Verified Service Provider in South Africa
Genomics Core Facilities in South Africa
Engineering Excellence & Technical Support
Genomics Core Facilities solutions for Research & Discovery (R&D). High-standard technical execution following OEM protocols and local regulatory frameworks.
High-Throughput Sequencing Capabilities
Empowering South African researchers with state-of-the-art Illumina NovaSeq and MiSeq platforms, enabling large-scale genomic projects from whole-genome sequencing to targeted gene panels, accelerating discovery in infectious diseases, agricultural genomics, and human health.
Advanced Bioinformatics and Data Analysis
Providing robust computational infrastructure and expert bioinformaticians to process, analyze, and interpret complex genomic datasets, delivering actionable insights for diverse research areas including population genetics, cancer genomics, and environmental sequencing.
Specialized Omics Services
Offering comprehensive services beyond genomics, including transcriptomics (RNA-Seq), epigenomics (ChIP-Seq, ATAC-Seq), and metagenomics, facilitating multi-omics integration for a holistic understanding of biological systems and advancing translational research in South Africa.
What Is Genomics Core Facilities In South Africa?
Genomics Core Facilities in South Africa represent specialized centers that provide access to advanced genomic technologies, expertise, and computational resources for research and development. These facilities are crucial for enabling a wide spectrum of biological and medical investigations by offering services that are often beyond the scope or budget of individual research laboratories. They are designed to democratize access to cutting-edge genomic capabilities, fostering innovation and driving scientific discovery across various disciplines. The services offered are typically fee-for-service, ensuring sustainable operation and continuous upgrades to maintain state-of-the-art instrumentation and methodologies.
| Category | Description | Examples in South Africa |
|---|---|---|
| Academic Research | Driving fundamental biological understanding, disease mechanisms, and translational research. | University-based research groups, National Health Laboratory Service (NHLS) research arms. |
| Public Health | Monitoring infectious disease outbreaks, understanding disease epidemiology, and developing public health interventions. | National Institute for Communicable Diseases (NICD), provincial public health labs. |
| Biotechnology & Pharmaceuticals | Drug discovery, development of novel diagnostics, and biomarker identification. | Local biotech startups, multinational pharmaceutical research divisions. |
| Agriculture & Food Security | Improving crop yields, livestock health, and developing climate-resilient varieties. | Agricultural Research Council (ARC), university agricultural departments. |
| Conservation Biology | Understanding biodiversity, population genetics, and conservation strategies for endangered species. | South African National Biodiversity Institute (SANBI), environmental research organizations. |
Typical Use Cases for Genomics Core Facilities
- Disease gene discovery and variant identification in human genetic disorders.
- Cancer genomics: Profiling tumor genomes, transcriptomes, and epigenomes for personalized medicine and therapeutic target identification.
- Infectious disease research: Pathogen surveillance, outbreak investigation, and understanding antimicrobial resistance through whole-genome sequencing.
- Agrigenomics: Crop and livestock improvement through trait discovery, breeding programs, and genome-assisted selection.
- Evolutionary biology and phylogenomics: Reconstructing evolutionary histories and understanding species diversification.
- Environmental genomics: Studying microbial communities in various ecosystems (metagenomics) and understanding biodiversity.
- Developmental biology: Investigating gene regulation and cellular differentiation during development.
- Epigenomics: Studying DNA methylation, histone modifications, and chromatin accessibility to understand gene regulation.
- Pharmacogenomics: Identifying genetic variations that influence drug response and optimize treatment strategies.
- Metabolomics and proteomics integration with genomics: Understanding the interplay between different 'omics' layers.
Who Needs Genomics Core Facilities In South Africa?
