CPGR BRIEF DESCRIPTION – 2013

Service provision, innovation eco-system creation, Translational research & development…

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CPGR brief description

CPGR background

The CPGR is based on an initiative by the South African Department of Science and Technology

(DST), and funded by the Technology Innovation Agency (TIA), to support the development of an

internationally competitive bio-economy in South Africa.

The organisation was created in 2006 with a vision of establishing a modern, world-class facility that

serves the needs of the scientific community in South Africa by providing state-of-the-art services,

technical expertise and collaborative research capabilities in the Genomics and Proteomics arena.

The CPGR was established as a non-profit organisation, working as a contract research organisation

when providing support and services to the life science and biotech community. Based in Cape

Town, the organisation combines state-of-the-art information rich genomic and proteomic ('omics')

technologies with bio-computational pipelines to create unique solutions for biological problems.

By applying principles of network orchestration the CPGR is combining internal and external

resources to create economies of scale and scope necessary for rendering genomic, proteomic and

bioinformatic support in a high-quality, cost-effective fashion1. Orchestrating capacity in a

networked fashion allows the CPGR to respond to a wide range of needs in an agile fashion and

render fit-for-purpose solutions; the network approach also facilities the creation and diffusion of

knowledge, a prerequisite for innovation in any sector but certainly in the rapidly evolving ‘omics’

arena. Ultimately, our aim is to create an eco-system conducive to stimulating life science innovation

in Africa!

The CPGR's vision is to be a key driver in South Africa's effort to become one of the leading bio-

economies of the 21st century. Our mission is to be an 'omics' technology platform that provides

solutions to innovation gaps and identified opportunities in the development of the SA modern

biotech sector!

CPGR offering

A highly skilled laboratory staff complement maintains and runs the key pieces of genomic and

proteomic equipment in providing critical support in services and projects to clients. The

organization can handle samples and isolates from most biological sources, including human, animal,

plant, yeast, bacteria and viruses in a secure Biohazard Class II (BSL II) environment. To create

effective solutions in complex biological projects, the CPGR employs a wide range of validated

genomic, proteomic and bioinformatic workflows. These include array-based RNA expression

profiling and DNA genotyping using Affymetrix cartridge- and GeneTitan-arrays; whole-genome,

exome and transcriptome sequencing on a variety of high-throughput sequencing platforms

(Illumina, LifeTech, 454); quantitative DNA and RNA detection on digital and qRT-PCR platforms;

protein identification and biomarker discovery using a suite of state-of-the-art mass spectrometers

(MALDI-ToF/ToF, Q-Exactive, TSQ Vantage, Q-ToF, amongst others); and multiplex biomarker

profiling using solid protein arrays and bead-based suspension arrays. Computational workflows for

high-throughput analysis of genomic and proteomic data-sets, including standard DNA and next-

generation sequencing (NGS) data analysis complete the portfolio.

1 For a detailed discussion of the approach, visit http://www.cpgr.org.za/blogspot/?p=367

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CPGR brief description

Complete Genomics & Proteomics services

The efficient integration of a range of technologies and workflows allows us to render complete

Genomics and Proteomics services. The value we add to scientists is based on the fact that we can

choose from a range of options and devise custom solutions that meet diverse requirements such as

throughput, coverage, depth, and costs in genomic and proteomic projects. In response to clients’

needs, we can assemble available know-how and resources into fit-for-purpose value propositions.

Through the flexible combination of technologies, and adherence to stage-specific quality

management principles, we have the ability to render support and services across the entire

genomic and proteomic innovation chain (Figures 1 and 2).

Figure 1: Complete Genomics offering

Figure 2: Complete Proteomics offering

Quality is an intrinsic part of all of the organisation’s endeavours; it is part of service processes,

product development, and all of our communication. In support of generating good quality outputs,

the CPGR employs a modular approach to quality assurance and control. Overall, the organisation is

based on ISO approach to quality management while in projects we adhere to G(C)LP principles. In

2013, the CPGR prepares for certification according to ISO 9001:2008, building the foundation for

the accreditation of individual workflows, as needed. Relevant CPGR staff is trained in G(C)LP and in

lean management principles, amongst others.

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CPGR brief description

Project management in support of life science innovation

Technological versatility is relevant in projects aimed at the development of biomarkers for diagnosis

and treatment of human diseases. Biomarker development is a lengthy process unfolding over 3

essential stages: analytical validity, clinical validity and clinical utility. Often, initially promising

discoveries fail to pass later development hurdles owing to problems in the design, execution or

reporting of genomic and proteomic projects. Often, ‘omics’-driven innovation does not occur for

lack of validation of research outputs2.

We believe that genuine capacity development in the modern life sciences, aimed at genomics-and

proteomics-driven innovation on the African continent, rests on the triple pillars of access to world-

class infrastructure, provision of high-quality affordable services, and empowerment through

training, in particular in the field of data-analysis and interpretation (Bioinformatics).

