Context

CPGR has implemented and provided Precision Medicine solutions over the last two years to the South African health care market. In doing so, it has encountered challenges and opportunities.

We believe that these can be addressed by creating an integrated Precision Medicine Centre of Excellence. We propose that this can be achieved by collaborating with a Hospital (Group) and have outlined a dedicated concept on the following pages.

Such a Center shall be in South Africa, with very strong linkages into the African continent, to create and leverage value derived from ‘the African Genome’.

A Precision Medicine eco-system analysis, an exemplary Africa project, and background information about the CPGR, is provided at the end of this post (Addendum).

Challenges

South Africa has a unique disease profile, challenged by one of the world’s highest TB and HIV burden. In addition, the country experiences a rapid shift towards Non-Communicable Diseases (NCDs), a trend caused by urbanization and life style changes. Currently, NCDs account for 60% of the ten leading underlying causes of death in South Africa.

This increase in ‘Western’ diseases is complicated by a lack in understanding of the contribution of the African ‘genome’ to disease development owing to a historical focus on Caucasian populations for biomedical research and clinical development. Currently, only 2.5% of the global pharmaceutical R&D spend goes towards Africa.

Cutting edge diagnostic solutions and advanced therapies are presently not available to the majority of (South) Africa’s population. This is mainly due to a lack of infrastructure (buildings, systems, people, and processes used in the provision of health care), human resources (such as medical specialists, geneticists, and genetic counselors), and financial resources (to recover the costs of medical interventions, fund research, or invest into startups). Availability of knowledgeable medical specialists is a key impediment to the broad-based adaptation of Precision Medicine in the South African context.

Opportunities

Novel molecular techniques in Genomics, such as next-generation DNA sequencing, are being used globally to enhance diagnosis and treatment of NCDs. This has given rise to a novel medical paradigm, i.e. Precision Medicine. It can achieve health care efficiencies (cost savings) through more accurate diagnosis and effective selection of treatments.

The ability to manage and analyze large and complex data-sets has grown tremendously over the last few years, stimulating dedicated ‘big data’ initiatives and population health initiatives. New technologies, such as blockchain, Artificial Intelligence (AI), and machine learning, are increasingly becoming commonplace in biomedical research and innovation. These can be used to aggregate, manage and mine large data-sets, creating the basis for levering the value inherent to (South) African genomes.

Cutting-edge Genomics expertise is available in South Africa through the CPGR and can be used to develop and implement applications with advanced clinical utility in areas such as oncology, reproductive health, pediatrics, or pharmacogenetics (a summary of tests is available here). Data generated can be captured and aggregated in a systematic manner, laying the basis for future discovery and medical innovation.

South Africa has high quality clinical infrastructure and resources, mainly provided by private hospital groups; with the caveat that it only serves a minority of the population (ca 16%). Such capacity can be utilised in a collaborative manner, to develop a bespoke Precision Medicine Centre of Excellence.

Goals

• To make Genomic Medicine applications available to the entire population in South Africa in the most affordable manner, maximising individual patient benefits, health system efficiencies, and socio-economic impact.
• To create a premiere hub for developing, implementing and providing Precision Medicine solutions in the African context, with utility for clinicians and high value to patients.
• To develop a Precision Medicine ecosystem that fosters research, innovation, and economic development in South Africa.
• To build the go-to-place for world-class Precision Medicine solutions in Africa, creating a centre of gravity for medical tourism (for people of African descent, such as African Americans) and biomedical research (attracting clinical research).

Objectives

• To enter into a partnership with a Hospital (Group) aimed at creating an excellence centre for Precision Medicine (which can be replicated in other locations in the future).
• To raise the funding required for the creation of a world-class Precision Medicine infrastructure environment, as conceptualised below.
• To adapt or build a hospital and integrate multi-disciplinary expertise by marry high-end laboratory, and data analysis capacity, with relevant clinical expertise.

Center of Excellence: Conceptual description

A Precision Medicine Center is an integrated facility that brings together multi-disciplinary expertise in a seamless, patient-centric manner. A representative example of this can be found here.

The Center is embedded in a quality standard clinical environment that facilitates patient engagement, diagnosis and treatment in an effective manner.

It is also part of a larger Precision Medicine eco-system, contributing to and benefitting from ongoing innovation in this space, as conceptually summarised in Figure 1 and further expanded below.

Figure 1: Precision Medicine Center of Excellence

Clinical environment: High quality environment to receive, register and manage patients throughout the entire Precision Medicine ‘patient journey’ process.