Genomics core facilities in South Africa are essential for advancing a wide range of scientific research and industrial applications. Their services are not a luxury but a necessity for numerous entities seeking to leverage the power of genomic technologies. These facilities provide access to cutting-edge equipment, specialized expertise, and standardized protocols that are often beyond the scope of individual laboratories.
| Customer Type | Key Departments/Research Areas | Specific Needs/Applications |
|---|---|---|
| Academic and Research Institutions | Biology (Molecular, Cell, Evolutionary), Genetics, Biochemistry, Medicine, Agriculture, Environmental Science, Zoology, Botany, Public Health | De novo sequencing, whole-genome sequencing (WGS), RNA sequencing (RNA-Seq) for gene expression, ChIP-seq for protein-DNA interactions, metagenomics for microbial communities, population genetics, phylogenomics, epigenomics (e.g., methylation sequencing) |
| Government Research Agencies and Institutes | National Health Laboratory Service (NHLS), South African Medical Research Council (SAMRC), Council for Scientific and Industrial Research (CSIR), Agricultural Research Council (ARC), South African National Biodiversity Institute (SANBI) | Epidemiology of infectious diseases (e.g., HIV, TB, COVID-19), antimicrobial resistance surveillance, cancer genomics, agricultural genomics for food security, biodiversity assessment, conservation genetics |
| Biotechnology and Pharmaceutical Companies | R&D departments, drug discovery, preclinical development, diagnostics development | Target identification and validation, biomarker discovery, personalized medicine, development of molecular diagnostics, sequencing of drug targets and resistance mechanisms |
| Agricultural Sector | Crop science departments, animal science departments, seed development companies | Marker-assisted selection (MAS) for crop and livestock breeding, genome-wide association studies (GWAS) for trait discovery, identification of genes for disease resistance and yield improvement, pathogen genomics for crop protection |
| Conservation and Environmental Agencies | Ecology departments, conservation biology units, wildlife management agencies | Species identification and barcoding, population structure and connectivity analysis, studies of adaptation to environmental change, monitoring of invasive species, ancient DNA analysis |
| Clinical Diagnostics Laboratories | Pathology departments, genetic counseling services, specialized diagnostic centers | Somatic mutation profiling for cancer treatment, germline mutation analysis for inherited disorders, carrier screening, prenatal diagnosis, infectious disease diagnostics (e.g., rapid pathogen identification and sequencing) |
| Forensic Science Laboratories | DNA analysis units, criminal investigation support | DNA profiling for identification, kinship analysis, degraded DNA analysis, forensic metagenomics for environmental trace evidence |
| Public Health Organizations | Epidemiology units, infectious disease control centers, national health institutes | Genomic surveillance of pathogens for outbreak detection and tracking, understanding viral and bacterial evolution, antimicrobial resistance profiling, vaccine development support |
Target Customers and Departments for Genomics Core Facilities in South Africa
- {"title":"Academic and Research Institutions","description":"The primary users, encompassing a broad spectrum of scientific inquiry."}
- {"title":"Government Research Agencies and Institutes","description":"Critical for national research priorities, public health, and conservation efforts."}
- {"title":"Biotechnology and Pharmaceutical Companies","description":"Driving innovation in drug discovery, development, and diagnostics."}
- {"title":"Agricultural Sector (Large-scale farming, Seed Companies)","description":"Improving crop yields, disease resistance, and livestock management."}
- {"title":"Conservation and Environmental Agencies","description":"Understanding biodiversity, managing endangered species, and monitoring ecosystems."}
- {"title":"Clinical Diagnostics Laboratories (hospitals and private)","description":"Enabling advanced genetic testing for inherited diseases, cancer, and infectious agents."}
- {"title":"Forensic Science Laboratories","description":"Supporting criminal investigations and identification."}
- {"title":"Public Health Organizations","description":"Tracking disease outbreaks, understanding pathogen evolution, and developing public health strategies."}
Genomics Core Facilities Process In South Africa
Genomics core facilities in South Africa play a crucial role in supporting research by providing access to advanced genomic technologies and expertise. The workflow from initial inquiry to the final execution of genomic services typically involves several distinct stages. This process ensures that researchers' needs are clearly understood, experiments are designed effectively, samples are prepared and processed accurately, and data is delivered in a usable format. Collaboration between the researcher and the core facility staff is paramount throughout this workflow.
