI 1·66, 5·45; prevalence=74 %) and 4·24 times more likely to be obese (95 % CI 2·23, 8·05; prevalence=44 %) than women in this pattern’s lowest tertile (both PConclusionsWe identified two major dietary patterns in several African populations, a Mixed Diet pattern and a Processed Diet pattern. The Processed Diet pattern was associated with obesity.
Published: 2018

31. Spatial organization and molecular correlation of tumor-infiltrating lymphocytes using deep learning on pathology images

Author: Joel Saltz, Rajarsi Gupta, Le Hou, Tahsin Kurc, Pankaj Singh, Vu Nguyen, Dimitris Samaras, Kenneth R. Shroyer, Tianhao Zhao, Rebecca Batiste, John Van Arnam, Ilya Shmulevich, Arvind U.K. Rao, Alexander J. Lazar, Ashish Sharma, Vésteinn Thorsson, Samantha J. Caesar-Johnson, John A. Demchok, Ina Felau, Melpomeni Kasapi, Martin L. Ferguson, Carolyn M. Hutter, Heidi J. Sofia, Roy Tarnuzzer, Zhining Wang, Liming Yang, Jean C. Zenklusen, Jiashan (Julia) Zhang, Sudha Chudamani, Jia Liu, Laxmi Lolla, Rashi Naresh, Todd Pihl, Qiang Sun, Yunhu Wan, Ye Wu, Juok Cho, Timothy DeFreitas, Scott Frazer, Nils Gehlenborg, Gad Getz, David I. Heiman, Jaegil Kim, Michael S. Lawrence, Pei Lin, Sam Meier, Michael S. Noble, Gordon Saksena, Doug Voet, Hailei Zhang, Brady Bernard, Nyasha Chambwe, Varsha Dhankani, Theo Knijnenburg, Roger Kramer, Kalle Leinonen, Yuexin Liu, Michael Miller, Sheila Reynolds, Vesteinn Thorsson, Wei Zhang, Rehan Akbani, Bradley M. Broom, Apurva M. Hegde, Zhenlin Ju, Rupa S. Kanchi, Anil Korkut, Jun Li, Han Liang, Shiyun Ling, Wenbin Liu, Yiling Lu, Gordon B. Mills, Kwok-Shing Ng, Arvind Rao, Michael Ryan, Jing Wang, John N. Weinstein, Jiexin Zhang, Adam Abeshouse, Joshua Armenia, Debyani Chakravarty, Walid K. Chatila, Ino de Bruijn, Jianjiong Gao, Benjamin E. Gross, Zachary J. Heins, Ritika Kundra, Konnor La, Marc Ladanyi, Augustin Luna, Moriah G. Nissan, Angelica Ochoa, Sarah M. Phillips, Ed Reznik, Francisco Sanchez-Vega, Chris Sander, Nikolaus Schultz, Robert Sheridan, S. Onur Sumer, Yichao Sun, Barry S. Taylor, Jioajiao Wang, Hongxin Zhang, Pavana Anur, Myron Peto, Paul Spellman, Christopher Benz, Joshua M. Stuart, Christopher K. Wong, Christina Yau, D. Neil Hayes, Joel S. Parker, Matthew D. Wilkerson, Adrian Ally, Miruna Balasundaram, Reanne Bowlby, Denise Brooks, Rebecca Carlsen, Eric Chuah, Noreen Dhalla, Robert Holt, Steven J.M. Jones, Katayoon Kasaian, Darlene Lee, Yussanne Ma, Marco A. Marra, Michael Mayo, Richard A. Moore, Andrew J. Mungall, Karen Mungall, A. Gordon Robertson, Sara Sadeghi, Jacqueline E. Schein, Payal Sipahimalani, Angela Tam, Nina Thiessen, Kane Tse, Tina Wong, Ashton C. Berger, Rameen Beroukhim, Andrew D. Cherniack, Carrie Cibulskis, Stacey B. Gabriel, Galen F. Gao, Gavin Ha, Matthew Meyerson, Steven E. Schumacher, Juliann Shih, Melanie H. Kucherlapati, Raju S. Kucherlapati, Stephen Baylin, Leslie Cope, Ludmila Danilova, Moiz S. Bootwalla, Phillip H. Lai, Dennis T. Maglinte, David J. Van Den Berg, Daniel J. Weisenberger, J. Todd Auman, Saianand Balu, Tom Bodenheimer, Cheng Fan, Katherine A. Hoadley, Alan P. Hoyle, Stuart R. Jefferys, Corbin D. Jones, Shaowu Meng, Piotr A. Mieczkowski, Lisle E. Mose, Amy H. Perou, Charles M. Perou, Jeffrey Roach, Yan Shi, Janae V. Simons, Tara Skelly, Matthew G. Soloway, Donghui Tan, Umadevi Veluvolu, Huihui Fan, Toshinori Hinoue, Peter W. Laird, Hui Shen, Wanding Zhou, Michelle Bellair, Kyle Chang, Kyle Covington, Chad J. Creighton, Huyen Dinh, HarshaVardhan Doddapaneni, Lawrence A. Donehower, Jennifer Drummond, Richard A. Gibbs, Robert Glenn, Walker Hale, Yi Han, Jianhong Hu, Viktoriya Korchina, Sandra Lee, Lora Lewis, Wei Li, Xiuping Liu, Margaret Morgan, Donna Morton, Donna Muzny, Jireh Santibanez, Margi Sheth, Eve Shinbrot, Linghua Wang, Min Wang, David A. Wheeler, Liu Xi, Fengmei Zhao, Julian Hess, Elizabeth L. Appelbaum, Matthew Bailey, Matthew G. Cordes, Li Ding, Catrina C. Fronick, Lucinda A. Fulton, Robert S. Fulton, Cyriac Kandoth, Elaine R. Mardis, Michael D. McLellan, Christopher A. Miller, Heather K. Schmidt, Richard K. Wilson, Daniel Crain, Erin Curley, Johanna Gardner, Kevin Lau, David Mallery, Scott Morris, Joseph Paulauskis, Robert Penny, Candace Shelton, Troy Shelton, Mark Sherman, Eric Thompson, Peggy Yena, Jay Bowen, Julie M. Gastier-Foster, Mark Gerken, Kristen M. Leraas, Tara M. Lichtenberg, Nilsa C. Ramirez, Lisa Wise, Erik Zmuda, Niall Corcoran, Tony Costello, Christopher Hovens, Andre L. Carvalho, Ana C. de Carvalho, José H. Fregnani, Adhemar Longatto-Filho, Rui M. Reis, Cristovam Scapulatempo-Neto, Henrique C.S. Silveira, Daniel O. Vidal, Andrew Burnette, Jennifer Eschbacher, Beth Hermes, Ardene Noss, Rosy Singh, Matthew L. Anderson, Patricia D. Castro, Michael Ittmann, David Huntsman, Bernard Kohl, Xuan Le, Richard Thorp, Chris Andry, Elizabeth R. Duffy, Vladimir Lyadov, Oxana Paklina, Galiya Setdikova, Alexey Shabunin, Mikhail Tavobilov, Christopher McPherson, Ronald Warnick, Ross Berkowitz, Daniel Cramer, Colleen Feltmate, Neil Horowitz, Adam Kibel, Michael Muto, Chandrajit P. Raut, Andrei Malykh, Jill S. Barnholtz-Sloan, Wendi Barrett, Karen Devine, Jordonna Fulop, Quinn T. Ostrom, Kristen Shimmel, Yingli Wolinsky, Andrew E. Sloan, Agostino De Rose, Felice Giuliante, Marc Goodman, Beth Y. Karlan, Curt H. Hagedorn, John Eckman, Jodi Harr, Jerome Myers, Kelinda Tucker, Leigh Anne Zach, Brenda Deyarmin, Hai Hu, Leonid Kvecher, Caroline Larson, Richard J. Mural, Stella Somiari, Ales Vicha, Tomas Zelinka, Joseph Bennett, Mary Iacocca, Brenda Rabeno, Patricia Swanson, Mathieu Latour, Louis Lacombe, Bernard Têtu, Alain Bergeron, Mary McGraw, Susan M. Staugaitis, John Chabot, Hanina Hibshoosh, Antonia Sepulveda, Tao Su, Timothy Wang, Olga Potapova, Olga Voronina, Laurence Desjardins, Odette Mariani, Sergio Roman-Roman, Xavier Sastre, Marc-Henri Stern, Feixiong Cheng, Sabina Signoretti, Andrew Berchuck, Darell Bigner, Eric Lipp, Jeffrey Marks, Shannon McCall, Roger McLendon, Angeles Secord, Alexis Sharp, Madhusmita Behera, Daniel J. Brat, Amy Chen, Keith Delman, Seth Force, Fadlo Khuri, Kelly Magliocca, Shishir Maithel, Jeffrey J. Olson, Taofeek Owonikoko, Alan Pickens, Suresh Ramalingam, Dong M. Shin, Gabriel Sica, Erwin G. Van Meir, Hongzheng Zhang, Wil Eijckenboom, Ad Gillis, Esther Korpershoek, Leendert Looijenga, Wolter Oosterhuis, Hans Stoop, Kim E. van Kessel, Ellen C. Zwarthoff, Chiara Calatozzolo, Lucia Cuppini, Stefania Cuzzubbo, Francesco DiMeco, Gaetano Finocchiaro, Luca Mattei, Alessandro Perin, Bianca Pollo, Chu Chen, John Houck, Pawadee Lohavanichbutr, Arndt Hartmann, Christine Stoehr, Robert Stoehr, Helge Taubert, Sven Wach, Bernd Wullich, Witold Kycler, Dawid Murawa, Maciej Wiznerowicz, Ki Chung, W. Jeffrey Edenfield, Julie Martin, Eric Baudin, Glenn Bubley, Raphael Bueno, Assunta De Rienzo, William G. Richards, Steven Kalkanis, Tom Mikkelsen, Houtan Noushmehr, Lisa Scarpace, Nicolas Girard, Marta Aymerich, Elias Campo, Eva Giné, Armando López Guillermo, Nguyen Van Bang, Phan Thi Hanh, Bui Duc Phu, Yufang Tang, Howard Colman, Kimberley Evason, Peter R. Dottino, John A. Martignetti, Hani Gabra, Hartmut Juhl, Teniola Akeredolu, Serghei Stepa, Dave Hoon, Keunsoo Ahn, Koo Jeong Kang, Felix Beuschlein, Anne Breggia, Michael Birrer, Debra Bell, Mitesh Borad, Alan H. Bryce, Erik Castle, Vishal Chandan, John Cheville, John A. Copland, Michael Farnell, Thomas Flotte, Nasra Giama, Thai Ho, Michael Kendrick, Jean-Pierre Kocher, Karla Kopp, Catherine Moser, David Nagorney, Daniel O’Brien, Brian Patrick O’Neill, Tushar Patel, Gloria Petersen, Florencia Que, Michael Rivera, Lewis Roberts, Robert Smallridge, Thomas Smyrk, Melissa Stanton, R. Houston Thompson, Michael Torbenson, Ju Dong Yang, Lizhi Zhang, Fadi Brimo, Jaffer A. Ajani, Ana Maria Angulo Gonzalez, Carmen Behrens, Jolanta Bondaruk, Russell Broaddus, Bogdan Czerniak, Bita Esmaeli, Junya Fujimoto, Jeffrey Gershenwald, Charles Guo, Christopher Logothetis, Funda Meric-Bernstam, Cesar Moran, Lois Ramondetta, David Rice, Anil Sood, Pheroze Tamboli, Timothy Thompson, Patricia Troncoso, Anne Tsao, Ignacio Wistuba, Candace Carter, Lauren Haydu, Peter Hersey, Valerie Jakrot, Hojabr Kakavand, Richard Kefford, Kenneth Lee, Georgina Long, Graham Mann, Michael Quinn, Robyn Saw, Richard Scolyer, Kerwin Shannon, Andrew Spillane, onathan Stretch, Maria Synott, John Thompson, James Wilmott, Hikmat Al-Ahmadie, Timothy A. Chan, Ronald Ghossein, Anuradha Gopalan, Douglas A. Levine, Victor Reuter, Samuel Singer, Bhuvanesh Singh, Nguyen Viet Tien, Thomas Broudy, Cyrus Mirsaidi, Praveen Nair, Paul Drwiega, Judy Miller, Jennifer Smith, Howard Zaren, Joong-Won Park, Nguyen Phi Hung, Electron Kebebew, W. Marston Linehan, Adam R. Metwalli, Karel Pacak, Peter A. Pinto, Mark Schiffman, Laura S. Schmidt, Cathy D. Vocke, Nicolas Wentzensen, Robert Worrell, Hannah Yang, Marc Moncrieff, Chandra Goparaju, Jonathan Melamed, Harvey Pass, Natalia Botnariuc, Irina Caraman, Mircea Cernat, Inga Chemencedji, Adrian Clipca, Serghei Doruc, Ghenadie Gorincioi, Sergiu Mura, Maria Pirtac, Irina Stancul, Diana Tcaciuc, Monique Albert, Iakovina Alexopoulou, Angel Arnaout, John Bartlett, Jay Engel, Sebastien Gilbert, Jeremy Parfitt, Harman Sekhon, George Thomas, Doris M. Rassl, Robert C. Rintoul, Carlo Bifulco, Raina Tamakawa, Walter Urba, Nicholas Hayward, Henri Timmers, Anna Antenucci, Francesco Facciolo, Gianluca Grazi, Mirella Marino, Roberta Merola, Ronald de Krijger, Anne-Paule Gimenez-Roqueplo, Alain Piché, Simone Chevalier, Ginette McKercher, Kivanc Birsoy, Gene Barnett, Cathy Brewer, Carol Farver, Theresa Naska, Nathan A. Pennell, Daniel Raymond, Cathy Schilero, Kathy Smolenski, Felicia Williams, Carl Morrison, Jeffrey A. Borgia, Michael J. Liptay, Mark Pool, Christopher W. Seder, Kerstin Junker, Larsson Omberg, Mikhail Dinkin, George Manikhas, Domenico Alvaro, Maria Consiglia Bragazzi, Vincenzo Cardinale, Guido Carpino, Eugenio Gaudio, David Chesla, Sandra Cottingham, Michael Dubina, Fedor Moiseenko, Renumathy Dhanasekaran, Karl-Friedrich Becker, Klaus-Peter Janssen, Julia Slotta-Huspenina, Mohamed H. Abdel-Rahman, Dina Aziz, Sue Bell, Colleen M. Cebulla, Amy Davis, Rebecca Duell, J. Bradley Elder, Joe Hilty, Bahavna Kumar, James Lang, Norman L. Lehman, Randy Mandt, Phuong Nguyen, Robert Pilarski, Karan Rai, Lynn Schoenfield, Kelly Senecal, Paul Wakely, Paul Hansen, Ronald Lechan, James Powers, Arthur Tischler, William E. Grizzle, Katherine C. Sexton, Alison Kastl, Joel Henderson, Sima Porten, Jens Waldmann, Martin Fassnacht, Sylvia L. Asa, Dirk Schadendorf, Marta Couce, Markus Graefen, Hartwig Huland, Guido Sauter, Thorsten Schlomm, Ronald Simon, Pierre Tennstedt, Oluwole Olabode, Mark Nelson, Oliver Bathe, Peter R. Carroll, June M. Chan, Philip Disaia, Pat Glenn, Robin K. Kelley, Charles N. Landen, Joanna Phillips, Michael Prados, Jeffry Simko, Karen Smith-McCune, Scott VandenBerg, Kevin Roggin, Ashley Fehrenbach, Ady Kendler, Suzanne Sifri, Ruth Steele, Antonio Jimeno, Francis Carey, Ian Forgie, Massimo Mannelli, Michael Carney, Brenda Hernandez, Benito Campos, Christel Herold-Mende, Christin Jungk, Andreas Unterberg, Andreas von Deimling, Aaron Bossler, Joseph Galbraith, Laura Jacobus, Michael Knudson, Tina Knutson, Deqin Ma, Mohammed Milhem, Rita Sigmund, Andrew K. Godwin, Rashna Madan, Howard G. Rosenthal, Clement Adebamowo, Sally N. Adebamowo, Alex Boussioutas, David Beer, Thomas Giordano, Anne-Marie Mes-Masson, Fred Saad, Therese Bocklage, Lisa Landrum, Robert Mannel, Kathleen Moore, Katherine Moxley, Russel Postier, Joan Walker, Rosemary Zuna, Michael Feldman, Federico Valdivieso, Rajiv Dhir, James Luketich, Edna M. Mora Pinero, Mario Quintero-Aguilo, Carlos Gilberto Carlotti, Jose Sebastião Dos Santos, Rafael Kemp, Ajith Sankarankuty, Daniela Tirapelli, James Catto, Kathy Agnew, Elizabeth Swisher, Jenette Creaney, Bruce Robinson, Carl Simon Shelley, Eryn M. Godwin, Sara Kendall, Cassaundra Shipman, Carol Bradford, Thomas Carey, Andrea Haddad, Jeffey Moyer, Lisa Peterson, Mark Prince, Laura Rozek, Gregory Wolf, Rayleen Bowman, Kwun M. Fong, Ian Yang, Robert Korst, W. Kimryn Rathmell, J. Leigh Fantacone-Campbell, Jeffrey A. Hooke, Albert J. Kovatich, Craig D. Shriver, John DiPersio, Bettina Drake, Ramaswamy Govindan, Sharon Heath, Timothy Ley, Brian Van Tine, Peter Westervelt, Mark A. Rubin, Jung Il Lee, Natália D. Aredes, Armaz Mariamidze, SAIC-F-Frederick, Inc, and Leidos Biomedical Research, Inc.
Subjects: 0301 basic medicine, lymphocytes, Genetics and Molecular Biology (all), MELANOMA, Cancer Genome Atlas Research Network, Biochemistry, computer vision, SUBTYPES, Correlation, GENOMIC ANALYSES, PROPOSAL, Neoplasms, lcsh:QH301-705.5, Spatial organization, LINFÓCITOS, Spatial structure, Melanoma, bioinformatics, artificial intelligence, SOLID TUMORS, CANCER, Editorial Commentary, machine learning, tumor-infiltrating lymphocytes, SQUAMOUS-CELL CARCINOMA, Life Sciences & Biomedicine, deep learning, digital pathology, immuno-oncology, tumor microenvironment, Biochemistry, Genetics and Molecular Biology (all), chemical and pharmacologic phenomena, Computational biology, Biology, BREAST, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, STANDARDIZED METHOD, Lymphocytes, Tumor-Infiltrating, Image Interpretation, Computer-Assisted, medicine, Humans, Tumor microenvironment, Science & Technology, Tumor-infiltrating lymphocytes, business.industry, Deep learning, Digital pathology, Cell Biology, medicine.disease, IMMUNE CONTEXTURE, 030104 developmental biology, lcsh:Biology (General), Artificial intelligence, business
Abstract: Summary: Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumor-infiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment. : Tumor-infiltrating lymphocytes (TILs) were identified from standard pathology cancer images by a deep-learning-derived “computational stain” developed by Saltz et al. They processed 5,202 digital images from 13 cancer types. Resulting TIL maps were correlated with TCGA molecular data, relating TIL content to survival, tumor subtypes, and immune profiles. Keywords: digital pathology, immuno-oncology, machine learning, lymphocytes, tumor microenvironment, deep learning, tumor-infiltrating lymphocytes, artificial intelligence, bioinformatics, computer vision
Published: 2018