In order to facilitate a seamless conversion of project ideas into robust project plans, the CPGR has

devised an integrated framework for the design and management of genomic and proteomic

projects2. This framework is based on the categorisation of key areas of activity in these projects into

domains and functions (Figure 3). The framework was developed by taking into account CPGR

expertise and inputs from external experts in the field of genomic and proteomic biomarker

development. Ultimately, it is a risk-mitigation framework developed to facilitate a more effective

migration of early-stage research outputs into downstream development, and translation into

products and services.

Figure 3: CPGR project management framework

Following this approach, we strive to enhance quality, turnaround and cost-effectiveness of genomic

and proteomic projects. In addition, we take a long-term perspective to planning the early stages of

the research & development life cycle, thereby enhancing our ability to support translational

outcomes.

2 For a discussion of the corresponding problems, visit http://www.cpgr.org.za/blogspot/?p=201

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CPGR brief description

Customer engagement

CPGR customer engagement occurs through a 3-stage process (Figure 4). The first step, bio-

consultation, is aimed at clearly assessing project needs and requirements. The main output of this

stage is a mutually agreed analytical study design and project plan, both aimed at ensuring seamless

and high-quality turn-around of project deliverables. The second stage, bio-analysis, is where

biological samples are converted into analytical data, generated on one or more of the CPGR’s

technological platforms. The main output of this stage is a robust set of raw data, including primary

analysis and quality control, and an analytical report. The last stage, bio-informatics, is comprised of

a more-in-depth analysis and interpretation of data and, if required, down-stream data-mining. The

scope of this last stage is dependent on the needs and requirements specified in the initial study

plan but can vary with the outcomes generated in stage 2, bio-analysis.

Figure 4: CPGR customer engagement

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CPGR brief description

Memberships & networking

The CPGR embraces networking and collaboration in the interest of creating capacity in Africa for

innovation in diagnostics, health and drug development. To date, the organisation is a member of

the following organisations:

Society / organisation Type of affiliation Description

EMBNET (European Molecular Biology Network)

Associated Node Network aimed at enhancing capacity in Bioinformatics worldwide

SASBi (South African Society for Bioinformatics)

Elected representative for industry in South Africa

Society aimed at coordinating Bioinformatics activities in South Africa

ISCB (International Society for Computational Biology)

Education and training committee member

The ISCB addresses scientific policies, provides access to high quality publications, organizes meetings, and serves as a portal to information about training, education, employment and news from related fields

PGENI (Pharmacogenomics for Every Nation Initiative)

Partner Global initiative aimed at enhancing the development of improved drug treatments through Pharmacogenomics

ITFoM (IT Future of Medicine) Associated partner European Commission (EC) funded program to develop improved diagnostic tests through a combination of IT-based and ‘omics’ approaches

GOBLET (Global Organization for Bioinformatics Learning, Education and Training)

Partner Initiative aimed at coordinating world-wide bioinformatics training activities

ASBCB (African Society for Bioinformatics and Computational Biology)

Member Non-profit professional association dedicated to the advancement of bioinformatics and computational biology in Africa

Accordia network of African Centres of Excellence in Health

member Initiative aimed at creating sustainable centres of innovation in health on the African continent

ANDI (African Network for Drugs and Diagnostics Innovation) Centre of Excellence in Proteomics and Genomics

Partner Initiative that aims at promoting and sustaining African-led health product innovation to address African public health needs through efficient use of local knowledge, assembly of research networks, and building of capacity to support economic development.

H3ABioNet Member NIH/Welcome Trust funded pan-African initiative to create capacity in Bioinformatics across the continent

The Biomarkers Consortium Member Public-private biomedical research partnership managed by the Foundation for the National Institutes of Health that endeavours to discover, develop, and qualify biological markers (biomarkers) to support new drug development, preventive medicine, and medical diagnostics

ABRF (Association of Biomolecular Resource facilities)

Member International society dedicated to advancing core and research biotechnology laboratories through research, communication, and education.

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CPGR brief description

Institutional support

The CPGR is supported by grants from the following institutional investors in South Africa:

DST (Department of Science & Technology) TIA (Technology Innovation Agency)

Contact

Specific

Area Contact

Genomics genomics@cpgr.org.za

Proteomics proteomics@cpgr.org.za

Bioinformatics bioinformatics@cpgr.org.za

Human Capital Development (HCD) hcd@cpgr.org.za

General info@cpgr.org.za

General

Centre for Proteomic & Genomic Research (CPGR) Upper Level, St Peter’s Mall Cnr Anzio Road & Lower Main Road Observatory Cape Town 7925 South Africa Tel: +27 21 447 5669 Fax: +27 21 404 7657 WWW: http://www.cpgr.org.za Blog: www.cpgr.org.za/blogspot/

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CPGR brief description