| Stage | Description | Key Activities | Typical Turnaround Time (Approx.) |
|---|---|---|---|
| Inquiry & Consultation | Initial contact and discussion to understand researcher's project goals and requirements. | Email/phone inquiry, scheduled meeting with core facility staff, discussion of research questions, experimental feasibility assessment. | 1-3 business days |
| Project Design & Quoting | Detailed planning of the experiment, including choosing appropriate technologies and services, and providing a cost estimate. | Defining sample types, experimental design (e.g., sequencing depth, target region), selecting assays, developing a formal quote based on services and consumables, formalizing service agreement. | 3-7 business days |
| Sample Submission & Quality Control (QC) | Researcher submits biological samples, and the core facility assesses their suitability for downstream processing. | Adherence to sample submission guidelines (e.g., DNA/RNA concentration, purity, integrity), visual inspection, Qubit/Nanodrop quantification, gel electrophoresis, Bioanalyzer/TapeStation analysis. | 1-5 business days (depending on sample volume and QC complexity) |
| Library Preparation | Converting raw biological samples into libraries suitable for sequencing or genotyping platforms. | DNA/RNA extraction (if not provided), fragmentation, adapter ligation, amplification, library quantification. | 3-10 business days (highly dependent on assay and sample number) |
| Sequencing/Genotyping | Running the prepared libraries on the chosen genomic technology platform. | Loading libraries onto sequencers (e.g., Illumina NovaSeq/MiSeq, PacBio), running genotyping arrays, operating other relevant instrumentation. | 2-14 business days (dependent on platform, run time, and throughput) |
| Data Analysis & Interpretation | Processing raw data from the instruments to generate meaningful biological insights. | Raw data de-multiplexing, quality assessment of sequencing reads, alignment to reference genome, variant calling, gene expression analysis, pathway analysis, statistical analysis. (Note: The extent of analysis can vary greatly based on the quote). | 7-30+ business days (highly dependent on data volume and complexity of analysis) |
| Data Delivery & Reporting | Providing the processed data and a summary of the results to the researcher. | Delivery of raw data (FASTQ files), processed data (BAM, VCF files), analysis reports, figures, interpretation of findings, consultation on next steps. | 2-5 business days |
| Billing & Follow-up | Finalizing the financial aspects of the project and ensuring researcher satisfaction. | Issuing final invoices, addressing any post-delivery queries, gathering feedback for continuous improvement. | Ongoing |
Genomics Core Facilities Process in South Africa: Workflow Stages
- Inquiry & Consultation
- Project Design & Quoting
- Sample Submission & Quality Control (QC)
- Library Preparation
- Sequencing/Genotyping
- Data Analysis & Interpretation
- Data Delivery & Reporting
- Billing & Follow-up
Genomics Core Facilities Cost In South Africa
Genomics core facilities in South Africa offer a range of services crucial for research and development. The cost of these services is influenced by several factors, including the specific technology employed, the complexity of the assay, the volume of samples, and the expertise required for data analysis. Commonly offered services include DNA sequencing (Sanger and Next-Generation Sequencing - NGS), RNA sequencing, genotyping, and bioinformatics support. Pricing is typically quoted in South African Rand (ZAR).
| Service Type | Typical Pricing Range (ZAR) | Notes |
|---|---|---|
| Sanger Sequencing (per reaction/capillary) | R 300 - R 700 | Includes basic read processing. Longer reads or special primers may increase cost. |
| DNA Extraction (basic, per sample) | R 200 - R 500 | Varies with sample type (blood, tissue, saliva). |
| NGS Library Preparation (per sample) | R 1,000 - R 4,000 | Depends on library type (e.g., TruSeq, Nextera) and target size (e.g., exome, genome). |
| Whole Genome Sequencing (WGS) - 30x coverage (per sample) | R 8,000 - R 15,000+ | Excludes data analysis. Price is heavily dependent on sequencing platform and run size. |
| Whole Exome Sequencing (WES) - ~100x coverage (per sample) | R 5,000 - R 10,000 | Excludes data analysis. Target enrichment kit costs are significant. |
| RNA Sequencing (RNA-Seq) - mRNA library (per sample) | R 5,000 - R 12,000 | Includes library prep and sequencing. Data analysis is extra. |
| Genotyping (SNP arrays, per sample) | R 1,000 - R 3,000 | Price varies with the density and type of SNP array. |
| Basic Bioinformatics Analysis (QC, alignment, variant calling) | R 1,500 - R 5,000 (per project/sample) | Hourly rates for custom analysis are typically R 800 - R 1,500/hour. |
Factors Influencing Genomics Core Facility Costs in South Africa
- Technology Type: Different sequencing platforms (e.g., Illumina NovaSeq, PacBio Sequel) and assay methodologies have vastly different capital and operational costs, which translate to service prices.
