CPGR

Genomics

Our Genomic services enable a diverse range of cutting-edge solutions aimed at decoding an organism’s genomic DNA. This also includes analysis of the full complement of coding and non-coding RNA in a given biological system, otherwise known as Transcriptomics. As technology continues to advance, genomic services hold great promise in revolutionizing healthcare and genetic research.

The Nucleic Acid Extraction platform is dedicated to the isolation and purification of nucleic acids, specifically DNA and/or RNA. This process involves employing a variety of physical and/or chemical methods to effectively separate genetic material from cell membranes, proteins, and other cellular components.  The quality of nucleic acids recovered by this process is crucial for downstream applications. This includes assessing integrity, purity, and quantity of the extracted nucleic acids.

Applications

The platform supports the extraction of nucleic acids from diverse sample types, including but not limited to:

Whole blood

Sputum

Dried Blood Spots (DBS)

Bronchial Lavage

Serum

Buccal cells

Plasma

Mouth rinse

Tissue

Stool

FFPE (Formalin-Fixed Paraffin-Embedded) tissue

Urine

Respiratory secretions

Cervical Lavage

Saliva

Cell Culture (Mammalian, Bacterial, Viral, Fungal)

Quality control analyses include:

DNA & RNA Quantification

Purity Assessment

Integrity and Size Assessment

Contamination Check

Concentration Normalization

Current Services
  • CPGR’s extraction and QC laboratory provides validated workflows that ensures reliability and reproducibility in downstream analytical procedures. We are committed to delivering high-quality nucleic acids for various applications, including but not limited to genomics, transcriptomics, and molecular diagnostics.


Instruments
  • KingFisher™ Flex Purification System

  • QIAcube Connect and various manual extraction methods

  • NanoDrop™ 8000 Spectrophotometer

  • Glomax Explorer System, Qubit™ 4 Fluorometer

  • 4200 TapeStation system, Agilent Bioanalyzer 2100 Expert

  • Syngene Gel Documentation System

The Microarray platform specialises in a collection of high-throughput, streamlined array processing, specifically looking at gene expression studies and genome-wide analytics. Various assays are available for genotyping and copy number variation (CNV) analysis. The platform also hosts DNA Methylation pattern analysis and Cytogenetics analysis capabilities.

Applications

  • Pharmacogenomics
  • Genome-Wide Associated Study (GWAS)
  • CNV analysis
  • Ancestry marker analysis
  • Methylation pattern
  • Cytogenetics analysis


Validated Workflows & Current Services

  • Pharmacogenomics testing using the Precision Medicine Diversity Array (PMDA/PMDA Plus)
  • GWAS and Methylation pattern analysis
  • CytoScan Optima array to enable the detection of aneuploidies, sub microscopic aberrations, and mosaic events

Instruments 

  • GeneTitan™ MC Instrument
  • iScan™ System

Next Generation Sequencing (NGS) has propelled discoveries in rare disease research; allowed monitoring of cancer immunotherapy treatment efficacy; and helped us understand that our gut health as humans is at the core of our susceptibility to disease. In the era of the genome, the CPGR is poised to be an enabler and driver of efforts in utilising NGS to elucidate not only the African genome but our rich biodiversity.

Applications

  • DNA sequencing
  • RNA sequencing


Validated Workflows & Current Services

  • Whole Genome Sequencing.
  • Whole transcriptome Sequencing
  • mRNA Sequencing
  • small RNA sequencing
  • Metatransciptomic sequencing
  • Targeted metagenomic sequencing
  • Shotgun metagenomics


Instruments

  • NovaSeq™ 6000 System
  • NextSeq ™500
  • NextSeq ™550
  • MiSeq™
  • Ion GeneStudio™ S5 System with Ion Chef™ Instrument.

The Real-Time PCR platform offers custom qPCR services for targeted gene expression analysis, genotyping and miRNA Profiling.