32. Burden of depressive symptoms and non-alcohol substance abuse; and their association with alcohol use and partner violence: a cross-sectional study in four sub-Saharan Africa countries

Author: Shona Dalal, Marina Njelekela, Faraja S. Chiwanga, Carien Laurence, David Guwatudde, Clement Adebamowo, IkeOluwapo O. Ajayi, Todd G. Reid, S. Maling, Joan Nankya-Mutyoba, Michelle D. Holmes, Francis Bajunirwe, Jimmy Volmink, and Hans-Olov Adami
Subjects: Interpersonal Violence and Mental Health, sub-Saharan Africa, Etiology, Cross-sectional study, prevalence, Psychological intervention, 03 medical and health sciences, 0302 clinical medicine, Environmental health, substance abuse, Medicine, 030212 general & internal medicine, biology, business.industry, Odds ratio, biology.organism_classification, Simple random sample, medicine.disease, Mental health, 030227 psychiatry, Original Research Paper, Substance abuse, Tanzania, Domestic violence, business, mental health
Abstract: In sub-Saharan Africa, there are limited data on burden of non-alcohol substance abuse (NAS) and depressive symptoms (DS), yet potential risk factors such as alcohol and intimate partner violence (IPV) are common and NAS abuse may be the rise. The aim of this study was to measure the burden of DS and NAS abuse, and determine whether alcohol use and IPV are associated with DS and/or NAS abuse. We conducted a cross-sectional study at five sites in four countries: Nigeria (nurses), South Africa (teachers), Tanzania (teachers) and two sites in Uganda (rural and peri-urban residents). Participants were selected by simple random sampling from a sampling frame at each of the study sites. We used a standardized tool to collect data on demographics, alcohol use and NAS use, IPV and DS and calculated prevalence ratios (PR). We enrolled 1415 respondents and of these 34.6% were male. DS occurred among 383 (32.3%) and NAS use among 52 (4.3%). In the multivariable analysis, being female (PR = 1.49, p = 0.008), NAS abuse (PR = 2.06, p = 0.02) and IPV (PR = 2.93, p p p = 0.036) were protective of NAS but current smokers (OR = 2.98, p p = 0.024) were more likely to use NAS. Longitudinal studies should be done to establish temporal relationships with these risk factors to provide basis for interventions.
Published: 2018
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33. An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

