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CAF DNA Sequencer Unit is still growing after 21 years
Author: CAF
Published: 05/04/2019

​The CAF DNA Sequencer Unit reached new milestones in 2018, the year in which the staff celebrated the Unit's 21st birthday. Their Next Generation Sequencing (NGS) division, which was started in 2011, boasted a record amount of R653 121 in revenue for December 2018 and together with the capillary division's revenue contribution of R500 899, this resulted in the unit posting a monthly income of more than R1 million for the fifth time in 2018. As a whole, the facility invoiced >R10 000 000 in analytical services during 2018 which is a first for any CAF facility.

These milestones represent a commitment from the facility to provide analysis at the lowest cost possible to a large number of researchers and postgraduate students, while also ensuring the long term sustainability of the unit. The facility had 491 users in 2018, of which 471 were academics and 20 were clients from industry.


Offering a sustainable, reliable and affordable analytical service, whilst also aiming to not make a significant profit, is an exceptionally difficult task. Several factors like unpredictable use patterns, volatile exchange rates, long-term devaluation of the Rand, logistical problems related to shipment of temperature sensitive reagents along with competition from large international service suppliers cause a multitude of problems. To minimise the impact of some of these factors, reagents are mostly ordered in bulk before they are needed to reach the facility in time for analysing the samples. According to Carel van Heerden, manager of the facility, there is a fine line between oversupply or undersupply of expensive reagents due to the unpredictability in the number of analysis requested from day to day. "We make careful predictions for the medium to long term and plan our purchases so that we can save money and offer competitive prices to our users," explains Van Heerden. Sometimes quotes for large quantities of work are rendered but the samples only arrive more than six months later. The facility must be ready with enough reagents regardless of when the work is submitted. "Our aim is to advance research, therefor we put research first and business second", says Van Heerden.

The CAF DNA Sequencer Unit not only works for Stellenbosch University, but also for many other universities and research institutions in South Africa. The facility competes with much larger international service providers in terms of price, data quality and speed of delivery. A substantial amount of research funding is kept within South Africa because of the facility's ability to deliver internationally competitive services.

“It took us about six years to build the NGS service to where we are today and have clients' trust in our NGS services" says Van Heerden. Over the last two years all the hard work has started to bear fruit resulting in the volume of work nearly doubling between 2017 and 2018. This has allowed the facility to almost completely eliminate losses through expired reagents. Furthermore, the facility uses a combination of optical density and fluorescence readings to determine the concentration of nucleic acids in a sample while at the same time also detecting the level of impurities in the samples. Samples are also subjected to microfluidic electrophoresis to determine the nucleic acid quality and the combined results from these tests are used to predict which samples are likely to fail analysis. This avoids analysis of samples that cannot be successfully analysed, saving the client money and saving the facility time and reagents. Given that the cost of a single NGS analysis is typically more than R5000, this pre-screening of sample quality is invaluable to researchers and confirms the facility's commitment to research support.