- Service Scope: Basic DNA extraction is less expensive than a full genome sequencing project with extensive bioinformatic analysis.
- Sample Type and Preparation: The complexity of sample lysis, DNA/RNA extraction, and library preparation can impact costs. For example, difficult-to-lyse tissues or FFPE samples may incur higher charges.
- Sequencing Depth/Read Length: Higher sequencing depth (coverage) and longer read lengths, while providing more information, require more sequencing capacity and thus higher costs.
- Data Analysis and Bioinformatics: The level of bioinformatic analysis required, from basic quality control to complex variant calling and interpretation, significantly influences pricing. Custom analysis projects will be more expensive.
- Consumables and Reagents: The cost of specialized kits, enzymes, and other reagents is a direct component of service pricing.
- Facility Overhead: Operational costs of the facility, including equipment maintenance, staff salaries, and infrastructure, are factored into the pricing.
- Volume Discounts: Larger projects or ongoing collaborations often benefit from volume-based discounts.
- Academic vs. Commercial Pricing: Many core facilities offer tiered pricing, with academic institutions often receiving preferential rates compared to commercial entities.
- Turnaround Time: Expedited services may come with a premium charge.
Affordable Genomics Core Facilities Options
Affordable genomics core facilities are crucial for researchers with limited budgets to access cutting-edge technologies. This often involves understanding how core facilities structure their services and exploring various cost-saving strategies. Value bundles are a key mechanism for this, offering a package of services or reagents at a reduced price compared to individual purchases. This encourages users to commit to a certain volume or set of experiments, allowing the core to achieve economies of scale and pass on savings. Cost-saving strategies can range from proactive planning and efficient experimental design to leveraging internal resources and exploring collaborative opportunities.
| Value Bundle Type | Description | Potential Cost Savings |
|---|---|---|
| Library Prep + Sequencing Bundle | Includes the cost of preparing DNA/RNA libraries and performing sequencing. Often offers a discount on the combined services. | 10-20% off individual service costs |
| Single-Cell RNA-Seq Bundle | Covers cell isolation, library preparation, and sequencing for single-cell experiments. | Can reduce per-cell costs significantly, especially for large cell numbers. |
| Genotyping Array Bundle | Includes DNA extraction, array hybridization, and basic data processing for genotyping arrays. | 15-25% off individual costs |
| Exome/Genome Sequencing Package | Combines library preparation, sequencing, and initial data alignment/variant calling. | Economies of scale can lead to substantial savings per gigabase. |
| Customizable Project Bundles | Core facilities may work with users to create tailored bundles based on specific experimental workflows and required services. | Variable, but can offer flexibility and targeted discounts. |
Key Strategies for Affordable Genomics Core Facilities
- Value Bundles: Core facilities often offer bundled services, such as sequencing runs with library preparation, or multiple array analyses, at a discounted rate compared to individual service costs. These bundles can be pre-defined or customizable based on project needs.
- Volume Discounts: Similar to value bundles, cores may offer tiered pricing based on the volume of samples or experiments processed. Committing to larger projects can unlock significant cost reductions.
- Service Tiering: Cores might offer different levels of service (e.g., basic data analysis vs. comprehensive bioinformatics support) allowing users to select the level that best fits their budget and expertise.
- Collaborative Projects: Joining forces with other labs or departments to share costs for large-scale projects can significantly reduce individual financial burdens.
- Internal Expertise Utilization: Leveraging in-house bioinformatics or wet-lab expertise can reduce reliance on expensive core facility support for certain tasks.
- Efficient Experimental Design: Optimizing experimental protocols, sample preparation, and data acquisition strategies can minimize reagent usage and processing time, leading to lower costs.
- Reagent Sharing and Bulk Purchasing: When possible, coordinate with other users to purchase reagents in bulk for shared experiments, often leading to discounts.