Author: Jianfang Liu, Tara Lichtenberg, Katherine A. Hoadley, Laila M. Poisson, Alexander J. Lazar, Andrew D. Cherniack, Albert J. Kovatich, Christopher C. Benz, Douglas A. Levine, Adrian V. Lee, Larsson Omberg, Denise M. Wolf, Craig D. Shriver, Vesteinn Thorsson, Hai Hu, Samantha J. Caesar-Johnson, John A. Demchok, Ina Felau, Melpomeni Kasapi, Martin L. Ferguson, Carolyn M. Hutter, Heidi J. Sofia, Roy Tarnuzzer, Zhining Wang, Liming Yang, Jean C. Zenklusen, Jiashan (Julia) Zhang, Sudha Chudamani, Jia Liu, Laxmi Lolla, Rashi Naresh, Todd Pihl, Qiang Sun, Yunhu Wan, Ye Wu, Juok Cho, Timothy DeFreitas, Scott Frazer, Nils Gehlenborg, Gad Getz, David I. Heiman, Jaegil Kim, Michael S. Lawrence, Pei Lin, Sam Meier, Michael S. Noble, Gordon Saksena, Doug Voet, Hailei Zhang, Brady Bernard, Nyasha Chambwe, Varsha Dhankani, Theo Knijnenburg, Roger Kramer, Kalle Leinonen, Yuexin Liu, Michael Miller, Sheila Reynolds, Ilya Shmulevich, Wei Zhang, Rehan Akbani, Bradley M. Broom, Apurva M. Hegde, Zhenlin Ju, Rupa S. Kanchi, Anil Korkut, Jun Li, Han Liang, Shiyun Ling, Wenbin Liu, Yiling Lu, Gordon B. Mills, Kwok-Shing Ng, Arvind Rao, Michael Ryan, Jing Wang, John N. Weinstein, Jiexin Zhang, Adam Abeshouse, Joshua Armenia, Debyani Chakravarty, Walid K. Chatila, Ino de Bruijn, Jianjiong Gao, Benjamin E. Gross, Zachary J. Heins, Ritika Kundra, Konnor La, Marc Ladanyi, Augustin Luna, Moriah G. Nissan, Angelica Ochoa, Sarah M. Phillips, Ed Reznik, Francisco Sanchez-Vega, Chris Sander, Nikolaus Schultz, Robert Sheridan, S. Onur Sumer, Yichao Sun, Barry S. Taylor, Jioajiao Wang, Hongxin Zhang, Pavana Anur, Myron Peto, Paul Spellman, Christopher Benz, Joshua M. Stuart, Christopher K. Wong, Christina Yau, D. Neil Hayes, Joel S. Parker, Matthew D. Wilkerson, Adrian Ally, Miruna Balasundaram, Reanne Bowlby, Denise Brooks, Rebecca Carlsen, Eric Chuah, Noreen Dhalla, Robert Holt, Steven J.M. Jones, Katayoon Kasaian, Darlene Lee, Yussanne Ma, Marco A. Marra, Michael Mayo, Richard A. Moore, Andrew J. Mungall, Karen Mungall, A. Gordon Robertson, Sara Sadeghi, Jacqueline E. Schein, Payal Sipahimalani, Angela Tam, Nina Thiessen, Kane Tse, Tina Wong, Ashton C. Berger, Rameen Beroukhim, Carrie Cibulskis, Stacey B. Gabriel, Galen F. Gao, Gavin Ha, Matthew Meyerson, Steven E. Schumacher, Juliann Shih, Melanie H. Kucherlapati, Raju S. Kucherlapati, Stephen Baylin, Leslie Cope, Ludmila Danilova, Moiz S. Bootwalla, Phillip H. Lai, Dennis T. Maglinte, David J. Van Den Berg, Daniel J. Weisenberger, J. Todd Auman, Saianand Balu, Tom Bodenheimer, Cheng Fan, Alan P. Hoyle, Stuart R. Jefferys, Corbin D. Jones, Shaowu Meng, Piotr A. Mieczkowski, Lisle E. Mose, Amy H. Perou, Charles M. Perou, Jeffrey Roach, Yan Shi, Janae V. Simons, Tara Skelly, Matthew G. Soloway, Donghui Tan, Umadevi Veluvolu, Huihui Fan, Toshinori Hinoue, Peter W. Laird, Hui Shen, Wanding Zhou, Michelle Bellair, Kyle Chang, Kyle Covington, Chad J. Creighton, Huyen Dinh, HarshaVardhan Doddapaneni, Lawrence A. Donehower, Jennifer Drummond, Richard A. Gibbs, Robert Glenn, Walker Hale, Yi Han, Jianhong Hu, Viktoriya Korchina, Sandra Lee, Lora Lewis, Wei Li, Xiuping Liu, Margaret Morgan, Donna Morton, Donna Muzny, Jireh Santibanez, Margi Sheth, Eve Shinbro, Linghua Wang, Min Wang, David A. Wheeler, Liu Xi, Fengmei Zhao, Julian Hess, Elizabeth L. Appelbaum, Matthew Bailey, Matthew G. Cordes, Li Ding, Catrina C. Fronick, Lucinda A. Fulton, Robert S. Fulton, Cyriac Kandoth, Elaine R. Mardis, Michael D. McLellan, Christopher A. Miller, Heather K. Schmidt, Richard K. Wilson, Daniel Crain, Erin Curley, Johanna Gardner, Kevin Lau, David Mallery, Scott Morris, Joseph Paulauskis, Robert Penny, Candace Shelton, Troy Shelton, Mark Sherman, Eric Thompson, Peggy Yena, Jay Bowen, Julie M. Gastier-Foster, Mark Gerken, Kristen M. Leraas, Tara M. Lichtenberg, Nilsa C. Ramirez, Lisa Wise, Erik Zmuda, Niall Corcoran, Tony Costello, Christopher Hovens, Andre L. Carvalho, Ana C. de Carvalho, José H. Fregnani, Adhemar Longatto-Filho, Rui M. Reis, Cristovam Scapulatempo-Neto, Henrique C.S. Silveira, Daniel O. Vidal, Andrew Burnette, Jennifer Eschbacher, Beth Hermes, Ardene Noss, Rosy Singh, Matthew L. Anderson, Patricia D. Castro, Michael Ittmann, David Huntsman, Bernard Kohl, Xuan Le, Richard Thorp, Chris Andry, Elizabeth R. Duffy, Vladimir Lyadov, Oxana Paklina, Galiya Setdikova, Alexey Shabunin, Mikhail Tavobilov, Christopher McPherson, Ronald Warnick, Ross Berkowitz, Daniel Cramer, Colleen Feltmate, Neil Horowitz, Adam Kibel, Michael Muto, Chandrajit P. Raut, Andrei Malykh, Jill S. Barnholtz-Sloan, Wendi Barrett, Karen Devine, Jordonna Fulop, Quinn T. Ostrom, Kristen Shimmel, Yingli Wolinsky, Andrew E. Sloan, Agostino De Rose, Felice Giuliante, Marc Goodman, Beth Y. Karlan, Curt H. Hagedorn, John Eckman, Jodi Harr, Jerome Myers, Kelinda Tucker, Leigh Anne Zach, Brenda Deyarmin, Leonid Kvecher, Caroline Larson, Richard J. Mural, Stella Somiari, Ales Vicha, Tomas Zelinka, Joseph Bennett, Mary Iacocca, Brenda Rabeno, Patricia Swanson, Mathieu Latour, Louis Lacombe, Bernard Têtu, Alain Bergeron, Mary McGraw, Susan M. Staugaitis, John Chabot, Hanina Hibshoosh, Antonia Sepulveda, Tao Su, Timothy Wang, Olga Potapova, Olga Voronina, Laurence Desjardins, Odette Mariani, Sergio Roman-Roman, Xavier Sastre, Marc-Henri Stern, Feixiong Cheng, Sabina Signoretti, Andrew Berchuck, Darell Bigner, Eric Lipp, Jeffrey Marks, Shannon McCall, Roger McLendon, Angeles Secord, Alexis Sharp, Madhusmita Behera, Daniel J. Brat, Amy Chen, Keith Delman, Seth Force, Fadlo Khuri, Kelly Magliocca, Shishir Maithel, Jeffrey J. Olson, Taofeek Owonikoko, Alan Pickens, Suresh Ramalingam, Dong M. Shin, Gabriel Sica, Erwin G. Van Meir, Hongzheng Zhang, Wil Eijckenboom, Ad Gillis, Esther Korpershoek, Leendert Looijenga, Wolter Oosterhuis, Hans Stoop, Kim E. van Kessel, Ellen C. Zwarthoff, Chiara Calatozzolo, Lucia Cuppini, Stefania Cuzzubbo, Francesco DiMeco, Gaetano Finocchiaro, Luca Mattei, Alessandro Perin, Bianca Pollo, Chu Chen, John Houck, Pawadee Lohavanichbutr, Arndt Hartmann, Christine Stoehr, Robert Stoehr, Helge Taubert, Sven Wach, Bernd Wullich, Witold Kycler, Dawid Murawa, Maciej Wiznerowicz, Ki Chung, W. Jeffrey Edenfield, Julie Martin, Eric Baudin, Glenn Bubley, Raphael Bueno, Assunta De Rienzo, William G. Richards, Steven Kalkanis, Tom Mikkelsen, Houtan Noushmehr, Lisa Scarpace, Nicolas Girard, Marta Aymerich, Elias Campo, Eva Giné, Armando López Guillermo, Nguyen Van Bang, Phan Thi Hanh, Bui Duc Phu, Yufang Tang, Howard Colman, Kimberley Evason, Peter R. Dottino, John A. Martignetti, Hani Gabra, Hartmut Juhl, Teniola Akeredolu, Serghei Stepa, Dave Hoon, Keunsoo Ahn, Koo Jeong Kang, Felix Beuschlein, Anne Breggia, Michael Birrer, Debra Bell, Mitesh Borad, Alan H. Bryce, Erik Castle, Vishal Chandan, John Cheville, John A. Copland, Michael Farnell, Thomas Flotte, Nasra Giama, Thai Ho, Michael Kendrick, Jean-Pierre Kocher, Karla Kopp, Catherine Moser, David Nagorney, Daniel O’Brien, Brian Patrick O’Neill, Tushar Patel, Gloria Petersen, Florencia Que, Michael Rivera, Lewis Roberts, Robert Smallridge, Thomas Smyrk, Melissa Stanton, R. Houston Thompson, Michael Torbenson, Ju Dong Yang, Lizhi Zhang, Fadi Brimo, Jaffer A. Ajani, Ana Maria Angulo Gonzalez, Carmen Behrens, Jolanta Bondaruk, Russell Broaddus, Bogdan Czerniak, Bita Esmaeli, Junya Fujimoto, Jeffrey Gershenwald, Charles Guo, Christopher Logothetis, Funda Meric-Bernstam, Cesar Moran, Lois Ramondetta, David Rice, Anil Sood, Pheroze Tamboli, Timothy Thompson, Patricia Troncoso, Anne Tsao, Ignacio Wistuba, Candace Carter, Lauren Haydu, Peter Hersey, Valerie Jakrot, Hojabr Kakavand, Richard Kefford, Kenneth Lee, Georgina Long, Graham Mann, Michael Quinn, Robyn Saw, Richard Scolyer, Kerwin Shannon, Andrew Spillane, Jonathan Stretch, Maria Synott, John Thompson, James Wilmott, Hikmat Al-Ahmadie, Timothy A. Chan, Ronald Ghossein, Anuradha Gopalan, Victor Reuter, Samuel Singer, Bhuvanesh Singh, Nguyen Viet Tien, Thomas Broudy, Cyrus Mirsaidi, Praveen Nair, Paul Drwiega, Judy Miller, Jennifer Smith, Howard Zaren, Joong-Won Park, Nguyen Phi Hung, Electron Kebebew, W. Marston Linehan, Adam R. Metwalli, Karel Pacak, Peter A. Pinto, Mark Schiffman, Laura S. Schmidt, Cathy D. Vocke, Nicolas Wentzensen, Robert Worrell, Hannah Yang, Marc Moncrieff, Chandra Goparaju, Jonathan Melamed, Harvey Pass, Natalia Botnariuc, Irina Caraman, Mircea Cernat, Inga Chemencedji, Adrian Clipca, Serghei Doruc, Ghenadie Gorincioi, Sergiu Mura, Maria Pirtac, Irina Stancul, Diana Tcaciuc, Monique Albert, Iakovina Alexopoulou, Angel Arnaout, John Bartlett, Jay Engel, Sebastien Gilbert, Jeremy Parfitt, Harman Sekhon, George Thomas, Doris M. Rassl, Robert C. Rintoul, Carlo Bifulco, Raina Tamakawa, Walter Urba, Nicholas Hayward, Henri Timmers, Anna Antenucci, Francesco Facciolo, Gianluca Grazi, Mirella Marino, Roberta Merola, Ronald de Krijger, Anne-Paule Gimenez-Roqueplo, Alain Piché, Simone Chevalier, Ginette McKercher, Kivanc Birsoy, Gene Barnett, Cathy Brewer, Carol Farver, Theresa Naska, Nathan A. Pennell, Daniel Raymond, Cathy Schilero, Kathy Smolenski, Felicia Williams, Carl Morrison, Jeffrey A. Borgia, Michael J. Liptay, Mark Pool, Christopher W. Seder, Kerstin Junker, Mikhail Dinkin, George Manikhas, Domenico Alvaro, Maria Consiglia Bragazzi, Vincenzo Cardinale, Guido Carpino, Eugenio Gaudio, David Chesla, Sandra Cottingham, Michael Dubina, Fedor Moiseenko, Renumathy Dhanasekaran, Karl-Friedrich Becker, Klaus-Peter Janssen, Julia Slotta-Huspenina, Mohamed H. Abdel-Rahman, Dina Aziz, Sue Bell, Colleen M. Cebulla, Amy Davis, Rebecca Duell, J. Bradley Elder, Joe Hilty, Bahavna Kumar, James Lang, Norman L. Lehman, Randy Mandt, Phuong Nguyen, Robert Pilarski, Karan Rai, Lynn Schoenfield, Kelly Senecal, Paul Wakely, Paul Hansen, Ronald Lechan, James Powers, Arthur Tischler, William E. Grizzle, Katherine C. Sexton, Alison Kastl, Joel Henderson, Sima Porten, Jens Waldmann, Martin Fassnacht, Sylvia L. Asa, Dirk Schadendorf, Marta Couce, Markus Graefen, Hartwig Huland, Guido Sauter, Thorsten Schlomm, Ronald Simon, Pierre Tennstedt, Oluwole Olabode, Mark Nelson, Oliver Bathe, Peter R. Carroll, June M. Chan, Philip Disaia, Pat Glenn, Robin K. Kelley, Charles N. Landen, Joanna Phillips, Michael Prados, Jeffry Simko, Karen Smith-McCune, Scott VandenBerg, Kevin Roggin, Ashley Fehrenbach, Ady Kendler, Suzanne Sifri, Ruth Steele, Antonio Jimeno, Francis Carey, Ian Forgie, Massimo Mannelli, Michael Carney, Brenda Hernandez, Benito Campos, Christel Herold-Mende, Christin Jungk, Andreas Unterberg, Andreas von Deimling, Aaron Bossler, Joseph Galbraith, Laura Jacobus, Michael Knudson, Tina Knutson, Deqin Ma, Mohammed Milhem, Rita Sigmund, Andrew K. Godwin, Rashna Madan, Howard G. Rosenthal, Clement Adebamowo, Sally N. Adebamowo, Alex Boussioutas, David Beer, Thomas Giordano, Anne-Marie Mes-Masson, Fred Saad, Therese Bocklage, Lisa Landrum, Robert Mannel, Kathleen Moore, Katherine Moxley, Russel Postier, Joan Walker, Rosemary Zuna, Michael Feldman, Federico Valdivieso, Rajiv Dhir, James Luketich, Edna M. Mora Pinero, Mario Quintero-Aguilo, Carlos Gilberto Carlotti, Jr, Jose Sebastião Dos Santos, Rafael Kemp, Ajith Sankarankuty, Daniela Tirapelli, James Catto, Kathy Agnew, Elizabeth Swisher, Jenette Creaney, Bruce Robinson, Carl Simon Shelley, Eryn M. Godwin, Sara Kendall, Cassaundra Shipman, Carol Bradford, Thomas Carey, Andrea Haddad, Jeffey Moyer, Lisa Peterson, Mark Prince, Laura Rozek, Gregory Wolf, Rayleen Bowman, Kwun M. Fong, Ian Yang, Robert Korst, W. Kimryn Rathmell, J. Leigh Fantacone-Campbell, Jeffrey A. Hooke, John DiPersio, Bettina Drake, Ramaswamy Govindan, Sharon Heath, Timothy Ley, Brian Van Tine, Peter Westervelt, Mark A. Rubin, Jung Il Lee, Natália D. 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Subjects: 0301 basic medicine, Genetics and Molecular Biology (all), Cancer Genome Atlas Research Network, Kaplan-Meier Estimate, Biochemistry, DEFINITIONS, Neoplasms, Databases, Genetic, SUFFICIENT FOLLOW-UP, LS2_1, LS4_6, 11 Medical and Health Sciences, COMPREHENSIVE GENOMIC CHARACTERIZATION, Cox proportional hazards regression model, TAXA DE SOBREVIVÊNCIA, follow-up time, Genomics, 3. Good health, TIME, Life Sciences & Biomedicine, PROGRESSION-FREE SURVIVAL, Human, Biochemistry & Molecular Biology, overall survival, The Cancer Genome Atlas, Translational research, Computational biology, Biology, clinical data resource, disease-free interval, disease-specific survival, progression-free interval, TCGA, translational research, Article, General Biochemistry, Genetics and Molecular Biology, CLASSIFICATION, NO, 03 medical and health sciences, Annotation, Breast cancer, END-POINTS, medicine, BREAST-CANCER, Humans, Progression-free survival, RECURRENCE, Biochemistry, Genetics and Molecular Biology (all), Proportional Hazards Models, Data collection, Science & Technology, business.industry, MOLECULAR PORTRAITS, Biochemistry, Genetics and Molecular Biology(all), Cancer, Cell Biology, 06 Biological Sciences, medicine.disease, 030104 developmental biology, Analytics, Genomic, Neoplasm, business, The Cancer Genome Atla, Genetics and Molecular Biology(all), Developmental Biology
Abstract: SUMMARY For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale., Graphical abstract In Brief Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types.
Published: 2018

