Genomics

Service Providers

Genomic sequencing services are available at numerous local labs. There are several DNA sequencers spread out across the country. These facilities offer high-quality data generation and analysis capacity, with expert assistance at competitive prices. Contact our help centre or the providers in your area to discuss your needs.

CPGR-High-Res-Logo.png

Center for Proteomic and Genomic Research

The Centre for Proteomic and Genomic Research (CPGR) is a non-profit organisation providing state-of-the-art ‘omics’ services to the life science and biotech communities in South Africa.

Location

Western Cape

CPGR-High-Res-Logo.png

SAMRC Genomics Centre

"Latest sequencing technology and cutting-edge facility design."

Location

Western Cape

CPGR-High-Res-Logo.png

Agricultural Research Council Biotechnology Platform

The Agricultural Research Council is a premier science institution that conducts research with partners, develops human capital and fosters innovation to support and develop the agricultural sector.

Location

Pretoria

CPGR-High-Res-Logo.png

KwaZulu-Natal Research Innovation and Sequencing Platform

Challenging status quo & creating a scientific environment that drives innovation & reverses brain drain.

Location

KwaZulu-Natal

CPGR-High-Res-Logo.png

Plant & Pathogen Genomic Services

CenGen offers various genomic related services to plant breeders, producers and agricultural-related industries.

Location

Western Cape

 

It has become a requirement of publication to make the data generated for publication, publicly available. There are several genomic data repositories for data deposition. These data are processed, compiled, and made accessible via genome browsers. Omics experiments often rely heavily on available data as a starting point. Sometimes it may even be possible to make use of existing data rather than needing to generate new data. The first step in any Omics experiment is therefore to check what data are available.
 
The two primary genomics databases are the NCBI Genome Database and the Ensemble Genome Database. These databases contain genomes across all kingdoms of organisms. Most of the sequences, though are focused on model organisms. There are already thousands of organisms for which we have genomic sequences, as well as thousands of human genomes. There are also several databases for specific purposes like the cancer genome databases, that focus on genomes of a variety of cancers.

Ensembl

Ensembl is a genome browser for vertebrate genomes that supports research in comparative genomics, evolution, sequence variation and transcriptional regulation.

NCBI Genomes

NCBI's databases of genome sequences, maps, chromosomes, assemblies and annotations

1000 Genomes

The 1000 Genomes Project ran between 2008 and 2015, creating the largest public catalogue of human variation and genotype data.

 

Data Generation

Depending on the amount of information required, there are a variety of ways to generate genomics data. If a small specific area of the genome such as a gene or control sequence needs to be studied, the region is amplified by polymerase chain reaction (PCR), quantitated and characterised. Recently this has been shown to be useful in identifying infection by SARS-CoV-2 in the COVID-19 pandemic.

If more global information about the genome is required, commercial or custom DNA microarrays are available to determine the prevalence of known genomic variances. Sanger sequencing used initially to sequence the human genome, has been automated using fluorescent tags to allow high throughput applications. Small genomes are easily sequenced by Sanger sequencing. Next-generation sequencing (NGS), which covers a variety of modern parallel sequencing techniques, allows sequencing of an entire human genome within a day. Depending on the information required, NGS is used to sequence the whole-genome or just the exomes.

Sequencing

DNA and RNA sequencing technologies

ReadMore.png
thebrain-c.png

Array Based

Commercial or custom DNA micro-arrays designed for genotyping

ReadMore.png

PCR Based

Polymerase change reaction; amplification of specific genetic sequences to determine their abundance

ReadMore.png
 
 
 

Analysis Tool Collections

Genomic sequencing produces a large amount of data and the data analysis consists of multiple steps. To ensure that data is processed in a consistent manner H3ABioNet and others have compiled several trusted tools and workflows. Due to the large amount of data needing to be processed, access to extensive data storage and high-performance computing resources may be required. Many of these tools are open source and only run on Linux. Combining these tools into robust pipelines can be complicated and may require the assistance of a bioinformatician. Consult the bioinformatician section to get help.

H3ABioNet

"H3ABioNet has developed a number of tools and services for H3Africa and the broader bioinformatics community"

Broad Institure

"Broad Institute of MIT and Harvard, collection of genomics tools"

EBI Tools

"The European Bioinformatics Institute (EMBL-EBI) maintains the world’s most comprehensive range of freely available and up-to-date molecular data resources."

Bio Tools

"Essential scientific and technical information about software tools, databases and services for bioinformatics and the life sciences."

Bioinformaticians are available through DIPLOMICS to assist you with your project.

The earlier you contact them, the more assistance they will be able to offer. Omics research is costly, choosing the most appropriate technology for your experiment, and budget is, therefore, crucial. In particular, it is essential to discuss the experimental design with a statistician to ensure your experiment has sufficient statistical power.

It is advisable to run a pilot study and have an expert check the quality of the results before continuing with the bulk of the analysis. The pilot project will familiarise you with the sample processing, data generated, and data processing, before embarking on the main project. Issues identified at this point can improve the quality of the data generated thereby making better use of the funds spent.

Omics technologies produce masses of data and require expertise for processing. Fortunately, Bioinformatics tools and resources are available to store and process omics data. Contact our team of expert bioinformaticians for assistance on all levels of your project. The earlier, the better.

Dr Katie Lennard

Bioinformatician at the Institute of Infectious Diseases & Molecular Medicine

email_icon.png
linkedin_edited.jpg
ResearchGate.jpg

Fields

  • Genomics

  • Transcriptomics

  • Differential Abundance Statistics

Expertise

  • 16S rRNA gene amplicon sequencing

  • WGS metagenomics sequencing

  • RNAseq

  • Pathogen isolate profiling

Tools

  • Nextflow

  • R : edgeR, metagenomeSeq


Literature

High-depth African genomes inform human migration and health

Nature (2020)

PMC.gif

Bensellak, Taoufik., Wells, Gordon., Kumuthini, Judit., Shriner, Daniel., Fakim, Yasmina J

 

©2018 by SA-DIPLOMICS. Proudly created with Wix.com