31 October 2018, Cape Town, South Africa
Microsoft – through its 4Afrika initiative – and the Centre for Proteomic & Genomic Research (CPGR) have embarked on a joint project bringing together the intelligent cloud and genomics research to create a scalable, cost-effective technology platform to power cutting-edge medical analysis and research. This platform will be enabled by Microsoft Azure – to support the data transfer, storage and processing capabilities for genomics data-sets. The partnership will allow African scientists and academics to perform and efficiently collaborate on ground-breaking genomics research.
The platform aims to make genomic applications, such as, non-invasive prenatal testing (NIPT), BRCA sequencing for breast cancer, HLA typing for stem cell match making and ancestry profiling available on an accessible, secure and versatile cloud-based platform. This will enhance the analysis of data, the dissemination of information and the aggregation of data to support genomic research, innovation and health provision in (South) Africa.
This will be the first such initiative in Africa and could have enormous social and health care provision benefits by avoiding prescription of ineffective drugs and sidestepping potential side effects. It will also be an important step in enhancing the South African genomics ecosystem and the government’s Precision Medicine strategy.
Partnering for health
Based in Cape Town, the CPGR provides advanced ‘omics’ services to the life science and biotech communities in South Africa. ‘Omics’ groups, together with several specialities within the field of biology – including proteomics and genomics, which ‘zoom in’ on the proteome (the proteins output of an organism) and genome (the genetic makeup of an organism) respectively. This non-profit organisation uses leading technologies and bio-computational data pipelines to create and support tailored services for both academia and industry customers alike.
Combined with the power and stability of Azure (Microsoft’s dynamic cloud computing service) and coupled with technical and financial support from Microsoft 4Afrika, this project will boost the depth and breadth of the African medical sciences research community’s output and nurture the establishment of a stronger and sustainable medical research community on the continent.
A universe of data within us
Arguably the most famous of omics projects – to a broader, non-specialist audience – was the “Human Genome Project” which set out to map the entire human genome. This ambitious inward journey of discovery took 15 years to be declared ‘complete’ and uncovered, among other things, that the length of the average human genome – measured in base pairs (letters of the DNA sequence) – is approximately three billion. If we think of this as kilobytes of data, we’re talking about three terabytes of data points to be unpacked and explored per person.
To analyse this amount of information, a robust technology platform for analytics is needed. Azure cloud provides a cost-effective and regulation-compliant architecture for these big data projects.
From data to utility
Given the often-incomplete access to cutting edge medical solutions for many people in South Africa and Africa, building a platform that (i) enhances access to patient eco-systems; (ii) eases collection and transfer of information; (iii) facilitates the processing and down-stream analysis of genomic (eg DNA sequencing) data; (iv) allows for the secure, efficient and safe aggregation of such data; and (v) provides a means to combine and mine such data for research purposes is an important step towards enhancing (South) Africa’s Genomics and Precision Medicine eco-system.
Common diseases, such as cancer or diabetes, are influenced by the interplay of many different genetic markers, not caused by single gene mutations. To study these linkages requires the aggregation and analysis of very large data-sets. Also, provision of gene-based diagnostic testing requires the careful comparison of an individual’s data with appropriate reference data sets. Given the rapidly expanding nature of biomedical science and the genetic diversity found in African populations, having a means to store and analyse data is a key pillar of Africa-led research and innovation. Such a solution will aid in reducing “data drain” from Africa as researchers will have solutions to better manage and analyse their data which in turn works towards building research capacity in Africa.
‘Working with Microsoft Azure gives us an opportunity to explore data management solutions that are flexible in scope and scale when supporting large-scale research projects or developing Precision Medicine solutions’, says Reinhard Hiller, Managing Director at CPGR. ‘The project allows us to leverage an existing cloud-based data management ecosystem, while amplifying our own expertise in developing and running a Genomics technology platform, to further develop our innovation support and service provision capabilities. We envisage creating a system that allows us to deliver value, and collaborate with others, across the African continent.’
Microsoft for medicine
This project speaks directly to the potential of cloud technologies enabling cutting-edge science and medicine. With a scalable platform like Azure as the backbone of a project, medical researchers can get to work on unlocking the secrets embedded in our cells – a giant leap for mankind into ‘inner space’ – and towards a literal better, healthier life.
“For Microsoft 4Afrika, it is one of the most exciting fruits of our long-term investment into Africa’s economic, social and technological development,” says Ryno Rijnsburger, chief technology officer at Microsoft 4Afrika. “We are providing both financial and technical support to the CPGR and also intend to bring out Microsoft experts to work with the team through our MySkills4Afrika volunteer programme.”
“Another of the intended outcomes is to stimulate interest and support the CPGR in accessing additional funding to continue operationalising the platform, which will in turn lead to additional technology investments into things like mobile apps and reporting capabilities.”
“The sheer volume of data that can flow through the system will drive genomic research and medical innovation, and public health across Africa will reap the benefits,” concludes Rijnsburger.
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About Microsoft
Microsoft (Nasdaq “MSFT” @microsoft) enables digital transformation for the era of an intelligent cloud and an intelligent edge. Its mission is to empower every person and every organization on the planet to achieve more.let
The 4Afrika Initiative is Microsoft’s business and market development engine in Africa. Launched in 2013, it promotes affordable access to the internet, world-class skills and innovation to unlock and accelerate Africa’s potential to create technology not only for the continent, but for the world.
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 incubator 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.
In support of Genomics capacity development in Africa, CPGR has launched an iScan system for high-end genotyping studies in early 2018. In April 2018, CPGR announced a new partnership to form a bespoke African biotech incubator, OneBio.
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