34. The Immune Landscape of Cancer

Author: Vésteinn Thorsson, David L. Gibbs, Scott D. Brown, Denise Wolf, Dante S. Bortone, Tai-Hsien Ou Yang, Eduard Porta-Pardo, Galen F. Gao, Christopher L. Plaisier, James A. Eddy, Elad Ziv, Aedin C. Culhane, Evan O. Paull, I.K. Ashok Sivakumar, Andrew J. Gentles, Raunaq Malhotra, Farshad Farshidfar, Antonio Colaprico, Joel S. Parker, Lisle E. Mose, Nam Sy Vo, Jianfang Liu, Yuexin Liu, Janet Rader, Varsha Dhankani, Sheila M. Reynolds, Reanne Bowlby, Andrea Califano, Andrew D. Cherniack, Dimitris Anastassiou, Davide Bedognetti, Younes Mokrab, Aaron M. Newman, Arvind Rao, Ken Chen, Alexander Krasnitz, Hai Hu, Tathiane M. Malta, Houtan Noushmehr, Chandra Sekhar Pedamallu, Susan Bullman, Akinyemi I. Ojesina, Andrew Lamb, Wanding Zhou, Hui Shen, Toni K. Choueiri, John N. Weinstein, Justin Guinney, Joel Saltz, Robert A. Holt, Charles S. Rabkin, Alexander J. Lazar, Jonathan S. Serody, Elizabeth G. Demicco, Mary L. Disis, Benjamin G. Vincent, Ilya Shmulevich, Samantha J. Caesar-Johnson, John A. Demchok, Ina Felau, Melpomeni Kasapi, Martin L. Ferguson, Carolyn M. Hutter, Heidi J. Sofia, Roy Tarnuzzer, Zhining Wang, Liming Yang, Jean C. Zenklusen, Jiashan (Julia) Zhang, Sudha Chudamani, Jia Liu, Laxmi Lolla, Rashi Naresh, Todd Pihl, Qiang Sun, Yunhu Wan, Ye Wu, Juok Cho, Timothy DeFreitas, Scott Frazer, Nils Gehlenborg, Gad Getz, David I. Heiman, Jaegil Kim, Michael S. Lawrence, Pei Lin, Sam Meier, Michael S. Noble, Gordon Saksena, Doug Voet, Hailei Zhang, Brady Bernard, Nyasha Chambwe, Theo Knijnenburg, Roger Kramer, Kalle Leinonen, Michael Miller, Sheila Reynolds, Vesteinn Thorsson, Wei Zhang, Rehan Akbani, Bradley M. Broom, Apurva M. Hegde, Zhenlin Ju, Rupa S. Kanchi, Anil Korkut, Jun Li, Han Liang, Shiyun Ling, Wenbin Liu, Yiling Lu, Gordon B. Mills, Kwok-Shing Ng, Michael Ryan, Jing Wang, Jiexin Zhang, Adam Abeshouse, Joshua Armenia, Debyani Chakravarty, Walid K. Chatila, Ino de Bruijn, Jianjiong Gao, Benjamin E. Gross, Zachary J. Heins, Ritika Kundra, Konnor La, Marc Ladanyi, Augustin Luna, Moriah G. Nissan, Angelica Ochoa, Sarah M. Phillips, Ed Reznik, Francisco Sanchez-Vega, Chris Sander, Nikolaus Schultz, Robert Sheridan, S. Onur Sumer, Yichao Sun, Barry S. Taylor, Jioajiao Wang, Hongxin Zhang, Pavana Anur, Myron Peto, Paul Spellman, Christopher Benz, Joshua M. Stuart, Christopher K. Wong, Christina Yau, D. Neil Hayes, Matthew D. Wilkerson, Adrian Ally, Miruna Balasundaram, Denise Brooks, Rebecca Carlsen, Eric Chuah, Noreen Dhalla, Robert Holt, Steven J.M. Jones, Katayoon Kasaian, Darlene Lee, Yussanne Ma, Marco A. Marra, Michael Mayo, Richard A. Moore, Andrew J. Mungall, Karen Mungall, A. Gordon Robertson, Sara Sadeghi, Jacqueline E. Schein, Payal Sipahimalani, Angela Tam, Nina Thiessen, Kane Tse, Tina Wong, Ashton C. Berger, Rameen Beroukhim, Carrie Cibulskis, Stacey B. Gabriel, Gavin Ha, Matthew Meyerson, Steven E. Schumacher, Juliann Shih, Melanie H. Kucherlapati, Raju S. Kucherlapati, Stephen Baylin, Leslie Cope, Ludmila Danilova, Moiz S. Bootwalla, Phillip H. Lai, Dennis T. Maglinte, David J. Van Den Berg, Daniel J. Weisenberger, J. Todd Auman, Saianand Balu, Tom Bodenheimer, Cheng Fan, Katherine A. Hoadley, Alan P. Hoyle, Stuart R. Jefferys, Corbin D. Jones, Shaowu Meng, Piotr A. Mieczkowski, Amy H. Perou, Charles M. Perou, Jeffrey Roach, Yan Shi, Janae V. Simons, Tara Skelly, Matthew G. Soloway, Donghui Tan, Umadevi Veluvolu, Huihui Fan, Toshinori Hinoue, Peter W. Laird, Michelle Bellair, Kyle Chang, Kyle Covington, Chad J. Creighton, Huyen Dinh, HarshaVardhan Doddapaneni, Lawrence A. Donehower, Jennifer Drummond, Richard A. Gibbs, Robert Glenn, Walker Hale, Yi Han, Jianhong Hu, Viktoriya Korchina, Sandra Lee, Lora Lewis, Wei Li, Xiuping Liu, Margaret Morgan, Donna Morton, Donna Muzny, Jireh Santibanez, Margi Sheth, Eve Shinbrot, Linghua Wang, Min Wang, David A. Wheeler, Liu Xi, Fengmei Zhao, Julian Hess, Elizabeth L. Appelbaum, Matthew Bailey, Matthew G. Cordes, Li Ding, Catrina C. Fronick, Lucinda A. Fulton, Robert S. Fulton, Cyriac Kandoth, Elaine R. Mardis, Michael D. McLellan, Christopher A. Miller, Heather K. Schmidt, Richard K. Wilson, Daniel Crain, Erin Curley, Johanna Gardner, Kevin Lau, David Mallery, Scott Morris, Joseph Paulauskis, Robert Penny, Candace Shelton, Troy Shelton, Mark Sherman, Eric Thompson, Peggy Yena, Jay Bowen, Julie M. Gastier-Foster, Mark Gerken, Kristen M. Leraas, Tara M. Lichtenberg, Nilsa C. Ramirez, Lisa Wise, Erik Zmuda, Niall Corcoran, Tony Costello, Christopher Hovens, Andre L. Carvalho, Ana C. de Carvalho, José H. Fregnani, Adhemar Longatto-Filho, Rui M. Reis, Cristovam Scapulatempo-Neto, Henrique C.S. Silveira, Daniel O. Vidal, Andrew Burnette, Jennifer Eschbacher, Beth Hermes, Ardene Noss, Rosy Singh, Matthew L. Anderson, Patricia D. Castro, Michael Ittmann, David Huntsman, Bernard Kohl, Xuan Le, Richard Thorp, Chris Andry, Elizabeth R. Duffy, Vladimir Lyadov, Oxana Paklina, Galiya Setdikova, Alexey Shabunin, Mikhail Tavobilov, Christopher McPherson, Ronald Warnick, Ross Berkowitz, Daniel Cramer, Colleen Feltmate, Neil Horowitz, Adam Kibel, Michael Muto, Chandrajit P. Raut, Andrei Malykh, Jill S. Barnholtz-Sloan, Wendi Barrett, Karen Devine, Jordonna Fulop, Quinn T. Ostrom, Kristen Shimmel, Yingli Wolinsky, Andrew E. Sloan, Agostino De Rose, Felice Giuliante, Marc Goodman, Beth Y. Karlan, Curt H. Hagedorn, John Eckman, Jodi Harr, Jerome Myers, Kelinda Tucker, Leigh Anne Zach, Brenda Deyarmin, Leonid Kvecher, Caroline Larson, Richard J. Mural, Stella Somiari, Ales Vicha, Tomas Zelinka, Joseph Bennett, Mary Iacocca, Brenda Rabeno, Patricia Swanson, Mathieu Latour, Louis Lacombe, Bernard Têtu, Alain Bergeron, Mary McGraw, Susan M. Staugaitis, John Chabot, Hanina Hibshoosh, Antonia Sepulveda, Tao Su, Timothy Wang, Olga Potapova, Olga Voronina, Laurence Desjardins, Odette Mariani, Sergio Roman-Roman, Xavier Sastre, Marc-Henri Stern, Feixiong Cheng, Sabina Signoretti, Andrew Berchuck, Darell Bigner, Eric Lipp, Jeffrey Marks, Shannon McCall, Roger McLendon, Angeles Secord, Alexis Sharp, Madhusmita Behera, Daniel J. Brat, Amy Chen, Keith Delman, Seth Force, Fadlo Khuri, Kelly Magliocca, Shishir Maithel, Jeffrey J. Olson, Taofeek Owonikoko, Alan Pickens, Suresh Ramalingam, Dong M. Shin, Gabriel Sica, Erwin G. Van Meir, Hongzheng Zhang, Wil Eijckenboom, Ad Gillis, Esther Korpershoek, Leendert Looijenga, Wolter Oosterhuis, Hans Stoop, Kim E. van Kessel, Ellen C. Zwarthoff, Chiara Calatozzolo, Lucia Cuppini, Stefania Cuzzubbo, Francesco DiMeco, Gaetano Finocchiaro, Luca Mattei, Alessandro Perin, Bianca Pollo, Chu Chen, John Houck, Pawadee Lohavanichbutr, Arndt Hartmann, Christine Stoehr, Robert Stoehr, Helge Taubert, Sven Wach, Bernd Wullich, Witold Kycler, Dawid Murawa, Maciej Wiznerowicz, Ki Chung, W. Jeffrey Edenfield, Julie Martin, Eric Baudin, Glenn Bubley, Raphael Bueno, Assunta De Rienzo, William G. Richards, Steven Kalkanis, Tom Mikkelsen, Lisa Scarpace, Nicolas Girard, Marta Aymerich, Elias Campo, Eva Giné, Armando López Guillermo, Nguyen Van Bang, Phan Thi Hanh, Bui Duc Phu, Yufang Tang, Howard Colman, Kimberley Evason, Peter R. Dottino, John A. Martignetti, Hani Gabra, Hartmut Juhl, Teniola Akeredolu, Serghei Stepa, Dave Hoon, Keunsoo Ahn, Koo Jeong Kang, Felix Beuschlein, Anne Breggia, Michael Birrer, Debra Bell, Mitesh Borad, Alan H. Bryce, Erik Castle, Vishal Chandan, John Cheville, John A. 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Ajani, Ana Maria Angulo Gonzalez, Carmen Behrens, Jolanta Bondaruk, Russell Broaddus, Bogdan Czerniak, Bita Esmaeli, Junya Fujimoto, Jeffrey Gershenwald, Charles Guo, Christopher Logothetis, Funda Meric-Bernstam, Cesar Moran, Lois Ramondetta, David Rice, Anil Sood, Pheroze Tamboli, Timothy Thompson, Patricia Troncoso, Anne Tsao, Ignacio Wistuba, Candace Carter, Lauren Haydu, Peter Hersey, Valerie Jakrot, Hojabr Kakavand, Richard Kefford, Kenneth Lee, Georgina Long, Graham Mann, Michael Quinn, Robyn Saw, Richard Scolyer, Kerwin Shannon, Andrew Spillane, onathan Stretch, Maria Synott, John Thompson, James Wilmott, Hikmat Al-Ahmadie, Timothy A. Chan, Ronald Ghossein, Anuradha Gopalan, Douglas A. Levine, Victor Reuter, Samuel Singer, Bhuvanesh Singh, Nguyen Viet Tien, Thomas Broudy, Cyrus Mirsaidi, Praveen Nair, Paul Drwiega, Judy Miller, Jennifer Smith, Howard Zaren, Joong-Won Park, Nguyen Phi Hung, Electron Kebebew, W. Marston Linehan, Adam R. Metwalli, Karel Pacak, Peter A. Pinto, Mark Schiffman, Laura S. Schmidt, Cathy D. Vocke, Nicolas Wentzensen, Robert Worrell, Hannah Yang, Marc Moncrieff, Chandra Goparaju, Jonathan Melamed, Harvey Pass, Natalia Botnariuc, Irina Caraman, Mircea Cernat, Inga Chemencedji, Adrian Clipca, Serghei Doruc, Ghenadie Gorincioi, Sergiu Mura, Maria Pirtac, Irina Stancul, Diana Tcaciuc, Monique Albert, Iakovina Alexopoulou, Angel Arnaout, John Bartlett, Jay Engel, Sebastien Gilbert, Jeremy Parfitt, Harman Sekhon, George Thomas, Doris M. Rassl, Robert C. Rintoul, Carlo Bifulco, Raina Tamakawa, Walter Urba, Nicholas Hayward, Henri Timmers, Anna Antenucci, Francesco Facciolo, Gianluca Grazi, Mirella Marino, Roberta Merola, Ronald de Krijger, Anne-Paule Gimenez-Roqueplo, Alain Piché, Simone Chevalier, Ginette McKercher, Kivanc Birsoy, Gene Barnett, Cathy Brewer, Carol Farver, Theresa Naska, Nathan A. Pennell, Daniel Raymond, Cathy Schilero, Kathy Smolenski, Felicia Williams, Carl Morrison, Jeffrey A. Borgia, Michael J. Liptay, Mark Pool, Christopher W. Seder, Kerstin Junker, Larsson Omberg, Mikhail Dinkin, George Manikhas, Domenico Alvaro, Maria Consiglia Bragazzi, Vincenzo Cardinale, Guido Carpino, Eugenio Gaudio, David Chesla, Sandra Cottingham, Michael Dubina, Fedor Moiseenko, Renumathy Dhanasekaran, Karl-Friedrich Becker, Klaus-Peter Janssen, Julia Slotta-Huspenina, Mohamed H. Abdel-Rahman, Dina Aziz, Sue Bell, Colleen M. Cebulla, Amy Davis, Rebecca Duell, J. Bradley Elder, Joe Hilty, Bahavna Kumar, James Lang, Norman L. Lehman, Randy Mandt, Phuong Nguyen, Robert Pilarski, Karan Rai, Lynn Schoenfield, Kelly Senecal, Paul Wakely, Paul Hansen, Ronald Lechan, James Powers, Arthur Tischler, William E. Grizzle, Katherine C. Sexton, Alison Kastl, Joel Henderson, Sima Porten, Jens Waldmann, Martin Fassnacht, Sylvia L. Asa, Dirk Schadendorf, Marta Couce, Markus Graefen, Hartwig Huland, Guido Sauter, Thorsten Schlomm, Ronald Simon, Pierre Tennstedt, Oluwole Olabode, Mark Nelson, Oliver Bathe, Peter R. Carroll, June M. Chan, Philip Disaia, Pat Glenn, Robin K. Kelley, Charles N. Landen, Joanna Phillips, Michael Prados, Jeffry Simko, Karen Smith-McCune, Scott VandenBerg, Kevin Roggin, Ashley Fehrenbach, Ady Kendler, Suzanne Sifri, Ruth Steele, Antonio Jimeno, Francis Carey, Ian Forgie, Massimo Mannelli, Michael Carney, Brenda Hernandez, Benito Campos, Christel Herold-Mende, Christin Jungk, Andreas Unterberg, Andreas von Deimling, Aaron Bossler, Joseph Galbraith, Laura Jacobus, Michael Knudson, Tina Knutson, Deqin Ma, Mohammed Milhem, Rita Sigmund, Andrew K. Godwin, Rashna Madan, Howard G. Rosenthal, Clement Adebamowo, Sally N. Adebamowo, Alex Boussioutas, David Beer, Thomas Giordano, Anne-Marie Mes-Masson, Fred Saad, Therese Bocklage, Lisa Landrum, Robert Mannel, Kathleen Moore, Katherine Moxley, Russel Postier, Joan Walker, Rosemary Zuna, Michael Feldman, Federico Valdivieso, Rajiv Dhir, James Luketich, Edna M. Mora Pinero, Mario Quintero-Aguilo, Carlos Gilberto Carlotti, Jose Sebastião Dos Santos, Rafael Kemp, Ajith Sankarankuty, Daniela Tirapelli, James Catto, Kathy Agnew, Elizabeth Swisher, Jenette Creaney, Bruce Robinson, Carl Simon Shelley, Eryn M. Godwin, Sara Kendall, Cassaundra Shipman, Carol Bradford, Thomas Carey, Andrea Haddad, Jeffey Moyer, Lisa Peterson, Mark Prince, Laura Rozek, Gregory Wolf, Rayleen Bowman, Kwun M. Fong, Ian Yang, Robert Korst, W. Kimryn Rathmell, J. Leigh Fantacone-Campbell, Jeffrey A. Hooke, Albert J. Kovatich, Craig D. Shriver, John DiPersio, Bettina Drake, Ramaswamy Govindan, Sharon Heath, Timothy Ley, Brian Van Tine, Peter Westervelt, Mark A. Rubin, Jung Il Lee, Natália D. Aredes, Armaz Mariamidze, Thorsson V., Gibbs D.L., Brown S.D., Wolf D., Bortone D.S., Ou Yang T.