South Africa’s Centre for Proteomic & Genomic Research (CPGR) launches the Illumina iScan system in support of the H3Africa consortium and Genomics research in Africa

The Illumina iScan system will enhance population and disease-related genetic research in African populations and support Genomics capacity development on the continent

April 17, 2018 —Cape Town, South Africa—The Centre for Proteomic and Genomic Research (CPGR) today announced the successful implementation of an Illumina iScan system, as part of an effort to strengthen the capacity for high-end Genomics research on the African continent. CPGR’s endeavor emanates from an initiative by the H3Africa Consortium and Illumina (through their Elite Channel Partner, Whitehead Scientific (Pty) Ltd), to place an iScan instrument in Africa to support genome-wide association studies with the H3Africa Consortium Array. CPGR was granted an opportunity to host the platform and will make the instrument available to all scientists involved in Genomics research in Africa.

CPGR has been involved in numerous projects on the African continent, including a large-scale prostate cancer risk study, MADCaP, where capacity development is also a major focus. CPGR puts a strong emphasis on impact through the application of high-end Genomics, as exemplified by a recent partnership with The Sunflower Fund to make high-resolution stem cell (HLA) typing more accessible and affordable across the African continent.

‘We are very excited to be part of this initiative because it builds on our existing commitment to advance Genomics capacity in Africa’, said Dr Desiree Petersen, Senior Research Officer and CPGR’s iScan specialist. ‘Realizing the impact of Genomics on research, innovation, and healthcare will only be possible if projects are conducted in entirety on the continent, and scientists are involved in the whole process from design to execution and downstream data analysis’.

In addition to rendering support to H3Africa, the CPGR has made the iScan part of a bigger vision for expanding ‘omics’ capacity in Africa. CPGR supports a growing number of projects in other African countries and plans to integrate these through effective sample and data logistics. CPGR endeavors to achieve this by utilizing BAOBAB LIMS, an open-source laboratory information management system, developed by SANBI (South African National Bioinformatics Institute) and the B3Africa consortium. CPGR’s vision is to foster the creation of a connected ecosystem of cutting-edge research projects and laboratories across the African continent. To this end, CPGR will work closely with H3Africa and other stakeholders who are committed to capacity development in Africa.

About H3Africa

The Human Heredity and Health in Africa (H3Africa) Initiative aims to facilitate a contemporary research approach to the study of genomics and environmental determinants of common diseases with the goal of improving the health of African populations. An initiative of the National Institutes of Health (NIH) and Wellcome Trust, these two organizations implemented the phase I of the program. In October 2016, Wellcome Trust handed over its portfolio to the Alliance for Accelerating Excellence in Science in Africa (AESA) to manage and implement the phase II round of funding. AESA is now responsible for the delivery of the Wellcome’s Phase II portfolio of the awards and the management of the H3Africa Consortium in partnership with Wellcome Trust and the NIH. 

The CPGR iScan platform in a nutshell

  • The iScan supports Illumina assays for (among others):
    • SNP genotyping
    • Copy number variation (CNV) analysis
    • DNA methylation
  • Processing of any Illumina Infinium array at CPGR, including:
    • H3Africa array
    • Global Screening Array (GSA)


  • H3A & GSA array pricing provided in table below*
  • For all other Infinium applications and custom sample numbers, contact the CPGR
Array type Array cost (USD, ex VAT) Running fee (USD, ex VAT) Minimum sample number Number of markers
H3Africa member H3Africa 60 15 288 2.5M
Any African scientist H3Africa 60 20 288 2.5M
Any African scientist GSA 60 20 288 > 642k

*all prices are for the time being and to subject periodic change

About Whitehead Scientific

As one of Illumina’s elite partners, Whitehead Scientific (Pty) Ltd will be providing applications and service support to CPGR. Whitehead Scientific’s involvement with Illumina spans 10 years and our qualified and capable staff are committed to providing the support needed to ensure the success of this initiative.

 About CPGR

The CPGR is a non-profit company located in Cape Town, South Africa, based on an initiative by the Department of Science and Technology (DST), and financially supported by the Technology Innovation Agency (TIA). The CPGR combines state-of-the-art information-rich genomic and proteomic (‘omics’) technologies with bio-computational pipelines to render services and support projects in the life science and biomedical arena in (South) Africa, all run in an ISO 9001:2015 certified and ISO 17025 compliant quality management system.

Among others, the CPGR has recently launched an accelerator program to stimulate the creation of South African start-ups based on ‘omics’ technologies and set up Artisan Biomed to develop and implement Precision Medicine solutions in (South) Africa. The organization uses the open-source Baobab LIMS for sample and data tracking; and, it has recently implemented a DRAGEN platform to enhance the development and execution of high-speed/high-volume NGS data-sets. CPGR also hosts DIPLOMICS, a large infrastructure program initiated by the DST. In December 2017, CPGR entered into a partnership with the Sunflower Fund to enhance stem cell donor typing in Africa.

Information about the CPGR can be obtained at and


Desiree Petersen, Senior Research Officer