Introduction: Genomics Facility at Nelson Mandela School of Medicine, UKZN, Executive Summary

Mission: The mission of the Genomics and Bioinformatics Facility at Nelson R Mandela School of Medicine, UKZN is to setup one of the world’s most advanced and respected genetic sequencing systems in South Africa in order to enable and support world-class genomics research in Africa.





History: The University of KwaZulu-Natal was formed on 1 January 2004 as a result of the merger between the University of Durban-Westville and the University of Natal. The new university brings together the rich histories of both the former Universities (which are over 100 years old). The University of Natal was also home of the first Medical School for African, Indian and Coloured students in South Africa. It was granted Nelson Mandela's name on its 50th anniversary in 2000 in order to remind its important contribution to South Africa.

UKZN vision is to be a truly South African university that is academically excellent, innovative in research, critically engaged with society and demographically representative, redressing the disadvantages, inequities and imbalances of the past. It current ranks in forth position in the University rank in South Africa but it has been ranked in first position for research output in 2014 and 2015. UKZN and the Nelson R Mandela School of Medicine host a number of large research centres, including the NIH funded CAPRISA, the Howard Hughes funded K-RITH, the Wellcome Trust Africa Centre for Population Health and the newly developed Genomics and Bioinformatics unit, which is funded as a flagship program of the Medical Research Council and UKZN.

Genomics Laboratory Unit: The Genomics Unit is situated at the Doris Duke Medical Research Institute (DDMRI) of the Nelson R. Mandela School of Medicine, in Durban. It is a research unit and is staffed with 1 Professor, 5 post-docs, 3 PhD students, 5 MSc, 1 scientific manager and lab manager. The laboratory consists of a fully equipped RNA/DNA extraction, PCR and sequencing facility that contains all of the equipment needed to support most genomics research requirements. Technologies available include quantitative real-time assays for DNA and RNA detection of HIV-1, HCV and HTLV-1 and a variety of other viruses. The laboratory has extensive experience with RNA/DNA molecular tests using a range of biological samples types such as breast milk, plasma and dried blood spots (DBS). These include considerable experience at conducting qPCR on both RNA and DNA and extraction of RNA/DNA for sequencing.

The genomics laboratory has a robotic workstation for RNA/DNA extraction, an automated RNA/DNA quantification machine (GeneChip) and two next generation sequencers (e.g. Illumina MiSeq and Ion Torrent Life Technologies). These three pieces of machinery are commonly used in the leading genomic centres and allow sequencing to be done locally in the most efficient and cost-efficient manner. The end result is the production of high-quality genomic data that is altomatically assembled in Linux operation system pipelines (see bioinformatics unit information) and available to researchers in a relational database that is web accessible and password protected (RegaDB. Bioinformatics 2013).

Image: Robotics machinery for RNA/DNA extraction, quantification, NextGen sequencing & Linux bioinformatics server.

Bioinformatics Unit: The unit contains bioinformatics servers and applications needed for the generation and analysis of high-throughput genomic sequences produced the genomics unit. The main unit server is a medium enterprise server such as HP ProLiant BL685c G7 Server series with AMD Opteron™ chips (12 core, 4 processors, 2.8 GHz, 12MB L3, 80W), 256GB of memory RAM and 400 TB of storage. This system is ideal for deploying many applications at once (up to 48) and thus can cope with multiple users. This kind of server has a large memory footprint (256Gb) and maximum expandability for compute intensive workloads. The system CentOS linux, a flavour of linux (i.e. RPM) has been in use for the past decade to run some of the bioinformatics tools and databases that we developed (see below). The unit has also five top-of-the-range MacPro OS X servers (5 core, 4 processors, 3.5 GHz, 64GB memory), which is used by five post-doctoral researchers in the analysis of genomic data.

In addition to the IT infrastructure at Nelson R Mandela School of Medicine we have access to IT infrastructure developed through a long-standing and Flagship collaboration between at ourselves and the South African Medical Research Council (MRC). The MRC network has access to the fastest internet in Africa (academic internet ring), recently launched in 2011 providing internet speed of 1Gb per second). The MRC host our online bioinformatics server (bioafrica.net and bioafrica.mrc.ac.za), which provide access online to our databases and bioinformatics software applications.


MORE INFO

High-Throughput Genomics Facility at Nelson R Mandela School of Medicine, UKZN, Durban, South Africa

Videos that highlight the construction of our genomics facility.








Page last updated by Tulio de Oliveira, March 2015