The CPGR, together with a consortium of South African, African, and American scientists, has been awarded NCI (National Cancer Institute) funding in the order of USD 3M to study the genetic root causes of prostate cancer in African men. The project, known as MADCaP (Men of African Descent & Cancer of the Prostate), is formally led by Harvard TH Chan School of Public Health & Dana-Farber Cancer Institute Professor Tim Rebbeck (USA), together with a team of researchers at Stellenbosch University (SA), National Cancer Registry at the National Health Laboratory Services (NHLS) (SA), and several centres in Senegal, Nigeria and Ghana.
While Cancer of the Prostate (CaP) is the leading non-cutaneous cancer in the USA, African American (AA) men have the highest incidence and a significantly higher mortality rate than other men in the USA. Likewise, CaP is the leading cancer in terms of mortality in men from Africa and the Caribbean. The majority of Sub-Saharan African (SSA) CaP cases are diagnosed with aggressive disease, often at late (usually incurable) stages. In both SSA and AA men, this pattern may be due to a combination of tumor aggressiveness and late detection. Thus, there may be common features of CaP etiology in men of African descent that may explain observed mortality patterns. Knowledge gained from studies of CaP in SSA may in turn improve our understanding of aggressive CaP in men of African descent around the world.
Despite the clear public health implications of CaP in men of African descent, there have been few consistent associations of exposures, genetic susceptibility loci, or environmental factors with CaP etiology. In contrast, CaP has the highest heritability of any major cancer, and many genetic susceptibility loci have been identified in men of European and Asian descent. While numerous CaP genome-wide association studies (GWAS) have been reported, only one has been reported in an African population, and most of the GWAS-identified loci have not been replicated in men of African descent. There is a pressing need to identify African-specific alleles and thereby to elucidate the etiology of CaP with regards to risk and disease aggressiveness.
The NCI-funded MADCaP project aims to address this current knowledge disparity by conducting a Genome Wide Association Study (GWAS) with samples collected in South Africa, Senegal, Nigeria and Ghana. The CPGR will be leading the genotyping effort which will be enhanced by designing a custom high-density SNP array to interrogate 800.000 SNP genotyping markers at a time. This will be done in collaboration with Affymetrix and samples will be run on the CPGR’s GeneTitan® high throughput Axiom array platform. DNA collection and sample processing will commence towards the end of 2016 while the entire project will run over a 5-year period. Statistical data analysis will be done through a collaborative effort by the project consortium.
The project as a whole will be open to engagement with the SSA scientific community, with a particular emphasis on boosting cancer research capacity in Africa. Owing to the sample volume to be processed in the study, cancer researchers will benefit from having access to an African-centric cancer genotyping array application at affordable rates. This will facilitate the design and execution of small-to-medium size pilot studies which may in turn lead to further large-scale GWAS studies in African populations.
The CPGR is Africa’s first fully integrated ‘omics’ service provider, built to leapfrog South Africa’s ability to conduct information-rich biomedical research onto a globally competitive level. Amongst others, the organization offers the following ‘omics’ capacity: Next-Generation Sequencing: NextSeq500 (1x), MiSeq (1x), IonTorrent PGM (2x), IonProton (1x), for high-performance sequencing projects; Microarrays: Affymetrix GS 3000 and Affymetrix GeneTitan for genoytping and gene-expression analysis; Mass spectrometry: ABI 4800 MALDI-ToF/ToF and Thermo Q Exactive for MS-Proteomics; High-throughput PCR: ABI 7900 for qRT-PCR applications; Automated DNA/RNA QC, library handling and sample processing; dedicated IT infrastructure and bioinformatic applications for data analysis and interpretation.
The CPGR is a non-profit company based in Cape Town, South Africa, and based on an initiative by the Department of Science and Technology (DST), and financially supported by the Technology Innovation Agency (TIA), to boost the development of a bio-economy in South Africa. The CPGR combines state-of-the-art information rich genomic and proteomic (‘omics’) technologies with bio-computational pipelines to create unique solutions in the human health and the agri-biotech sectors. The CPGR has adopted a certified ISO 9001:2008 quality management system and is a BEE Level 2 contributor to economic transformation in South Africa. Information about the CPGR can be obtained at www.cpgr.org.za and www.cpgr.org.za/blogspot.
For questions, contact Dr Lindsay Petersen at email@example.com