-H., Porta-Pardo E., Gao G.F., Plaisier C.L., Eddy J.A., Ziv E., Culhane A.C., Paull E.O., Sivakumar I.K.A., Gentles A.J., Malhotra R., Farshidfar F., Colaprico A., Parker J.S., Mose L.E., Vo N.S., Liu J., Liu Y., Rader J., Dhankani V., Reynolds S.M., Bowlby R., Califano A., Cherniack A.D., Anastassiou D., Bedognetti D., Rao A., Chen K., Krasnitz A., Hu H., Malta T.M., Noushmehr H., Pedamallu C.S., Bullman S., Ojesina A.I., Lamb A., Zhou W., Shen H., Choueiri T.K., Weinstein J.N., Guinney J., Saltz J., Holt R.A., Rabkin C.E., Caesar-Johnson S.J., Demchok J.A., Felau I., Kasapi M., Ferguson M.L., Hutter C.M., Sofia H.J., Tarnuzzer R., Wang Z., Yang L., Zenklusen J.C., Zhang J.J., Chudamani S., Lolla L., Naresh R., Pihl T., Sun Q., Wan Y., Wu Y., Cho J., DeFreitas T., Frazer S., Gehlenborg N., Getz G., Heiman D.I., Kim J., Lawrence M.S., Lin P., Meier S., Noble M.S., Saksena G., Voet D., Zhang H., Bernard B., Chambwe N., Knijnenburg T., Kramer R., Leinonen K., Miller M., Reynolds S., Shmulevich I., Zhang W., Akbani R., Broom B.M., Hegde A.M., Ju Z., Kanchi R.S., Korkut A., Li J., Liang H., Ling S., Liu W., Lu Y., Mills G.B., Ng K.-S., Ryan M., Wang J., Zhang J., Abeshouse A., Armenia J., Chakravarty D., Chatila W.K., de Bruijn I., Gao J., Gross B.E., Heins Z.J., Kundra R., La K., Ladanyi M., Luna A., Nissan M.G., Ochoa A., Phillips S.M., Reznik E., Sanchez-Vega F., Sander C., Schultz N., Sheridan R., Sumer S.O., Sun Y., Taylor B.S., Anur P., Peto M., Spellman P., Benz C., Stuart J.M., Wong C.K., Yau C., Hayes D.N., Wilkerson M.D., Ally A., Balasundaram M., Brooks D., Carlsen R., Chuah E., Dhalla N., Jones S.J.M., Kasaian K., Lee D., Ma Y., Marra M.A., Mayo M., Moore R.A., Mungall A.J., Mungall K., Robertson A.G., Sadeghi S., Schein J.E., Sipahimalani P., Tam A., Thiessen N., Tse K., Wong T., Berger A.C., Beroukhim R., Cibulskis C., Gabriel S.B., Ha G., Meyerson M., Schumacher S.E., Shih J., Kucherlapati M.H., Kucherlapati R.S., Baylin S., Cope L., Danilova L., Bootwalla M.S., Lai P.H., Maglinte D.T., Van Den Berg D.J., Weisenberger D.J., Auman J.T., Balu S., Bodenheimer T., Fan C., Hoadley K.A., Hoyle A.P., Jefferys S.R., Jones C.D., Meng S., Mieczkowski P.A., Perou A.H., Perou C.M., Roach J., Shi Y., Simons J.V., Skelly T., Soloway M.G., Tan D., Veluvolu U., Fan H., Hinoue T., Laird P.W., Bellair M., Chang K., Covington K., Creighton C.J., Dinh H., Doddapaneni H., Donehower L.A., Drummond J., Gibbs R.A., Glenn R., Hale W., Han Y., Hu J., Korchina V., Lee S., Lewis L., Li W., Liu X., Morgan M., Morton D., Muzny D., Santibanez J., Sheth M., Shinbrot E., Wang L., Wang M., Wheeler D.A., Xi L., Zhao F., Hess J., Appelbaum E.L., Bailey M., Cordes M.G., Ding L., Fronick C.C., Fulton L.A., Fulton R.S., Kandoth C., Mardis E.R., McLellan M.D., Miller C.A., Schmidt H.K., Wilson R.K., Crain D., Curley E., Gardner J., Lau K., Mallery D., Morris S., Paulauskis J., Penny R., Shelton C., Shelton T., Sherman M., Thompson E., Yena P., Bowen J., Gastier-Foster J.M., Gerken M., Leraas K.M., Lichtenberg T.M., Ramirez N.C., Wise L., Zmuda E., Corcoran N., Costello T., Hovens C., Carvalho A.L., de Carvalho A.C., Fregnani J.H., Longatto-Filho A., Reis R.M., Scapulatempo-Neto C., Silveira H.C.S., Vidal D.O., Burnette A., Eschbacher J., Hermes B., Noss A., Singh R., Anderson M.L., Castro P.D., Ittmann M., Huntsman D., Kohl B., Le X., Thorp R., Andry C., Duffy E.R., Lyadov V., Paklina O., Setdikova G., Shabunin A., Tavobilov M., McPherson C., Warnick R., Berkowitz R., Cramer D., Feltmate C., Horowitz N., Kibel A., Muto M., Raut C.P., Malykh A., Barnholtz-Sloan J.S., Barrett W., Devine K., Fulop J., Ostrom Q.T., Shimmel K., Wolinsky Y., Sloan A.E., De Rose A., Giuliante F., Goodman M., Karlan B.Y., Hagedorn C.H., Eckman J., Harr J., Myers J., Tucker K., Zach L.A., Deyarmin B., Kvecher L., Larson C., Mural R.J., Somiari S., Vicha A., Zelinka T., Bennett J., Iacocca M., Rabeno B., Swanson P., Latour M., Lacombe L., Tetu B., Bergeron A., McGraw M., Staugaitis S.M., Chabot J., Hibshoosh H., Sepulveda A., Su T., Wang T., Potapova O., Voronina O., Desjardins L., Mariani O., Roman-Roman S., Sastre X., Stern M.-H., Cheng F., Signoretti S., Berchuck A., Bigner D., Lipp E., Marks J., McCall S., McLendon R., Secord A., Sharp A., Behera M., Brat D.J., Chen A., Delman K., Force S., Khuri F., Magliocca K., Maithel S., Olson J.J., Owonikoko T., Pickens A., Ramalingam S., Shin D.M., Sica G., Van Meir E.G., Eijckenboom W., Gillis A., Korpershoek E., Looijenga L., Oosterhuis W., Stoop H., van Kessel K.E., Zwarthoff E.C., Calatozzolo C., Cuppini L., Cuzzubbo S., DiMeco F., Finocchiaro G., Mattei L., Perin A., Pollo B., Chen C., Houck J., Lohavanichbutr P., Hartmann A., Stoehr C., Stoehr R., Taubert H., Wach S., Wullich B., Kycler W., Murawa D., Wiznerowicz M., Chung K., Edenfield W.J., Martin J., Baudin E., Bubley G., Bueno R., De Rienzo A., Richards W.G., Kalkanis S., Mikkelsen T., Scarpace L., Girard N., Aymerich M., Campo E., Gine E., Guillermo A.L., Van Bang N., Hanh P.T., Phu B.D., Tang Y., Colman H., Evason K., Dottino P.R., Martignetti J.A., Gabra H., Juhl H., Akeredolu T., Stepa S., Hoon D., Ahn K., Kang K.J., Beuschlein F., Breggia A., Birrer M., Bell D., Borad M., Bryce A.H., Castle E., Chandan V., Cheville J., Copland J.A., Farnell M., Flotte T., Giama N., Ho T., Kendrick M., Kocher J.-P., Kopp K., Moser C., Nagorney D., O'Brien D., O'Neill B.P., Patel T., Petersen G., Que F., Rivera M., Roberts L., Smallridge R., Smyrk T., Stanton M., Thompson R.H., Torbenson M., Yang J.D., Zhang L., Brimo F., Ajani J.A., Gonzalez A.M.A., Behrens C., Bondaruk J., Broaddus R., Czerniak B., Esmaeli B., Fujimoto J., Gershenwald J., Guo C., Lazar A.J., Logothetis C., Meric-Bernstam F., Moran C., Ramondetta L., Rice D., Sood A., Tamboli P., Thompson T., Troncoso P., Tsao A., Wistuba I., Carter C., Haydu L., Hersey P., Jakrot V., Kakavand H., Kefford R., Lee K., Long G., Mann G., Quinn M., Saw R., Scolyer R., Shannon K., Spillane A., Stretch O., Synott M., Thompson J., Wilmott J., Al-Ahmadie H., Chan T.A., Ghossein R., Gopalan A., Levine D.A., Reuter V., Singer S., Singh B., Tien N.V., Broudy T., Mirsaidi C., Nair P., Drwiega P., Miller J., Smith J., Zaren H., Park J.-W., Hung N.P., Kebebew E., Linehan W.M., Metwalli A.R., Pacak K., Pinto P.A., Schiffman M., Schmidt L.S., Vocke C.D., Wentzensen N., Worrell R., Yang H., Moncrieff M., Goparaju C., Melamed J., Pass H., Botnariuc N., Caraman I., Cernat M., Chemencedji I., Clipca A., Doruc S., Gorincioi G., Mura S., Pirtac M., Stancul I., Tcaciuc D., Albert M., Alexopoulou I., Arnaout A., Bartlett J., Engel J., Gilbert S., Parfitt J., Sekhon H., Thomas G., Rassl D.M., Rintoul R.C., Bifulco C., Tamakawa R., Urba W., Hayward N., Timmers H., Antenucci A., Facciolo F., Grazi G., Marino M., Merola R., de Krijger R., Gimenez-Roqueplo A.-P., Piche A., Chevalier S., McKercher G., Birsoy K., Barnett G., Brewer C., Farver C., Naska T., Pennell N.A., Raymond D., Schilero C., Smolenski K., Williams F., Morrison C., Borgia J.A., Liptay M.J., Pool M., Seder C.W., Junker K., Omberg L., Dinkin M., Manikhas G., Alvaro D., Bragazzi M.C., Cardinale V., Carpino G., Gaudio E., Chesla D., Cottingham S., Dubina M., Moiseenko F., Dhanasekaran R., Becker K.-F., Janssen K.-P., Slotta-Huspenina J., Abdel-Rahman M.H., Aziz D., Bell S., Cebulla C.M., Davis A., Duell R., Elder J.B., Hilty J., Kumar B., Lang J., Lehman N.L., Mandt R., Nguyen P., Pilarski R., Rai K., Schoenfield L., Senecal K., Wakely P., Hansen P., Lechan R., Powers J., Tischler A., Grizzle W.E., Sexton K.C., Kastl A., Henderson J., Porten S., Waldmann J., Fassnacht M., Asa S.L., Schadendorf D., Couce M., Graefen M., Huland H., Sauter G., Schlomm T., Simon R., Tennstedt P., Olabode O., Nelson M., Bathe O., Carroll P.R., Chan J.M., Disaia P., Glenn P., Kelley R.K., Landen C.N., Phillips J., Prados M., Simko J., Smith-McCune K., VandenBerg S., Roggin K., Fehrenbach A., Kendler A., Sifri S., Steele R., Jimeno A., Carey F., Forgie I., Mannelli M., Carney M., Hernandez B., Campos B., Herold-Mende C., Jungk C., Unterberg A., von Deimling A., Bossler A., Galbraith J., Jacobus L., Knudson M., Knutson T., Ma D., Milhem M., Sigmund R., Godwin A.K., Madan R., Rosenthal H.G., Adebamowo C., Adebamowo S.N., Boussioutas A., Beer D., Giordano T., Mes-Masson A.-M., Saad F., Bocklage T., Landrum L., Mannel R., Moore K., Moxley K., Postier R., Walker J., Zuna R., Feldman M., Valdivieso F., Dhir R., Luketich J., Pinero E.M.M., Quintero-Aguilo M., Carlotti C.G., Dos Santos J.S., Kemp R., Sankarankuty A., Tirapelli D., Catto J., Agnew K., Swisher E., Creaney J., Robinson B., Shelley C.S., Godwin E.M., Kendall S., Shipman C., Bradford C., Carey T., Haddad A., Moyer J., Peterson L., Prince M., Rozek L., Wolf G., Bowman R., Fong K.M., Yang I., Korst R., Rathmell W.K., Fantacone-Campbell J.L., Hooke J.A., Kovatich A.J., Shriver C.D., DiPersio J., Drake B., Govindan R., Heath S., Ley T., Van Tine B., Westervelt P., Rubin M.A., Lee J.I., Aredes N.D., Mariamidze A., Serody J.S., Demicco E.G., Disis M.L., Vincent B.G., Shmulevich L., SAIC-F-Frederick, Inc, and Leidos Biomedical Research, Inc.
Subjects: Neuroblastoma RAS viral oncogene homolog, Male, 0301 basic medicine, INFORMATION, PREDICTION, Macrophage, medicine.medical_treatment, Lymphocyte, Cell, Cancer Genome Atlas Research Network, COMPREHENSIVE ANALYSIS, computer.software_genre, GENOMIC ANALYSES, 0302 clinical medicine, Transforming Growth Factor beta, Neoplasms, Immunologie, LS2_1, immune subtypes, LS4_6, Immunology and Allergy, tumor immunology, 610 Medicine & health, Child, Th1-Th2 Balance, immunomodulatory, Aged, 80 and over, T-CELL-RECEPTOR, integrative network analysi, cancer genomic, Genomics, Middle Aged, Prognosis, medicine.anatomical_structure, cancer genomics, immuno-oncology, immunotherapy, integrative network analysis, tumor microenvironment, Infectious Diseases, 1107 Immunology, 030220 oncology & carcinogenesis, immune subtype, Female, GENÔMICA, Life Sciences & Biomedicine, Natural language processing, Sentence, Human, Adult, SEQUENCING DATA, Adolescent, Prognosi, Immunology, Cancer immunity, Biology, CLASSIFICATION, Article, NO, Set (abstract data type), Interferon-gamma, Young Adult, 03 medical and health sciences, Immune system, microRNA, REVEALS, medicine, Humans, Epigenetics, Aged, Tumor microenvironment, Wound Healing, Science & Technology, business.industry, REGULATORY NETWORK, Macrophages, Gene sets, Scoring methods, Immunotherapy, SOMATIC MUTATIONS, R package, 030104 developmental biology, Cancer research, Genomic, Artificial intelligence, business, computer
Abstract: We performed an extensive immunogenomic analysis of more than 10,000 tumors comprising 33 diverse cancer types by utilizing data compiled by TCGA. Across cancer types, we identified six immune subtypes—wound healing, IFN-γ dominant, inflammatory, lymphocyte depleted, immunologically quiet, and TGF-β dominant—characterized by differences in macrophage or lymphocyte signatures, Th1:Th2 cell ratio, extent of intratumoral heterogeneity, aneuploidy, extent of neoantigen load, overall cell proliferation, expression of immunomodulatory genes, and prognosis. Specific driver mutations correlated with lower (CTNNB1, NRAS, or IDH1) or higher (BRAF, TP53, or CASP8) leukocyte levels across all cancers. Multiple control modalities of the intracellular and extracellular networks (transcription, microRNAs, copy number, and epigenetic processes) were involved in tumor-immune cell interactions, both across and within immune subtypes. Our immunogenomics pipeline to characterize these heterogeneous tumors and the resulting data are intended to serve as a resource for future targeted studies to further advance the field. Thorsson et al. present immunogenomics analyses of more than 10,000 tumors, identifying six immune subtypes that encompass multiple cancer types and are hypothesized to define immune response patterns impacting prognosis. This work provides a resource for understanding tumor-immune interactions, with implications for identifying ways to advance research on immunotherapy., 0, info:eu-repo/semantics/published
Published: 2019
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35. Comparability, diagnostic validity and completeness of Nigerian cancer registries

