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Southern African Genome Diversity Study


Scientists at the J. Craig Venter Institute have a long history of leadership in human genomic research. Since the work in the early 1990's by Dr. Venter and colleagues at the National Institutes of Health in describing expressed sequence tags (ESTs) to rapidly discover human genes, to the sequence and analysis of the first draft human genome published in 2001, to the first complete diploid human genome published in 2007, JCVI scientists remain committed to research into the human genome.

In 2010 the JCVI Human Genomic Medicine Group was strengthened with the addition of geneticist, Vanessa Hayes, Ph.D., who joined JCVI as Professor of Genomic Medicine. Dr. Hayes, a native of South Africa, and her team (who were then at the University of New South Wales and the Children's Cancer Institute of Australia) were part of the seminal South African Genome Project. They, along with lead collaborators from the Pennsylvania State University and nearly 50 other scientists from nine other academic institutions, published their work in the journal Nature in February 2010. The researchers sequenced the complete genomes (and an additional four exomes) of a Bushman and a Bantu, the latter happening to be Archbishop Desmond Tutu.

The research, which garnered world-wide attention, was key to enhanced understanding of the extent of uncaptured human genetic variation, and the relevance of this variation in assessing disease risk, outcomes and the response to various medicines, in particular within the understudied populations of southern Africa. The work also gives insights into aging since all participants were in their late 70's. The study identified 1.3-million genetic variants that scientists previously had not observed. These genetic variations reveal that Southern Africans are quite distinct genetically from Europeans, Asians, and West Africans.

Principal Investigator

Vanessa Hayes

Analytical Team

Nicholas Schork
The SCRIPPS Research Institute, San Diego

Desiree Petersen
JCVI, San Diego

Ondrej Libiger
The SCRIPPS Research Institute, San Diego

Elizabeth Tindall
JCVI, San Diego

International PhD students and Visiting Scientists

Rae-Anne Hardie
University of New South Wales, Australia

Zolani Simayi
University of Limpopo, South Africa

Katherine Theron
University of Limpopo, South Africa

Ju/'hoan hunters setting a trap. Photo courtesy Chris Bennett.

Dr. Hayes was a crucial component to getting this project underway. It was born from her frustration in earlier human genomic studies when she found a complete lack of African reference genomes and susceptibility gene array profiles in existing databases. Africa, believed to be the birthplace of mankind with the oldest populations, offers a much greater diversity than found in individuals of European decent.

Dr. Hayes' passion to see African genomes have their rightful place in the world-wide databases continues to this day and is reflected in the work she and her team are doing at JCVI. They are working on a variety of projects one of which involves a formal collaborative agreement with the University of Limpopo (UL) in South Africa.

In May 2011 JCVI signed a memorandum of understanding with UL to expand ongoing research collaborations on a variety of levels including in human genomics and prostate cancer in indigenous African populations. The collaboration was named the "University of Limpopo (UL) — J. Craig Venter Institute (JCVI) Genomics Network".

Dr. Hayes, and UL's Philip Venter, Professor in the Faculty of Medical Sciences, Turfloop Campus, have had a long-standing collaboration since both were involved in the Southern African Genome Project. The new UL-JCVI Genomics Network will expand on this fruitful collaboration by formally enabling researchers at both institutions to utilize and learn from the experience and expertise of their colleagues. [Nature. 2011 Aug 11; 476: 152.]

Specific goals and projects established within the framework of the UL-JCVI Network include:

  • Defining the extent of genomic diversity in the Khoesan and Bantu populations of Southern Africa and establishing a genomic profile of prostate cancer disparities within South African populations
  • Promoting the exchange of scientific ideas, information and technology as it relates to improving the understanding of human genetic diversity and genomic medicine (not excluding possible pathogen related genomic relevance), and
  • Ensuring the protection of all human subject participants in the clinical research program by providing thorough and complete ethical review of the Research Studies.

The Network will also facilitate faculty and student exchanges, hosting visiting scholars and scholars in residence, and joint project, proposal and scientific manuscript development.