Precision Medicine environment:

1. Counselling & prioritization: Patients are selected and/or recommended into the Precision Medicine process based on a thorough clinical assessment and fit-for-purpose selection of molecular testing applications.
2. Data & sample consent: Patient will be counselled about the benefits of sharing data and/or samples. Ideally, they consent to both.
3. Sample collection: Samples will be collected in accordance with procedures defined in (1). Samples and data will be stored in a repository, in accordance with (2).
4. Sample to data generation: Using procedures defined in (1), data will be generated. This may include data that are used for reporting purposes as well as data for research purposes.
5. Data analysis: This is the process used to convert raw data into high quality data sets (eg from raw sequencing data to VCF (variant call format) data), with a focus on standardisation, automation, turn-around, and scalability.
6. Interpretation & reporting: This is the process used to categorise, contextualise and interpret molecular data against the backdrop of a patient’s clinical presentation. In other words, it’s the key value-adding step in the entire process chain. This step is carried out by a multi-disciplinary team of experts.
7. Training & education: Considering existing knowledge and resource gaps, ongoing training and education is an essential component of a Precision Medicine Centre of Excellence. Such trainings can be delivered in a physical and virtual manner, as determined by user requirements.
8. Data repository: Any form of data linked to patients will be stored in accordance with a dedicated data capture and management framework. This is to enhance individual value-add (reporting) but also to stimulate research and innovation. Data may be derived from primary end-point testing (eg a DNA sequence in case of a BRCA test), but they may also be derived from secondary data analysis done with residual or in-process samples (eg high-end mass spectrometry analysis in tissue left after DNA extraction).
9. Sample repository: Residual samples (mainly DNA) will be stored for future research and development purposes, in accordance with (2).

Clinical environment: As applicable (defined in (6)), diagnosis, treatment, and/or monitoring are the pathways that can emanate from the Precision Medicine process. They are situated in dedicated medical domains, as exemplified by the green text boxes. The Centre may be linked to one or more medical domains, as defined by need and access to resources. Ongoing patient engagement forms a key part of this part in the process chain.

Continuous evaluation: This is aimed at continuously evaluating the effectiveness of Precision Medicine interventions and will require the statistical analysis of aggregate data-sets. It forms part of a systematic health economics assessment.

Socio-economic environment:

1. Research: Using samples, data and information generated by the Precision Medicine program, research can be conducted internally and externally. Access to samples and data will have to be governed effectively.
2. Clinical trials: The Precision Medicine centre ought to be involved in Clinical Trials, with an emphasis on benefitting local patients.
3. Incubation: Using the overall Precision Medicine ecosystem, we want to support biotech entrepreneurship and innovation, through a bespoke program.

4. Funding: Financial resources needed for patient care, diagnosis, treatment, prevention; for research programs; for start-up creation. This will require dedicated innovation efforts, considering the current lack of financial resources, eg by creating dedicated funding schemes.

Addendum

Precision Medicine ecosystem

A high-level Precision Medicine ecosystem description is available here.

HLA Africa Project

The HLA Africa Project is an extension of the CPGR’s partnership with The Sunflower Fund. The partnership has been created to tackle blood disorders, such as leukemia and sickle cell disease. The overview below is an executive summary of a project that is currently in development.