Author: Emmanuel A. Oga, Festus Igbinoba, Clement Adebamowo, CC Obiorah, Ame Nwofor, Emmanuel Ezeome, Abidemi Omonisi, Elima Jedy-Agba, Michael N. Okobia, Cornelius O Ukah, B.J.S. al-Haddad, and J. Olufemi Ogunbiyi
Subjects: Male, Cancer Research, Pediatrics, medicine.medical_specialty, Adolescent, Epidemiology, media_common.quotation_subject, Nigeria, Cancer registration, Validation Studies as Topic, Article, Neoplasms, Surveys and Questionnaires, Environmental health, Completeness (order theory), parasitic diseases, Humans, Medicine, Quality (business), Registries, Child, media_common, business.industry, Incidence, Comparability, Infant, Newborn, Infant, Cancer, medicine.disease, Infant newborn, Oncology, Work (electrical), Child, Preschool, Diagnostic validity, Female, business
Abstract: Like many countries in Africa, Nigeria is improving the quality and coverage of its cancer surveillance. This work is essential to address this growing category of chronic diseases, but is made difficult by economic, geographic and other challenges.To evaluate the completeness, comparability and diagnostic validity of Nigeria's cancer registries.Completeness was measured using children's age-specific incidence (ASI) and an established metric based on a modified Poisson distribution with regional comparisons. We used a registry questionnaire as well as percentages of death-certificate-only cases, morphologically verified cases, and case registration errors to examine comparability and diagnostic validity.Among the children's results, we found that over half of all cancers were non-Hodgkin lymphoma. There was also evidence of incompleteness. Considering the regional completeness comparisons, we found potential evidence of cancer-specific general incompleteness as well as what appears to be incompleteness due to inability to diagnose specific cancers. We found that registration was generally comparable, with some exceptions. Since autopsies are not common across Nigeria, coding for both them and death-certificate-only cases was also rare. With one exception, registries in our study had high rates of morphological verification of female breast, cervical and prostate cancers.Nigeria's registration procedures were generally comparable to each other and to international standards, and we found high rates of morphological verification, suggesting high diagnostic validity. There was, however, evidence of incompleteness.
Published: 2015
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36. Breast cancer risk after full‐term pregnancies among <scp>A</scp> frican women from <scp>N</scp> igeria, <scp>C</scp> ameroon, and <scp>U</scp> ganda

Author: Paul Ndom, Oladosu Ojengbede, Adeyinka Ademola, Imaria Anetor, Dominique Sighoko, Temidayo O. Ogundiran, Stella Odedina, Clement Adebamowo, Lin Chen, Antony Gakwaya, Dezheng Huo, and Olufunmilayo I. Olopade
Subjects: Adult, Cancer Research, medicine.medical_specialty, Epidemiology, media_common.quotation_subject, Population, Nigeria, Breast Neoplasms, Fertility, Discipline, breast cancer, Breast cancer, Pregnancy, Risk Factors, medicine, Humans, age at first full‐term pregnancy, Uganda, Cameroon, education, Aged, media_common, Gynecology, education.field_of_study, business.industry, African, case‐control studies, Case-control study, Original Articles, Odds ratio, Middle Aged, medicine.disease, Confidence interval, 3. Good health, Parity, Oncology, Case-Control Studies, Original Article, Female, Age of onset, business, Demography
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.
Published: 2015
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37. Genomic Research Data Generation, Analysis and Sharing – Challenges in the African Setting

