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CPGR BRIEF DESCRIPTION – 2013
Service provision, innovation eco-system creation, Translational research & development…
1 | P a g e
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
2 | P a g e
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.
3 | P a g e
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
4 | P a g e
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
5 | P a g e
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.
6 | P a g e
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/
7 | P a g e
CPGR brief description

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CPGR - Service provision, innovation eco-system creation, translational research & development - May 2013

  • 1. CPGR BRIEF DESCRIPTION – 2013 Service provision, innovation eco-system creation, Translational research & development…
  • 2. 1 | P a g e 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
  • 3. 2 | P a g e 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.
  • 4. 3 | P a g e 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
  • 5. 4 | P a g e 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
  • 6. 5 | P a g e 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.
  • 7. 6 | P a g e 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/
  • 8. 7 | P a g e CPGR brief description