Cancer Genomics and Genomic Data Science for East Africa

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PROJECT SUMMARY/ABSTRACT The 20 years since publication of the draft human genome sequence in 2001 have been a truly transformational era in the field of cancer research marked by ever more significant scientific milestones and a steadily accelerating rate of progress. Global scientific initiatives focused on comprehensive characterization of tumor genomes – such as The Cancer Genome Atlas (TCGA) and the Pan-Cancer Analysis of Whole Genomes (PCAWG) – are radically transforming our approach to the prevention, diagnosis, and treatment of cancer. Surprisingly, although both TCGA and PCAWG included tumors from patients on many continents, few tumors from Africa were included in their analyses. Moreover, the number of African scientists involved in the two projects was limited. The paucity of African tumors analyzed by TCGA and PCAWG, and the dearth of African scientists involved in their analysis, is concerning given that Africa is home to 1.4 of the world’s 7.9 billion inhabitants, and much of human genetic variation is found only on the African continent. The profound under- representation of African genomes and tumors – and of African scientists – in cancer genomics studies is attributable to many factors, but the lack of requisite infrastructure for genomic research in Africa and the limited number of genomics professionals in Africa who are trained in both the generation and analysis of genomic data are major contributors. To ensure that the transformative benefits of recent advances in cancer genomics to the prevention, diagnosis, and treatment of cancer will be realized in Africa, dedicated initiatives must be undertaken to increase the number of trained genomics professionals in Africa. In this application, the Fred Hutchinson Cancer Research Center in Seattle, WA and the Uganda Cancer Institute in Kampala, Uganda – two premier institutions that have been collaborating since 2004 to conduct cancer research and to increase the capacity for high-quality cancer research, training, and clinical care in Uganda and East Africa – propose to extend their well- established collaboration to address the critical shortage of African genomics professionals who are trained in the generation and the analysis of cancer genomic data. We hypothesize that improving the supply of African professionals who can both generate cancer genomic data of reproducibly high quality and analyze those data rigorously and comprehensively will accelerate the development of an Africa-based cancer genomics community and ensure that the advances of the cancer genomics revolution will maximally benefit African cancer patients. Over a period of 5 years, and in conjunction with the Infectious Diseases Institute of the College of Health Sciences, Makerere University, the Fred Hutch and UCI will support 4 Ugandan or East African individuals who will complete master’s degrees, and 2 who will complete doctoral degrees, in Bioinformatics with a focus on cancer genomics and genomic data science. We anticipate that graduates of the program will become the leaders of the cancer genomics community in Uganda and East Africa.