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December 12, 2013

Genomics Advances in Africa

Tiffany Trader
DNA Sequencing Africa 2013 graphic 220x

Scientists at Stellenbosch University (SU) in Africa have completed the first sequencing of the human genome on that continent with the help of a 5500xl Next Generation Sequencer, nicknamed MegaMind. This achievement was featured in a recent issue of Quest: Science for South Africa, a popular science magazine, published each quarter by the Academy of Science for South Africa.

In 2011, Stellenbosch University (SU) acquired MegaMind with a grant from the National Research Foundation. The sequencer was deployed in the DNA Sequencing Unit, part of the university’s Central Analytical Facilities (CAF). Earlier this year, scientists there sequenced a human genome, marking the first time that this has been done on the African continent.

As the world celebrates the 60th anniversary of the discovery of the DNA double helix, the sequencing of large genomes, like that of humans, requires “highly sophisticated instruments, technical expertise and supercomputing power,” notes Stellenbosch University science writer Wiida Fourie-Basson. The African continent has not had access to all the necessary resources to take on this challenge until now.

Sequencing of the first complete human genome under the Human Genome Project took place over a 13 year-period at a cost of $3 billion. The ground-breaking effort, requiring the work of over one-thousand scientists, culminated in 2001 with the first draft of the genome being published in two separate papers in Nature and Science. The project was declared complete in April 2003, and with that the world was welcomed the genome era.

In 2005, next-generation sequencing (aka next-gen) took sequencing to a new level. The pace of progress advanced to the point where it was possible to sequence the whole human genome in a matter of weeks, not years. In a similar trajectory, cost went from over a billion dollars to less than $100,000.

Now, genomes are routinely sequenced for around $6,000 and the “thousand-dollar genome” is rapidly approaching.

In the last five to ten years, numerous countries have successfully sequenced the human genome, but Africa had only been involved in sequencing smaller genomes, such as bacteria and fungi.

“Several resources had to be in place first,” writes Fourie-Basson, returning to the themes of “technical expertise, sophisticated instruments and supercomputing power.”

Once MegaMind was in place, the DNA Sequencing Unit at Stellenbosch University’s Central Analytical Facilities CAF was able to begin the complex process: preparation, loading the DNA fragments onto a special glass flow cell, and then beginning the actual sequencing process.

During sequencing, MegaMind deploys special primers containing fluorescent probes. These primers attach to the DNA fragments and emit a fluorescent signal when excited by a laser.

“Millions of these fluorescent data points are collected by a microscope lens and interpreted by software, similar to the way the Hubble telescope will interpret data from the stars,” explains the author.

The points are eventually consolidated into a single data file used for downstream analysis. Analyzing this data requires some serious hardware, says “For this purpose, Stellenbosch University acquired a high-performing computing cluster with over one Terabytes of RAM, more than 200 processors
and over 60 Terabytes of storage.”

Megamind completed the sequencing run in just two weeks.

According to Carel van Heerden, manager of the DNA Sequencing Unit, the sequencing work itself is pretty-straight forward, but “it must just be done correctly.”

“It is like playing a piano concerto,” says van Heerden. “You have to read the notes from the paper and do what it says. But just as it is with playing the piano, you have to practise until you get it right.”

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