Applications

  • Gene Expression Analysis with Real-Time PCR
  • Targeted Genotyping
  • miRNA Profiling services


Validated Workflows & Current Services

  • Gene Expression Analysis with Real-Time PCR for the quantitative measurement of mRNA expression of defined target genes. This service covers:
    • SYBR-Green or TaqMan primer design
    • qPCR Assay optimization and validation
    • Validation of reference (housekeeping) gene stability
    • Gene Expression Data Analysis
    • Profiling using multi-well plate-based gene expression arrays (e.g., RT2 Profiler PCR Arrays, TissueScan qPCR Arrays, etc)
    • Mid-to high-throughput custom gene expression profiling using the OpenArray® platform
    • Fixed Content TaqMan Specific Gene Expression Pathway Panels: Human Cancer Panel, Human and Mouse Inflammation Panels, Human Kinome Panel, Human Signal Transduction Panel and Stem Cell Panel
    • Pathogen detection
    • RNASeq Data Validation
    • Viral quantification
  • Targeted Genotyping to identify and validate genetic variations in DNA samples with the following services:
    • SNP Analysis
    • Mutation Detection
    • Copy Number Variation (CNV) with Real-Time PCR
    • Methylation-specific PCR
    • High Resolution Melting (HRM) analysis – (not sure if we should include this since we have not done these experiments yet)
    • Pharmacogenomic Profiling of ADME Gene Variants using the TaqMan™ OpenArray™ PGx Express Panel.
    • Human Barcoding


Instruments

  • QuantStudio™ 12K Flex Real-Time PCR System
    • FAST 96-well plates
    • 384-well plates and the OpenArray® chips with the QuantStudio™ AccuFill System loader for mid to high-throughput TaqMan assays.

Capillary Electrophoresis (CE) in genomic applications has surpassed conventional gel electrophoresis, providing unparalleled precision and efficiency for targeted or multiplexed genotyping. This analytical technique separates and analyzes DNA fragments based on their size and charge. At CPGR, CE facilitates applications that demand automated Sanger sequencing or fragment analysis workflows, offering flexibility to meet the unique requirements of your project outputs.

Applications

  • Targeted DNA sequencing
  • NGS confirmation
  • Microbial sequencing
  • Mitochondrial sequencing
  • Short tandem repeat (STR) analysis in human sample identification
  • Microsatellite marker analysis
  • Single-nucleotide polymorphism (SNP) genotyping
  • Quantitative fluorescence PCR (QF-PCR)
  • Restriction/Amplified fragment length polymorphism (RFLP/AFLP) analysis
  • Single-stranded conformation polymorphism (SSCP) analysis


Validated Workflows & Current Services

  • Human Identification for Paternity, Maternity or Kinship DNA testing (for Research use only)
  • Sanger Sequencing


Instruments

  • SeqStudio™ Genetic Analyzer System

Nucleic Acid Extraction & Quality Control

The Nucleic Acid Extraction platform at CPGR is dedicated to the isolation and purification of nucleic acids (DNA/RNA). This process involves employing a variety of physical and/or chemical methods to effectively separate genetic material from cell membranes, proteins, and other cellular components. The CPGR laboratory is equipped to ensure both efficiency and high-quality extraction, setting the stage for subsequent downstream analytical procedures.

  • Automated 

    Automated extraction processes utilize cutting-edge technology to streamline and enhance the efficiency of nucleic acid isolation. This method is particularly advantageous for high-throughput workflows, allowing for the processing of a large number of samples with precision and reproducibility.

  • Semi-Automated 

    Semi-automated extraction combines the benefits of automation with the flexibility of manual intervention. This approach is well-suited for projects that require a balance between precision and manual control, accommodating a range of sample types and sizes.

  • Manual extraction 

    Manual extraction provides a hands-on approach to nucleic acid isolation, offering researchers the flexibility to tailor the process to specific requirements. This method is suitable for smaller-scale projects or instances where a more customized approach is desired.

The Nucleic Acid Extraction platform at CPGR is equipped to handle a wide array of sample sources. The platform supports the extraction of nucleic acids from diverse sample types, including but not limited to:

Whole bloodSputum
Dried Blood Spots (DBS)Bronchial Lavage
SerumBuccal cells
PlasmaMouth rinse
TissueStool
FFPE (Formalin-Fixed Paraffin-Embedded) tissueUrine
Respiratory secretionsCervical Lavage
SalivaCell Culture (Mammalian, Bacterial, Viral, Fungal)

Current Services

  • CPGR’s extraction laboratory provides validated workflows for nucleic acid extraction, ensuring reliability and reproducibility in downstream analytical procedures. The platform is committed to delivering high-quality nucleic acids for various applications, including but not limited to genomics, transcriptomics, and molecular diagnostics.

    Clients can benefit from the expertise and advanced infrastructure at CPGR, facilitating cutting-edge research and analysis in the field of nucleic acids.

  • KingFisher™ Flex Purification System
  • QIAcube Connect and various manual methods.
  • Various manual methods.

