Genomics and Chronic Non-Communicable Diseases

Transition from Communicable to Chronic Non-Communicable Diseases

Global health research has often emphasized infectious diseases such as HIV/AIDS, TB, and malaria. As we continue to make gains in reducing deaths from deadly communicable diseases like HIV/AIDs, we are beginning to see a transition in this emphasis. Led by John Schneider, one of the first global health scholars nurtured by CGH, the Center for HIV Elimination (CCHE) seeks to eliminate new HIV transmission events over the next 30 years by using network science to target and integrate prevention as well as create structural and community-specific interventions ( While deaths from HIV/AIDs continue to decrease, giving rise to improved life expectancy and people living longer, we now have to deal with the emerging epidemic of chronic non-communicable diseases (NCD) and injuries that contribute to more than half of deaths in low- to middle-income countries (LMIC). The World Health Organization (WHO) predicts that deaths from cancer will rise by 2030 from approximately 8 million individuals/year to more than 13 million/year. Most of the increases in NCD diagnoses including diabetes, hypertension, strokes, depression, and cancer will occur in economically disadvantaged LMIC that are least able to detect and manage complications of NCD. Hence, the focus of our global health program is to integrate biologic and social determinants of health to improve health and wellness and prevent economically devastating chronic diseases in LMIC.

UChicago Research Bangladesh has established the world’s largest population-based cohort to study the health effects of arsenic poisoning. The research infrastructure they have developed in the process is already contributing new knowledge in cancer and other NCD. The burden of cancer and other NCD, such as diabetes, sickle cell disease, and cardio-pulmonary diseases in Africa remains poorly characterized. There is need for analysis of the population genetics of contemporary African populations in comparison to African Americans in the U.S. CGH has been successful in fostering the development of expertise in genomics research among African scientists and development of a networked community of African investigators who can collaborate with U.S. scientists. Funding from an NIH D43 training grant, for instance, brought Dr. Williams Balogun, an endocrinologist from the University of Ibadan (UI), together with Dr. Lou Philipson, Director of the Kovler Center, UCMedicine. Dr. Philipson provided capacity-building research mentoring on monogenic diabetes. Dr. Balogun facilitated access to a cohort of West Africans having genetic profiles that broadened Dr. Philipson’s program of research on insulin gene mutations. The D43 also enabled Dr. Funmi Olopade to mentor Dr. Atara Ntekim, a UI radiation oncologist, as they engaged in research on the genetic underpinnings of breast cancer in Nigerian women. These examples demonstrate mutual benefits to the two institutions. Most relevant to low resource settings, UChicago is poised to lead in the implementation and delivery of novel genomic technologies to improve global public health and, as well, address endemic NCD in our own communities.

Equity in Cancer Outcomes

Realizing full equity in cancer outcomes has long been a focus for faculty at the University of Chicago Comprehensive Cancer Center.  Here, the genetic and non-genetic risk factors in women’s breast, cervical, endometrial, and ovarian cancers are under study. Cancer care and research were identified as major institutional priorities in both the 2004 and 2011 strategic planning processes of the University. They continue to be a key focus of the ongoing University of Chicago Medicine Capital Campaign. UChicago has also been a particular leader in the investigation of the etiology and pathogenesis of breast cancer throughout the African Diaspora, with ongoing collaborations in Nigeria, Uganda, Cameroon, India, and Brazil. Elucidation of the molecular signature of breast cancer in populations of African Ancestry over decades of migration to the Americas and Brazil[6] led to important collaboration and mentoring of Rodrigo Guindalini from Brazil. This is just the beginning. Full elucidation of the genetic variables predisposing to breast cancer will require access to populations available to CGH partners at other sites in Africa as well as in Asia and South America. The CGH has partnered with the African Organization for Research and Training in Cancer (AORTIC), the American Cancer Society, Susan G. Komen for the Cure, the Breast Cancer Research Foundation, the Avon Foundation, and others—private sector, civil society, and governments—to build sustainable and scalable models for cancer control in LMIC.

Funmi Olopade, CGH Director and Associate Dean for Global Health, leads this initiative. As a previous presidential appointee to the National Cancer Advisory Board, she served on the highest governmental board overseeing the nation’s cancer research program, chairing the Subcommittee on Global Cancer Research. Dr. Olopade has long been committed to the goal of equity in cancer outcomes, focusing especially on Chicago’s Southside neighborhoods. The MacArthur Foundation recognized her achievements with a MacArthur Fellowship in 2005. Habib Ahsan, CGH Associate Director for Research, leads a team of cancer epidemiologists in the Center for Cancer Prevention that includes CGH-affiliated faculty Dezheng Huo, Brian Chiu, and Brandon Price. This team is committed to building on UChicago’s strengths in health equity research to create large-scale, prospective cohort projects to better understand the extent and manifestations of cancer locally and globally. Drs. Dezheng Huo and Funmi Olopade have collaborated with colleagues in Nigeria, Cameroon, Uganda for over a decade and have successfully built a risk prediction model for breast cancer.

Big Data Science

An exciting extension of this research in cancer genomics is the development of an international network of researchers, including experts in bioinformatics, having the goal of advancing “Big Data Science.” CGH partners in this endeavor include Ian Foster of the Computation Institute and Argonne Research Laboratories and Andrey Rzhetsky of the Department of Human Genetics. In 2018, Drs. Foster and Rzhetsky taught a Bioinformatics Master Class at CGH partner institution, University of Ibadan, Nigeria, with enrollment of more than 100 faculty, graduate and undergraduate students. They also visited several departments to assess computational capacities as planning for future collaborations. This effort is funded by the UChicago Center for Data and Computing for $90,000. The potential benefits of such capacity-building efforts are many. Using cloud computing, genome sequences can be analyzed in Chicago to personalize cancer treatment, a process that can be easily applied to other genetic diseases, such as sickle cell, neonatal diabetes, asthma, and obesity. This technology can also be used to monitor infectious disease outbreaks. The possibility exists to use clouds, genome sequences of affected individuals and non-affected relatives, evolutionary conservation information, and network analysis to identify the causative mutations in diseases of unknown genetic origin.