Author: Sally N. Adebamowo, Oussama Souiai, Faisal M. Fadlelmola, Mohamed Alibi, Mayowa O. Owolabi, Charles N. Rotimi, Fouzia Radouani, Osimhiarherhuo Adeleye, Alice Matimba, Hassan Ghazal, Nicola Mulder, Kais Ghedira, Oladimeji Adebayo, Clement Adebamowo, Dan J. Stein, Shakuntala Baichoo, Zahra Mungloo-Dilmohamud, Alia Benkahla, Ahmed Moussa, University of Cape Town, University of Maryland School of Medicine, University of Maryland System, University of Ibadan, Federal Medical Centre [Abeokuta], Laboratoire de Bioinformatique, biomathématiques, biostatistiques (BIMS) (LR11IPT09), Université de Tunis El Manar (UTM)-Institut Pasteur de Tunis, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), University of Mauritius, University of Khartoum, Université Mohammed Premier [Oujda], University of Zimbabwe (UZ), Université Abdelmalek Essaâdi (UAE), Institut Pasteur du Maroc, Réseau International des Instituts Pasteur (RIIP), National Human Genome Research Institute (NHGRI), and H3ABioNet is supported by the National Institutes of Health Common Fund (grant number U41HG006941). SNA and CAA are funded by H3Africa’s African Collaborative Center for Microbiome and Genomics Research (ACCME) grant supported by the National Institutes of Health (1U54HG006947). OA, OA and MOO are funded by H3Africa’s Stroke Investigative Research and Educational Network (U54HG007479).
Subjects: 0301 basic medicine, Test data generation, Process (engineering), Genetics, genomics, bioinformatics, Africa, health, media_common.quotation_subject, [SDV]Life Sciences [q-bio], Genomics, 03 medical and health sciences, 0302 clinical medicine, Computer Science (miscellaneous), Quality (business), 030212 general & internal medicine, lcsh:Science (General), genomics, bioinformatics, media_common, Research ethics, Management science, 1. No poverty, Data science, Human genetics, Computer Science Applications, Data sharing, 030104 developmental biology, Business, Return of results, lcsh:Q1-390
Abstract: International audience; Genomics is the study of the genetic material that constitutes the genomes of organisms. This genetic material can be sequenced and it provides a powerful tool for the study of human, plant and animal evolutionary history and diseases. Genomics research is becoming increasingly commonplace due to significant advances in and reducing costs of technologies such as sequencing. This has led to new challenges including increasing cost and complexity of data. There is, therefore, an increasing need for computing infrastructure and skills to manage, store, analyze and interpret the data. In addition, there is a significant cost associated with recruitment of participants and collection and processing of biological samples, particularly for large human genetics studies on specific diseases. As a result, researchers are often reluctant to share the data due to the effort and associated cost. In Africa, where researchers are most commonly at the study recruitment, determination of phenotypes and collection of biological samples end of the genomic research spectrum, rather than the generation of genomic data, data sharing without adequate safeguards for the interests of the primary data generators is a concern. There are substantial ethical considerations in the sharing of human genomics data. The broad consent for data sharing preferred by genomics researchers and funders does not necessarily align with the expectations of researchers, research participants, legal authorities and bioethicists. In Africa, this is complicated by concerns about comprehension of genomics research studies, quality of research ethics reviews and understanding of the implications of broad consent, secondary analyses of shared data, return of results and incidental findings. Additional challenges with genomics research in Africa include the inability to transfer, store, process and analyze large-scale genomics data on the continent, because this requires highly specialized skills and expensive computing infrastructure which are often unavailable. Recently initiatives such as H3Africa and H3ABioNet which aim to build capacity for large-scale genomics projects in Africa have emerged. Here we describe such initiatives, including the challenges faced in the generation, analysis and sharing of genomic data and how these challenges are being overcome.
Published: 2017
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38. Updating vital status by tracking in the community among patients with epidemic Kaposi sarcoma who are lost to follow-up in sub-Saharan Africa

Author: François Dabis, Kara Wools-Kaloustian, Clement Adebamowo, Julia Bohlius, Mwebesa Bwana, Elima Jedy-Agba, Matthias Egger, Constantin T. Yiannoutsos, Aggrey Semeere, Jeffrey N. Martin, Micheal Kanyesigye, Esther E. Freeman, Vivian Kwaghe, Naftali Busakhala, Elyne Rotich, Sam Phiri, David V. Glidden, Antoine Jaquet, Emmanuel A. Oga, Fredrick Chite Asirwa, Megan Wenger, and Kenneth Iregbu
Subjects: Male, Cancer Research, Survival, HIV Infections, Loss to follow-up, 0302 clinical medicine, Tracing, 030212 general & internal medicine, Medical diagnosis, Aetiology, Cancer, Sub-Saharan Africa, Tracking, Sarcoma, Updating vital status, lcsh:Neoplasms. Tumors. Oncology. Including cancer and carcinogens, 3. Good health, Oncology, 030220 oncology & carcinogenesis, Vital Status, Public Health and Health Services, HIV/AIDS, Female, Infection, Research Article, Adult, medicine.medical_specialty, Anti-HIV Agents, Oncology and Carcinogenesis, 610 Medicine & health, Kaposi, lcsh:RC254-282, 03 medical and health sciences, Rare Diseases, Acquired immunodeficiency syndrome (AIDS), Clinical Research, 360 Social problems & social services, Genetics, medicine, Humans, Oncology & Carcinogenesis, Lost to follow-up, Mortality, Epidemics, Sarcoma, Kaposi, Africa South of the Sahara, Estimation, AIDS-Related Opportunistic Infections, business.industry, Kaposi sarcoma, medicine.disease, Resource-limited settings, Surgery, Good Health and Well Being, Family medicine, Lost to Follow-Up, Tracking (education), business, 2.4 Surveillance and distribution
Abstract: Background Throughout most of sub-Saharan Africa (and, indeed, most resource-limited areas), lack of death registries prohibits linkage of cancer diagnoses and precludes the most expeditious approach to determining cancer survival. Instead, estimation of cancer survival often uses clinical records, which have some mortality data but are replete with patients who are lost to follow-up (LTFU), some of which may be caused by undocumented death. The end result is that accurate estimation of cancer survival is rarely performed. A prominent example of a common cancer in Africa for which survival data are needed but for which frequent LTFU has precluded accurate estimation is Kaposi sarcoma (KS). Methods Using electronic records, we identified all newly diagnosed KS among HIV-infected adults at 33 primary care clinics in Kenya, Uganda, Nigeria, and Malawi from 2009 to 2012. We determined those patients who were apparently LTFU, defined as absent from clinic for ≥90 days at database closure and unknown to be dead or transferred. Using standardized protocols which included manual chart review, telephone calls, and physical tracking in the community, we attempted to update vital status amongst patients who were LTFU. Results We identified 1222 patients with KS, of whom 440 were LTFU according to electronic records. Manual chart review revealed that 18 (4.1%) were classified as LFTU due to clerical error, leaving 422 as truly LTFU. Of these 422, we updated vital status in 78%; manual chart review was responsible for updating in 5.7%, telephone calls in 26%, and physical tracking in 46%. Among 378 patients who consented at clinic enrollment to be tracked if they became LTFU and who had sufficient geographic contact/locator information, we updated vital status in 88%. Duration of LTFU was not associated with success of tracking, but tracking success was better in Kenya than the other sites. Conclusion It is feasible to update vital status in a large fraction of patients with HIV-associated KS in sub-Saharan Africa who have become LTFU from clinical care. This finding likely applies to other cancers as well. Updating vital status amongst lost patients paves the way towards accurate determination of cancer survival.
Published: 2017
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39. Research Ethics Capacity Building in Sub-Saharan Africa: A Review of NIH Fogarty-Funded Programs 2000–2012

Author: Adnan A. Hyder, Mariana Kruger, Clement Adebamowo, Nancy E. Kass, Paul Ndebele, Solomon R. Benatar, Eric M. Meslin, Douglas Wassenaar, and Theodore Fleischer
Subjects: Research design, Capacity Building, Social Psychology, International Cooperation, Article, Ethics, Research, Education, Curriculum development, Humans, Medicine, Program Development, Duration (project management), Curriculum, Africa South of the Sahara, Research ethics, business.industry, Research, Communication, Capacity building, Bioethics, Public relations, Investment (macroeconomics), Management, Leadership, Research Design, business, Ethics Committees, Research
Abstract: The last fifteen years have witnessed a significant increase in investment in research ethics capacity development throughout the world. We examine nine research ethics training programs that are focused on Sub-Saharan Africa and supported by the US National Institutes of Health. We collected data from grants awards' documents and annual reports supplemented by questionnaires completed by the training program directors. Together, these programs provided long-term training in research ethics to 275 African professionals, strengthened research ethics committees in 19 countries in Sub-Saharan Africa, and created research ethics curricula at many institutions and bioethics centers within Africa. Trainees' leadership resulted in new national systems and policies on research ethics, human tissue storage and export, and methods of monitoring compliance with research ethics guidelines. Training programs adapted to challenges that arose due to varied trainees' background knowledge in ethics, duration of time available for training, spoken and written English language skills, administrative obstacles, and the need to sustain post-training research ethics activities. Our report showcases the development of awareness of research ethics and building/strengthening of basic research ethics infrastructure in Sub-Saharan Africa. Nevertheless, the increasing amount and complexity of health research being conducted in Sub-Saharan Africa suggests the need for continued investment in research ethics capacity development in this region. This paper is part of a collection of papers analyzing the Fogarty International Center's International Research Ethics Education and Curriculum Development program.
Published: 2014
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40. Association of HIV and ART with cardiometabolic traits in sub-Saharan Africa: a systematic review and meta-analysis

Author: Pontiano Kaleebu, Naomi S. Levitt, Kathryn Anastos, Elizabeth H. Young, Deepti Gurdasani, Phyllis C. Tien, Carla M.T. Fourie, Nigel J. Crowther, Liam Smeeth, Janet Seeley, Ousman Nyan, George PrayGod, Henrik Friis, Annamarie Kruger, Joel A. Dave, Livio Azzoni, Moffat J. Nyirenda, David G. Dillon, W Henry Boom, Chiratidzo E. Ndhlovu, Aletta E. Schutte, Johanna Riha, Nyagosya Range, Chris T. Longenecker, Anatoli Kamali, Billy N. Mayanja, O O Adewole, Rutendo Zinyama, John A Idoko, Eugene Mutimura, Ayesha A. Motala, Clement Adebamowo, Corinna M. Walsh, Fredirick Mashili, Caterina Compostella, Halima Dawood, Kaushik Ramaiya, Eric Walter Pefura Yone, Gershim Asiki, Suzanne Mbondi, Kenneth Ekoru, Marina Njelekela, Japheth E Mukaya, Karen Sliwa, Mar Pujades-Rodriguez, Eugene Sobngwi, Manjinder S. Sandhu, Mahmoud U Sani, Christian Erikstrup, Este H Vorster, 10062416 - Kruger, Annamarie, 10922180 - Schutte, Aletta Elisabeth, and 10055355 - Vorster, Hester Hendrina
Subjects: sub-Saharan Africa, medicine.medical_specialty, Anti-HIV Agents, Epidemiology, Human immunodeficiency virus (HIV), MEDLINE, HIV Infections, 030204 cardiovascular system & hematology, medicine.disease_cause, Body Mass Index, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, stomatognathic system, Antiretroviral Therapy, Highly Active, Diabetes mellitus, Internal medicine, parasitic diseases, Diabetes Mellitus, medicine, Humans, 030212 general & internal medicine, Africa South of the Sahara, Dyslipidemias, 2. Zero hunger, cardiometabolic disease, business.industry, virus diseases, HIV, General Medicine, medicine.disease, Corrigenda, Confidence interval, eye diseases, 3. Good health, Treatment, stomatognathic diseases, Blood pressure, chemistry, Non-communicable Disease Risk Factors and Mortality, Meta-analysis, Hypertension, Immunology, Glycated hemoglobin, business, Body mass index, 030217 neurology & neurosurgery, ART
Abstract: Background: Sub-Saharan Africa (SSA) has the highest burden of HIV in the world and a rising prevalence of cardiometabolic disease; however, the interrelationship between HIV, antiretroviral therapy (ART) and cardiometabolic traits is not well described in SSA populations. Methods: We conducted a systematic review and meta-analysis through MEDLINE and EMBASE (up to January 2012), as well as direct author contact. Eligible studies provided summary or individuallevel data on one or more of the following traits in HIVþ and HIV-, or ARTþ and ART- subgroups in SSA: body mass index (BMI), systolic blood pressure (SBP), diastolic blood pressure (DBP), high-density lipoprotein (HDL), low-density lipoprotein (LDL), triglycerides (TGs) and fasting blood glucose (FBG) or glycated hemoglobin (HbA1c). Information was synthesized under a random-effects model and the primary outcomes were the standardized mean differences (SMD) of the specified traits between subgroups of participants. Results: Data were obtained from 49 published and 3 unpublished studies which reported on 29 755 individuals. HIV infection was associated with higher TGs [SMD, 0.26; 95% confidence interval (CI), 0.08 to 0.44] and lower HDL (SMD, 0.59; 95% CI, 0.86 to 0.31), BMI (SMD, 0.32; 95% CI, 0.45 to 0.18), SBP (SMD, 0.40; 95% CI, 0.55 to 0.25) and DBP (SMD, 0.34; 95% CI, 0.51 to 0.17). Among HIVþ individuals, ART use was associated with higher LDL (SMD, 0.43; 95% CI, 0.14 to 0.72) and HDL (SMD, 0.39; 95% CI, 0.11 to 0.66), and lower HbA1c (SMD, 0.34; 95% CI, 0.62 to 0.06). Fully adjusted estimates from analyses of individual participant data were consistent with meta-analysis of summary estimates for most traits. Conclusions: Broadly consistent with results from populations of European descent, these results suggest differences in cardiometabolic traits between HIV-infected and uninfected individuals in SSA, which might be modified by ART use. In a region with the highest burden of HIV, it will be important to clarify these findings to reliably assess the need for monitoring and managing cardiometabolic risk in HIV-infected populations in SSA. http://ije.oxfordjournals.org/ http://dx.doi.org/10.1093/ije/dyt198
Published: 2014
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41. Patterns of Care and Survival in Stage III NSCLC Among Black and Latino Patients Compared With White Patients