- Utilize Older or Less Expensive Technologies: For certain applications, older or less technologically advanced platforms might offer sufficient data quality at a lower cost.
- Negotiate for Specific Needs: For very large or long-term collaborations, don't hesitate to discuss customized pricing or service agreements with the core facility manager.
- Seek External Funding: Explore grant opportunities specifically for core facility access or research projects that utilize core services.
Verified Providers In South Africa
In South Africa's evolving healthcare landscape, identifying verified providers is paramount for ensuring quality and trustworthy medical services. Franance Health has emerged as a leading entity, distinguishing itself through rigorous credentialing processes and a commitment to patient well-being. Their network of verified providers represents the best choice for individuals seeking reliable and competent healthcare professionals.
| Credential Type | Verification Standard | Franance Health Assurance |
|---|---|---|
| Medical Licensure | Current and valid registration with the Health Professions Council of South Africa (HPCSA). | Mandatory and regularly checked for all practicing doctors and allied health professionals. |
| Specialist Qualifications | Accredited postgraduate qualifications in their respective fields (e.g., MMed, FC, FCOG). | Verified through submission of certified academic records and professional board certifications. |
| Professional Indemnity Insurance | Up-to-date coverage against professional liability. | Proof of active and sufficient insurance is a prerequisite for inclusion. |
| Continuing Professional Development (CPD) | Demonstrated engagement in ongoing learning and skill enhancement. | Providers are required to show evidence of completed CPD points as mandated by the HPCSA. |
| Criminal Background Checks | Clean record with no history of medical malpractice or criminal convictions. | Conducted for all new providers joining the network. |
Why Franance Health Providers are the Best Choice:
- Rigorous Vetting Process: Franance Health employs a multi-stage verification process that scrutinizes the qualifications, experience, and licensure of all healthcare professionals in their network. This ensures that only highly competent and ethical practitioners are included.
- Commitment to Quality Care: Beyond basic credentials, Franance Health assesses providers on their commitment to delivering patient-centered, evidence-based care. This includes evaluating their communication skills, empathy, and adherence to ethical medical practices.
- Specialized Expertise: The network boasts a diverse range of specialists across various medical fields. This allows patients to find highly qualified professionals for their specific healthcare needs, whether it's general practice, surgery, pediatrics, or other specialized areas.
- Patient-Centric Approach: Franance Health prioritizes patient satisfaction and safety. Their verified providers are expected to maintain high standards of professionalism and patient care, fostering trust and positive health outcomes.
- Accessibility and Convenience: By partnering with a broad network of clinics and hospitals, Franance Health ensures that its verified providers are accessible across South Africa, offering convenient access to quality healthcare.
Scope Of Work For Genomics Core Facilities
This Scope of Work (SOW) outlines the services and deliverables provided by the Genomics Core Facility. It details the technical capabilities, standard specifications for common genomic applications, and the process for requesting services. The Genomics Core is dedicated to providing high-quality, reliable, and cost-effective genomic services to support research across the institution. This document serves as a reference for researchers planning experiments and ensures clear expectations for project execution and data delivery.