Project name	HLA Africa / Stem Cell Africa
Summary	Blood disorders, such as Leukaemia and sickle cell disease (SCD) affect 100s of thousands of individuals in Africa every year. Often, the only curative intervention is stem cell transplant, which requires the matching of suitable donors to patients. Access to donors is presently a life-threatening challenge for patients of African descent, who unlike patients in the developed world, have access to vast donor pools and advanced forms of diagnosis and treatment. HLA Africa aims to change the status quo by creating a pan-African registry with a minimum of 500,000 registered stem cell donors within a 5-year time-frame.
Partners	The project is a partnership between the CPGR and The Sunflower Fund, both established as NPCs in Cape Town, South Africa. It will also include partners from other African countries, for example in the form of local registries, as well as (potentially) the WMDA.
Governance	The project will be hosted at the CPGR and run as a consortium-based program, with accountability to the CPGR Board and the project ‘owners’. As applicable, the creation of special purpose vehicles, eg a dedicated NPC, will be considered. In addition, CPGR will consider the formation of dedicated entities in select African countries, either alone or in partnership with others, to implement project deliverables.
Market opportunity	To date, the only facility in Africa with advanced stem cell typing capabilities is located at CPGR. The only registry with typed donors is in South Africa (SABMR), with a few fledgling registries in other African countries. However, the donor numbers are so small that, statistically, they are literally insignificant in view of the problem (to put into context: Germany, with a population of 80M, has 8M registered donors; South Africa has hardly 70,000.) The only organisation with a dedicated program for stem cell donor funding and recruitment in Africa is The Sunflower Fund. Africa’s genetic diversity is huge, meaning that (i) an NGS-based donor typing program will have a medical impact and (ii) it will generate data of substantial scientific value (data that do not exist to date). Moreover, owing to shared ancestry, Africans in the diaspora (eg African Americans) will immediately benefit from having access to African donors when afflicted by a blood cancer or SCD, and vice-versa. This will generate novel avenues for value and income generation.
Solutions	Millions of African Americans, and other diaspora Africans, lack access to donors who match their own ancestry, should they fall ill. Finding a stem cell match requires access to a large pool of suitably characterised donors, owing to the underlying probabilities (ca 1/100,000). This is facilitated by a process of ‘molecular fingerprinting’ where a donor’s genetic information is mapped and combined with a patient’s. To date, registries across the world inadequately feature African donors, in number and quality of molecular profiling. For a blood disorder patient of African descent, this significantly diminishes his or her chance of finding a lifesaving donor. This problem can be addressed by recruiting a large number (healthy) African stem cell donors; (ii) creating adequate molecular profiles of these donors; (iii) and, facilitating donor-match-making through a proper African registry.
Our solution	We will roll out a large-scale donor typing program in (up to) 10 African countries, using South Africa as a base, in a hub-and-spoke-model. We will create a donor recruitment program; type donors at high resolution (to maximise match-making efficiency); create ancestry profiles of donors using high-density genotyping arrays; build an integrated data-centre to drive stem cell transplant R&D; develop a donor-recruitment and fund-raising program; and, foster the creation of regional stem cell and transplant centres of excellence.
Business model	The project will use project-specific funds to create a critical mass of capacity that will allow it to secure income from alternative sources to maintain, and expand, its activities. Therefore, it will use a hybrid approach to revenue generation, by continuously executing core donor funding initiatives; lobbying for government support in dedicated African countries; and, attracting private investments, eg by monetizing data or through algorithms developed through data comprehension.
Marketing	Marketing will be based on a multi-pronged strategy, including social media, web and TV channels; conferences; personal engagements with health officials; and, thought leadership activities through off- and online presentations.
Projections	The project will unravel in stages. Using a pilot that we’ll run in South Africa, to firmly test and establish the programs operational principles, we will implement further donor recruitment centres in select African countries, one at a time.
Investment	The program will require investment of at least USD 100 M, as elaborated in more detail below. This will go towards donor recruitment and capacity development across Africa; the bulk of the funds will be spent on stem cell donor typing.
Exit strategy / sustainability	During the project, we will develop extensive avenues for revenue generation to sustain the programs once the project has reached its conclusion. The avenues we’ll pursue will include the following and will all aim at continuing the project activities at a high level, through alternative income streams: •        Donor funding •        Research (philanthropic funding) •        Royalty income (from data utilisation) •        Productization (eg algorithms) •        Pharma / biotech projects
Summary	This is the first project that tackles donor recruitment and typing in Africans in a comprehensive and integrated manner. At this stage, this program is unparalleled on the African continent. It is a one of its kind Precision Medicine initiative, in how it employs cutting-edge technologies in a patient and donor-centric manner that maximises utility and health outcomes.

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. While situated in Cape Town, South Africa, the CPGR’s area of activity is increasingly the African continent, with a focus on biomedical research and innovation (eg MADCaP). 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.

Artisan Biomed

To bring Precision Medicine to Africa, CPGR has formed Artisan Biomed, Pyt Ltd. Artisan Biomed aims to develop Precision Medicine solutions by developing and implementing three distinct solutions: (i) provision of precision disease & health management services; (ii) translational research services; (iii) development of tailored medical solutions for people of African descent.

In support of this, Artisan has entered into a partnership with Lancet Laboratories, one of the biggest pathology laboratories in SA/Southern Africa. The partnership will start rolling-out a portfolio of unique molecular diagnostic applications, aimed at enhancing accessibility and affordability of Genomic Medicine in South Africa.

Information about the CPGR can be obtained at www.cpgr.org.za and www.cpgr.org.za/blogspot.