1 | P a g eCPGR brief descriptionCPGR backgroundThe 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 aninternationally competitive bio-economy in South Africa.The organisation was created in 2006 with a vision of establishing a modern, world-class facility thatserves 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 organisationwhen providing support and services to the life science and biotech community. Based in CapeTown, 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 externalresources to create economies of scale and scope necessary for rendering genomic, proteomic andbioinformatic support in a high-quality, cost-effective fashion1. Orchestrating capacity in anetworked fashion allows the CPGR to respond to a wide range of needs in an agile fashion andrender fit-for-purpose solutions; the network approach also facilities the creation and diffusion ofknowledge, 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 innovationin Africa!The CPGRs vision is to be a key driver in South Africas effort to become one of the leading bio-economies of the 21st century. Our mission is to be an omics technology platform that providessolutions to innovation gaps and identified opportunities in the development of the SA modernbiotech sector!CPGR offeringA highly skilled laboratory staff complement maintains and runs the key pieces of genomic andproteomic equipment in providing critical support in services and projects to clients. Theorganization 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 createeffective solutions in complex biological projects, the CPGR employs a wide range of validatedgenomic, proteomic and bioinformatic workflows. These include array-based RNA expressionprofiling 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 biomarkerprofiling using solid protein arrays and bead-based suspension arrays. Computational workflows forhigh-throughput analysis of genomic and proteomic data-sets, including standard DNA and next-generation sequencing (NGS) data analysis complete the portfolio.1For a detailed discussion of the approach, visit http://www.cpgr.org.za/blogspot/?p=367
2 | P a g eCPGR brief descriptionComplete Genomics & Proteomics servicesThe efficient integration of a range of technologies and workflows allows us to render completeGenomics and Proteomics services. The value we add to scientists is based on the fact that we canchoose from a range of options and devise custom solutions that meet diverse requirements such asthroughput, 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 qualitymanagement principles, we have the ability to render support and services across the entiregenomic and proteomic innovation chain (Figures 1 and 2).Figure 1: Complete Genomics offeringFigure 2: Complete Proteomics offeringQuality 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 isbased on ISO approach to quality management while in projects we adhere to G(C)LP principles. In2013, the CPGR prepares for certification according to ISO 9001:2008, building the foundation forthe accreditation of individual workflows, as needed. Relevant CPGR staff is trained in G(C)LP and inlean management principles, amongst others.
3 | P a g eCPGR brief descriptionProject management in support of life science innovationTechnological versatility is relevant in projects aimed at the development of biomarkers for diagnosisand treatment of human diseases. Biomarker development is a lengthy process unfolding over 3essential stages: analytical validity, clinical validity and clinical utility. Often, initially promisingdiscoveries fail to pass later development hurdles owing to problems in the design, execution orreporting of genomic and proteomic projects. Often, ‘omics’-driven innovation does not occur forlack of validation of research outputs2.We believe that genuine capacity development in the modern life sciences, aimed at genomics-andproteomics-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 throughtraining, 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 hasdevised an integrated framework for the design and management of genomic and proteomicprojects2. This framework is based on the categorisation of key areas of activity in these projects intodomains and functions (Figure 3). The framework was developed by taking into account CPGRexpertise and inputs from external experts in the field of genomic and proteomic biomarkerdevelopment. Ultimately, it is a risk-mitigation framework developed to facilitate a more effectivemigration of early-stage research outputs into downstream development, and translation intoproducts and services.Figure 3: CPGR project management frameworkFollowing this approach, we strive to enhance quality, turnaround and cost-effectiveness of genomicand proteomic projects. In addition, we take a long-term perspective to planning the early stages ofthe research & development life cycle, thereby enhancing our ability to support translationaloutcomes.2For a discussion of the corresponding problems, visit http://www.cpgr.org.za/blogspot/?p=201
4 | P a g eCPGR brief descriptionCustomer engagementCPGR 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 thisstage is a mutually agreed analytical study design and project plan, both aimed at ensuring seamlessand high-quality turn-around of project deliverables. The second stage, bio-analysis, is wherebiological samples are converted into analytical data, generated on one or more of the CPGR’stechnological platforms. The main output of this stage is a robust set of raw data, including primaryanalysis and quality control, and an analytical report. The last stage, bio-informatics, is comprised ofa more-in-depth analysis and interpretation of data and, if required, down-stream data-mining. Thescope of this last stage is dependent on the needs and requirements specified in the initial studyplan but can vary with the outcomes generated in stage 2, bio-analysis.Figure 4: CPGR customer engagement
5 | P a g eCPGR brief descriptionMemberships & networkingThe CPGR embraces networking and collaboration in the interest of creating capacity in Africa forinnovation in diagnostics, health and drug development. To date, the organisation is a member ofthe following organisations:Society / organisation Type of affiliation DescriptionEMBNET (European Molecular BiologyNetwork)Associated Node Network aimed at enhancing capacity inBioinformatics worldwideSASBi (South African Society forBioinformatics)Elected representative forindustry in South AfricaSociety aimed at coordinating Bioinformaticsactivities in South AfricaISCB (International Society forComputational Biology)Education and trainingcommittee memberThe ISCB addresses scientific policies, providesaccess to high quality publications, organizesmeetings, and serves as a portal to informationabout training, education, employment andnews from related fieldsPGENI (Pharmacogenomics for EveryNation Initiative)Partner Global initiative aimed at enhancing thedevelopment of improved drug treatmentsthrough PharmacogenomicsITFoM (IT Future of Medicine) Associated partner European Commission (EC) funded program todevelop improved diagnostic tests through acombination of IT-based and ‘omics’approachesGOBLET (Global Organization forBioinformatics Learning, Education andTraining)Partner Initiative aimed at coordinating world-widebioinformatics training activitiesASBCB (African Society forBioinformatics and ComputationalBiology)Member Non-profit professional association dedicatedto the advancement of bioinformatics andcomputational biology in AfricaAccordia network of African Centres ofExcellence in Healthmember Initiative aimed at creating sustainable centresof innovation in health on the AfricancontinentANDI (African Network for Drugs andDiagnostics Innovation) Centre ofExcellence in Proteomics and GenomicsPartner Initiative that aims at promoting and sustainingAfrican-led health product innovation toaddress African public health needs throughefficient use of local knowledge, assembly ofresearch networks, and building of capacity tosupport economic development.H3ABioNet Member NIH/Welcome Trust funded pan-Africaninitiative to create capacity in Bioinformaticsacross the continentThe Biomarkers Consortium Member Public-private biomedical research partnershipmanaged by the Foundation for the NationalInstitutes of Health that endeavours todiscover, develop, and qualify biologicalmarkers (biomarkers) to support new drugdevelopment, preventive medicine, andmedical diagnosticsABRF (Association of BiomolecularResource facilities)Member International society dedicated to advancingcore and research biotechnology laboratoriesthrough research, communication, andeducation.
6 | P a g eCPGR brief descriptionInstitutional supportThe CPGR is supported by grants from the following institutional investors in South Africa: DST (Department of Science & Technology) TIA (Technology Innovation Agency)ContactSpecificArea ContactGenomics firstname.lastname@example.orgProteomics email@example.comBioinformatics firstname.lastname@example.orgHuman Capital Development (HCD) email@example.comGeneral firstname.lastname@example.orgGeneralCentre for Proteomic & Genomic Research (CPGR)Upper Level, St Peter’s MallCnr Anzio Road & Lower Main RoadObservatoryCape Town 7925South AfricaTel: +27 21 447 5669Fax: +27 21 404 7657WWW: http://www.cpgr.org.zaBlog: www.cpgr.org.za/blogspot/