Author: Charles B. Simone, Melissa A.L. Vyfhuis, Shahed N. Badiyan, Pranshu Mohindra, Tejan Diwanji, Clement Adebamowo, Søren M. Bentzen, Jason K. Molitoris, and Surbhi Grover
Subjects: Adult, Male, 0301 basic medicine, Pulmonary and Respiratory Medicine, Oncology, Cancer Research, medicine.medical_specialty, Lung Neoplasms, Adolescent, medicine.medical_treatment, Black People, Disease, White People, Cohort Studies, Young Adult, 03 medical and health sciences, 0302 clinical medicine, Carcinoma, Non-Small-Cell Lung, Internal medicine, medicine, Humans, External beam radiotherapy, Practice Patterns, Physicians', Stage (cooking), Lung cancer, Socioeconomic status, Aged, Neoplasm Staging, Aged, 80 and over, Patterns of care, Chemotherapy, business.industry, Cancer, Hispanic or Latino, Middle Aged, medicine.disease, Survival Analysis, United States, 030104 developmental biology, Socioeconomic Factors, 030220 oncology & carcinogenesis, Female, business
Abstract: Race and socioeconomic status have continued to affect the survival and patterns of care of patients with non-small-cell lung cancer (NSCLC). However, data evaluating these associations in patients with stage III disease remain limited. Therefore, we investigated the patterns of care and overall survival (OS) of black and Latino patients with locally advanced NSCLC compared with white patients, using the National Cancer Database.All patients with stage III NSCLC from 2004 to 2013 who had undergone external beam radiotherapy (RT) alone, RT with chemotherapy (bimodality), or RT with chemotherapy followed by surgery (trimodality) were analyzed within the National Cancer Database according to race (n = 113,945). Univariate associations among the demographic, disease, and treatment characteristics within the 3 cohorts were assessed using χThe black and Latino patients were younger at diagnosis, had lower median household incomes, and were less likely to be insured than were the white patients. The black patients were more likely to receive RT alone (19.3% vs. 18%; P .001) and less likely to have undergone concurrent chemo-RT (53.6% vs. 56.1%; P .001) compared with the white patients. Black patients had improved OS (P .001). In contrast, the Latino patients had survival equivalent to that of the white patients (P = .920).Despite epidemiologic differences and a propensity for less aggressive treatment, black patients with locally advanced NSCLC had better OS than white patients and Latino patients had equivalent outcomes. Additional research is needed to elucidate this finding, perhaps focusing on biological differences among the cohorts.
Published: 2019
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42. Association of leisure time physical activity with breast cancer risk and breast cancer sub-types in Nigerian women

Author: Elima Jedy-Agba, Galya Bigman, Sally N. Adebamowo, Clement Adebamowo, and Izuchukwu Benerdin Achusi
Subjects: Oncology, Cancer Research, medicine.medical_specialty, business.industry, Leisure time, Physical activity, medicine.disease, Breast cancer, Internal medicine, Sub types, medicine, business, Association (psychology)
Abstract: e13085 Background: The association between physical activity and breast cancer has not been studied among Nigerian women and in particular by breast cancer sub-types. Therefore are studies aims are to examine the association between leisure time physical activity (LTPA) and breast cancer in Nigerian women and to examine the association between LTPA and estrogen receptor positive (ER+), triple negative breast cancer (TNBC+), Luminal A breast cancer in Nigerian women. Methods: We enrolled 739 newly diagnosed primary invasive breast cancer and 739 age-matched controls in Nigeria from 01/2014 to 07/2016. This analysis is restricted to the 40% of cases for whom we have complete ER, TNBC and Luminal-A data and their matched controls. We derived the average amount of time per week spent on LTPA over the past one year using a modified Nurses’ Health Study II PA questionnaire. LTPA was calculated from the total metabolic equivalent (METs) assigned for each reported physical activity hour/week (i.e. walking, cycling, and dancing). We examined LTPA by comparing participants who attained the WHO physical activity recommendations of at least 150 minutes of moderate-intensity or/and 75 minutes of vigorous-intensity aerobic activity weekly with those who did not. We used conditional logistic regression to estimate the adjusted Odds Ratio (OR) of LTPA and overall as well as subtypes of breast cancer. Results: The mean (SD) age of cases was 41.6 (9.1) and controls was 43.9 (11.8) years. Women who attained the WHO physical activity recommendations had 43% decreased risk of breast cancer (OR = 0.57 95% CI:0.42-0.77) compared with those who did not, after controlling for demographic, anthropometric and fertility related factors. LTPA was also associated with reduced risk of breast cancer subtypes by 41% for ER+, 59% for TNBC+ and 59% for Luminal A. Conclusions: Physical activity is associated with reduced risk of breast cancer overall and by subtypes in Nigerian women.
Published: 2019
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43. PE-1 Vaginal microbiota composition and persistent high-risk HPV infection in HIV negative and HIV positive women

Author: Jacques Ravel, Sally N. Adebamowo, Paul D.P. Pharoah, Clement Adebamowo, Bing Ma, and Eileen Dareng
Subjects: Infectious Diseases, High risk hpv, business.industry, Immunology, Human immunodeficiency virus (HIV), medicine, Pharmacology (medical), medicine.disease_cause, business, Microbiota composition
Published: 2019
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44. PC-10 Classical HLA alleles are associated with prevalent and persistent cervical high-risk HPV infection in African women

Author: Clement Adebamowo, Sally N. Adebamowo, and Adebowale Adeyemo
Subjects: Infectious Diseases, business.industry, High risk hpv, Immunology, Medicine, Pharmacology (medical), Human leukocyte antigen, Allele, business
Published: 2019
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45. PI-1 Age-specific HPV prevalence among adolescent girls in Jos, North-Central Nigeria

Author: Nanma Dashe, Clement Adebamowo, Lohya Nimzing, Daniel Z. Egah, and Sally N. Adebamowo
Subjects: Infectious Diseases, business.industry, North central, Medicine, Pharmacology (medical), business, Age specific, Hpv prevalence, Demography
Published: 2019
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46. PD-1 Genetic risk factors for high-risk human papillomavirus (HPV) infections and persistence among African women

Author: Adebowale Adeyemo, Sally N. Adebamowo, and Clement Adebamowo
Subjects: Persistence (psychology), Infectious Diseases, business.industry, Immunology, Medicine, Pharmacology (medical), Genetic risk, Human papillomavirus, business
Published: 2019
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47. PI-2 Comparison of type-specific HPV detection in urine and vulvo- vaginal samples from adeolescent girls in Jos, Nigeria

Author: Nanma Dashe, Clement Adebamowo, Sally N. Adebamowo, Lohya Nimzing, and Daniel Z. Egah
Subjects: Gynecology, medicine.medical_specialty, Infectious Diseases, business.industry, medicine, Type specific, Pharmacology (medical), Urine, Hpv detection, business
Published: 2019
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48. PF-3 Is nigerian breast cancer associated with endogenous retrovirus Xq21.33?

Author: Sally N. Adebamowo, Mark H. Kaplan, Clement Adebamowo, and Galya Bigman
Subjects: Infectious Diseases, Breast cancer, business.industry, Cancer research, Endogenous retrovirus, Medicine, Pharmacology (medical), business, medicine.disease
Published: 2019
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49. Abstract P3-06-13: Transient increase in breast cancer risk after a full term pregnancy among African women

Author: Ningqi Hou, Oladosu Ojengbede, S Akinleye, Adeyinka Ademola, T. O. Ogundiran, I Anetor, Antony Gakwaya, D Sighoko, Dezheng Huo, Clement Adebamowo, O. I. Olopade, and Paul Ndom
Subjects: Cancer Research, Pregnancy, medicine.medical_specialty, Pediatrics, Obstetrics, business.industry, medicine.disease, Logistic regression, Breast cancer, Oncology, Informed consent, medicine, Menarche, business, Live birth, Parity (mathematics), Body mass index
Abstract: Background African women affected by breast cancer (BC) have high parity with five children or more, are relatively young at first full term pregnancy (FFTP), are diagnosed at a young age and are often premenopausal at diagnosis. While several studies have assessed the role of reproductive factors for BC risk among African women, none of them have assessed whether there is dual effect of age at full term pregnancy (FTP). In this communications, using a large dataset from an on-going hospital-based case-control study, we examine the role of age at full term pregnancy on breast cancer risk among African women. Methods The study includes sites in Nigeria (University College Hospital, Ibadan), Cameroon (Yaoundé General Hospital) and Uganda (Breast Clinic of Mulago Hospital of Kampala). It was initiated in 1998 in Nigeria and extended to Cameroon and Uganda in 2011. Cases were consecutive females diagnosed with invasive BC. Controls were recruited from the community or within the hospital and have never being diagnosed with any cancer. Cases and controls were aged 18 years or more and gave informed consent. Full term pregnancy was defined as a pregnancy that lasted at least 7 months and included both live birth and stillbirth. Logistic regression models were used to assess the effects of age at first and second FTP, and their interaction with current age on BC risk. Age at menarche, parity, body mass index and hormone contraception use were included in the models. Results The study includes 1668 cases and 2399 controls recruited between 1998 and May 2013. Mean duration of live birth was 9 months (SD±0.52) and 8.8 months (SD±0.66) for a stillbirth. Overall, the mean age at FFTP was 23 years (SD±4.91) for both cases and controls. Compared to nulliparous women, parous women who had FFTP at 20 years have increased risk (OR = 1.59, CI 95%, 1.16-2.21) to develop BC in the year following the pregnancy. Up to 5 years following the FFTP, this OR is 1.38 (CI 95%, 1.06-1.80) while it is 0.77 (CI 95%, 0.62-0.95) 25 years later. This observation was also true for parous women who have had their FFTP at 25, 30, or 35 years. Moreover, a similar pattern was observed when comparing uniparous women to women with 2 or more children. Conclusion Our results show a transient increase in risk of BC after a full term pregnancy which declined and became protective over time. This observation is consistent with the effect of pregnancy on BC that has been described in other populations and may partially explain the current profile of breast cancer among African women. Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P3-06-13.
Published: 2013
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50. Risk factors for pregnancy-associated breast cancer: a report from the Nigerian Breast Cancer Study

Author: Stella Akinleye, Ningqi Hou, Oladosu Ojengbede, Dezheng Huo, Imran O. Morhason-Bello, Temidayo O. Ogundiran, Clement Adebamowo, Yonglan Zheng, Imaria Anetor, James D. Fackenthal, and Olufunmilayo I. Olopade
Subjects: Adult, medicine.medical_specialty, Epidemiology, Black People, Nigeria, Breast Neoplasms, Article, Body Mass Index, Young Adult, Breast cancer, Pregnancy, Risk Factors, Odds Ratio, Humans, Medicine, Prospective Studies, Young adult, skin and connective tissue diseases, Prospective cohort study, Gynecology, business.industry, Obstetrics, Postpartum Period, Case-control study, Odds ratio, medicine.disease, Parity, Logistic Models, Premenopause, Case-Control Studies, Female, business, Pregnancy Complications, Neoplastic, Body mass index, Postpartum period
Abstract: Little is known about risk factors for pregnancy-associated breast cancer (PABC), diagnosed during pregnancy or postpartum.We enrolled 1715 premenopausal women from the Nigerian Breast Cancer Study from 1998 to 2011. Based on recency of last pregnancy from diagnosis, breast cancer cases were categorized as (1) PABC diagnosed 2 years or longer postpartum, (2) PABC diagnosed 3 to 5 years postpartum, or (3) non-PABC diagnosed more than 5 years postpartum. Controls were matched to cases on recency of last pregnancy. Multiple logistic regressions were performed comparing cases and controls within each group.Of the 718 cases, 152 (21.2%) had PABC 2 or more years postpartum, and 145 (20.2%) 3 to 5 years postpartum. Although not statistically significant, women with higher parity tend to have an elevated risk of PABC but reduced risk of non-PABC (p for heterogeneity = 0.097). Family history of breast cancer might be a strong predictor particularly for PABC 2 or more years postpartum (odds ratio, 3.28; 95% confidence interval, 1.05-10.3). Compared with non-PABC cases, PABC 2 or more years postpartum cases were more likely to carry BRCA1/2 mutations (P = .03).Parity may have different roles in the development of PABC versus other premenopausal breast cancer in Nigerian women. Prospective mothers with multiple births and a family history of breast cancer may have an elevated risk of breast cancer during their immediate postpartum period.
Published: 2013
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