| Service Category | Standard Library Type | Sequencing Platform | Read Length (typical) | Data Output (approximate, per flow cell/lane) | Standard Deliverables | Turnaround Time (typical) |
|---|---|---|---|---|---|---|
| Whole Genome Sequencing (WGS) | Genomic DNA (gDNA) | Illumina NovaSeq/HiSeq | 150bp paired-end | 100-300 Gb | Raw sequencing reads (FASTQ), QC reports, aligned BAM files (optional) | 2-4 weeks |
| Whole Exome Sequencing (WES) | Genomic DNA (gDNA) | Illumina NovaSeq/HiSeq | 150bp paired-end | 50-100 Gb | Raw sequencing reads (FASTQ), QC reports, aligned BAM files (optional) | 2-3 weeks |
| RNA Sequencing (RNA-Seq) - Poly(A) selection | Total RNA | Illumina NovaSeq/HiSeq | 150bp paired-end | 100-200 Gb | Raw sequencing reads (FASTQ), QC reports, aligned BAM files (optional), gene counts (optional) | 2-3 weeks |
| RNA Sequencing (RNA-Seq) - rRNA depletion | Total RNA | Illumina NovaSeq/HiSeq | 150bp paired-end | 100-200 Gb | Raw sequencing reads (FASTQ), QC reports, aligned BAM files (optional), gene counts (optional) | 2-3 weeks |
| ChIP Sequencing (ChIP-Seq) | Chromatin | Illumina NovaSeq/HiSeq | 150bp paired-end | 50-100 Gb | Raw sequencing reads (FASTQ), QC reports, aligned BAM files (optional), peak calls (optional) | 3-5 weeks |
| ATAC Sequencing (ATAC-Seq) | Cellular nuclei | Illumina NovaSeq/HiSeq | 150bp paired-end | 50-100 Gb | Raw sequencing reads (FASTQ), QC reports, aligned BAM files (optional), peak calls (optional) | 3-5 weeks |
| Targeted Sequencing (Gene Panel) | Genomic DNA (gDNA) | Illumina MiSeq/NextSeq | 150bp paired-end | 5-20 Gb | Raw sequencing reads (FASTQ), QC reports, aligned BAM files (optional), variant calls (optional) | 1-2 weeks |
| Single Cell RNA-Seq (10X Genomics) | Single cells | Illumina NovaSeq/HiSeq | 150bp paired-end | Varies by cell count (e.g., 50,000 cells ~ 20-40 Gb) | Raw sequencing reads (FASTQ), QC reports, cellranger output (filtered feature-barcode matrices, etc.) | 3-5 weeks |
| Long-Read Sequencing (PacBio/Oxford Nanopore) | Genomic DNA (gDNA) or cDNA | PacBio Sequel II/Revio, Oxford Nanopore PromethION | Variable (kb to Mb) | Varies by instrument and run time | Raw sequencing reads (e.g., BAM, FASTQ formats), QC reports | 3-6 weeks |
Services Offered
- Next-Generation Sequencing (NGS) library preparation and sequencing
- Single-cell genomics library preparation and sequencing
- Long-read sequencing library preparation and sequencing
- Targeted sequencing (e.g., amplicon sequencing, gene panels)
- Genotyping and SNP analysis
- Gene expression analysis (e.g., RNA-Seq, qPCR)
- Epigenomics (e.g., ChIP-Seq, ATAC-Seq, Methyl-Seq)
- Genomic DNA extraction and quality control
- RNA extraction and quality control
- Bioinformatic analysis support (data QC, alignment, variant calling, differential expression, etc.)
- Custom assay design and validation
- Consultation on experimental design and service selection
Service Level Agreement For Genomics Core Facilities
This Service Level Agreement (SLA) outlines the guaranteed response times and uptime for services provided by the Genomics Core Facilities. This document is intended to ensure clarity and reliability for all users.
| Service Category | Uptime Guarantee | Response Time (Inquiries/Support) | Response Time (Technical Issues/Failures) |
|---|---|---|---|
| NGS Library Preparation | 98% Uptime | 2 business days | 4 business hours (initial acknowledgement), 24 business hours (resolution attempt) |
| NGS Sequencing (Illumina) | 99% Uptime | 2 business days | 4 business hours (initial acknowledgement), 24 business hours (resolution attempt) |
| Long-Read Sequencing | 97% Uptime | 2 business days | 4 business hours (initial acknowledgement), 36 business hours (resolution attempt) |
| qPCR and dPCR Services | 98% Uptime | 1 business day | 4 business hours (initial acknowledgement), 12 business hours (resolution attempt) |
| Genotyping Services | 98% Uptime | 2 business days | 4 business hours (initial acknowledgement), 24 business hours (resolution attempt) |
| Bioinformatics Support | N/A (Support availability defined by consultation) | 3 business days (initial response to consultation request) | N/A (Assistance with data analysis, not system uptime) |
Scope of Services Covered
- Next-Generation Sequencing (NGS) library preparation
- NGS sequencing (Illumina platforms)
- Long-read sequencing (e.g., PacBio, Oxford Nanopore)
- qPCR and dPCR services
- Genotyping services
- Bioinformatics support for data analysis
In-Depth Guidance
Frequently Asked Questions
Phase 02: Execution
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