Capillary Electrophoresis

Capillary Electrophoresis (CE) in genomic applications has surpassed conventional gel electrophoresis, providing unparalleled precision and efficiency for targeted or multiplexed genotyping. This analytical technique separates and analyzes DNA fragments based on their size and charge. At CPGR, CE facilitates applications that demand automated Sanger sequencing or fragment analysis workflows, offering flexibility to meet the unique requirements of your project outputs.

  • Targeted DNA sequencing
  • NGS confirmation
  • Microbial sequencing
  • Mitochondrial sequencing
  • Short tandem repeat (STR) analysis in human sample identification
  • Microsatellite marker analysis
  • Single-nucleotide polymorphism (SNP) genotyping
  • Quantitative fluorescence PCR (QF-PCR)
  • Restriction/Amplified fragment length polymorphism (RFLP/AFLP) analysis
  • Single-stranded conformation polymorphism (SSCP) analysis
  • Human Identification for Paternity, Maternity or Kinship DNA testing (for Research use only)
  • Sanger Sequencing
  • SeqStudio™ Genetic Analyzer System

Microarray

The Microarray platform specialises in a collection of high-throughput, streamlined array processing, specifically looking at gene expression studies and genome-wide analytics. Various assays are available for genotyping and copy number variation (CNV) analysis. The platform also hosts DNA Methylation pattern analysis and Cytogenetics analysis capabilities.

  • Pharmacogenomics
  • Genome-Wide Associated Study (GWAS)
  • CNV analysis
  • Ancestry marker analysis
  • Methylation pattern
  • Cytogenetics analysis
  • Pharmacogenomics testing using the Precision Medicine Diversity Array (PMDA/PMDA Plus)
  • GWAS and Methylation pattern analysis
  • CytoScan Optima array to enable the detection of aneuploidies, sub microscopic aberrations, and mosaic events
  • GeneTitan™ MC Instrument
  • iScan™ System

Next Generation Sequencing

Next Generation Sequencing (NGS) has propelled discoveries in rare disease research; allowed monitoring of cancer immunotherapy treatment efficacy; and helped us understand that our gut health as humans is at the core of our susceptibility to disease. In the era of the genome, the CPGR is poised to be an enabler and driver of efforts in utilising NGS to elucidate not only the African genome but our rich biodiversity.

  • DNA sequencing
  • RNA sequencing
  • Whole Genome Sequencing.
  • Whole transcriptome Sequencing
  • mRNA Sequencing
  • small RNA sequencing
  • Metatransciptomic sequencing
  • Targeted metagenomic sequencing
  • Shotgun metagenomics
  • NovaSeq™ 6000 System
  • NextSeq ™500
  • NextSeq ™550
  • MiSeq™
  • Ion GeneStudio™ S5 System with Ion Chef™ Instrument.

RT-PCR

The Real-Time PCR platform offers custom qPCR services for targeted gene expression analysis, genotyping and miRNA Profiling.

  • Gene Expression Analysis with Real-Time PCR
  • Targeted Genotyping
  • miRNA Profiling services
  • Gene Expression Analysis with Real-Time PCR for the quantitative measurement of mRNA expression of defined target genes. This service covers:
    • SYBR-Green or TaqMan primer design
    • qPCR Assay optimization and validation
    • Validation of reference (housekeeping) gene stability
    • Gene Expression Data Analysis
    • Profiling using multi-well plate-based gene expression arrays (e.g., RT2 Profiler PCR Arrays, TissueScan qPCR Arrays, etc)
    • Mid-to high-throughput custom gene expression profiling using the OpenArray® platform
    • Fixed Content TaqMan Specific Gene Expression Pathway Panels: Human Cancer Panel, Human and Mouse Inflammation Panels, Human Kinome Panel, Human Signal Transduction Panel and Stem Cell Panel
    • Pathogen detection
    • RNASeq Data Validation
    • Viral quantification
  • Targeted Genotyping to identify and validate genetic variations in DNA samples with the following services:
    • SNP Analysis
    • Mutation Detection
    • Copy Number Variation (CNV) with Real-Time PCR
    • Methylation-specific PCR
    • High Resolution Melting (HRM) analysis – (not sure if we should include this since we have not done these experiments yet)
    • Pharmacogenomic Profiling of ADME Gene Variants using the TaqMan™ OpenArray™ PGx Express Panel.
    • Human Barcoding
  • QuantStudio™ 12K Flex Real-Time PCR System
    • FAST 96-well plates
    • 384-well plates and the OpenArray® chips with the QuantStudio™ AccuFill System loader for mid to high-throughput TaqMan assays.