Geneticist Vanessa Hayes does not think small nor move slowly—from completing her post doc in six months (the US National average is 3 to 7 years) to completing the first South African Genome Project in 2010 with her goal set on defining the extent of human diversity in all populations, she is on a mission. Just 11 years outside her post doc she has the credentials of someone who has been in science much longer. Her work and talent has taken her to remote regions of Southern Africa, all over Australia, Europe, the U.S. and now to the J. Craig Venter Institute with her appointment as Professor of Genomic Medicine at the San Diego facility.
Of Cartoons and Men…
Born and raised in South Africa, Vanessa first headed a laboratory near Cape Town to investigate genetic susceptibility to HIV/AIDS after earning a Ph.D. in 1999 in Medical Genetics at the University of Groningen, Netherlands. After three years at the University of Stellenbosch she moved to Sydney, Australia to become group leader of Cancer Genetics first at the Garvan Institute of Medical Research, and later at the Children’s Cancer Institute of Australia. During those years she began two major cancer research projects that continue today. One is a study to assess how ethnicity impacts prostate cancer risk and outcomes by genetic profiling men with and without prostate cancer from different ethnic and geographical locations (initially South Africa and Australia). “I believe in going to the extremes of phenotypic diversity to understand genotype – for example the clinical disparities of prostate cancer in Africa compared to non-African populations has not been adequately explored,” she said explaining that the genetics of ethnic diversity is one of her main research interests. “We don’t always have clear clinical definitions to describe phenotype, but genomics can help to define disease,” she added.
This cancer research then led her to what might seem like an unlikely suspect–the Tasmanian devil. The inspiration for a much beloved Looney Toons character and the largest carnivorous marsupial indigenous to Australia, Vanessa became acquainted with the devil when learning that it was a good model for human cancers. She partnered with Stephan Schuster of Pennsylvania State University to sequence the animal using next-generation (gen) sequencing, in turn establishing the then first next-gen sequencing research laboratory in Australia. By establishing a Tasmanian devil genome, she and her team were able to define the extent of dwindling genetic diversity within the devil population as a result of an unusual infectious facial cancer. The hope is that this information and tools developed will be used for the insurance breeding program, which has been established by Australian authorities to save this iconic species from inevitable extinction within the next decade.
Putting Africa on the Genetic Map
In early 2010 Vanessa embarked on another collaborative effort with Schuster’s lab, this one to help get African populations represented in genetic databases and reap the benefits of human genomics research. The initiation of the South African Genome Project was a key step in helping to define the extent of human variation, the relevance to assessing disease risk, and the response to various medicines. The effort was conceived out of Vanessa’s frustration in earlier studies with African populations 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. Another issue with the existing databases was that the little African genetic data represented in early 2010 was based on one population – the Yoruba people from Nigeria. Demonstrating that the Yoruba people are clearly not representative of the majority of the over 500 different linguistic groups in central to southern Africa, Vanessa was determined to change the face of European-driven genomic research.
Ingenuity and perseverance led Vanessa to knock on the door of Nobel Peace Prize recipient Archbishop Desmond Tutu. He was, she knew, a critical step needed to gain access to a potential treasure trove of South African genetic data. She made her case directly to the Archbishop in front of a room of advisors who told him not to participate in a genetic study. However, much to her surprise, Tutu agreed to be the first South African to have his genome sequenced. Vanessa believes he did so, against the advice of his advisors, because he knew the importance of this type of research to the people of his country. The Archbishop’s participation was both critical and significant as he represents not only the Bantu linguistic group to which 80% of the South African population belongs, but he is also a survivor of TB, polio, and prostate cancer. The researchers were able to correlate his genetic markers (genotype) potentially associated with disease susceptibility with his family and medical history (phenotype), providing valuable information about the Bantu people. Vanessa and her team also sequenced the complete genome and three exomes (protein-coding genes only) from four individuals representing diverse ethnic groups of what are known as the Kalahari Bushmen. Bushmen (or San) is the term for the click-speaking hunter-gatherers who inhabit the Kalahari Desert, which spans parts of Botswana, Namibia, and Angola. Her studies, published in Nature in 2010, showed that two different linguistic groups of Kalahari Bushman were as genetically divergent as Europeans and Asians. Some found this finding surprising, however, the extent of the diversity should not be surprising considering these Bushman represent the oldest living lineage of modern humans.
By this time in 2010 Vanessa decided she had reached the technological limits of her research in human genomics in her current position in Australia. She was searching for a place to expand her capabilities, particularly in next generation (gen) sequencing and bioinformatics. She was interviewing last spring in Melbourne at the Walter and Eliza Hall Institute for Medical Research where Dr. Craig Venter happened to be giving a keynote lecture. The JCVI was not on her radar at the time as she had several job offers within and outside Australia, but Craig was able to convince her to come to work with him and the team at JCVI.
Sleep is overrated
The sequencing of Archbishop Tutu was only a start to Vanessa’s plans in human genomics research. She is continuing to expand her work with indigenous groups in Africa. Much like the aspirations (and accomplishments) of her new boss, she claims a ‘modest’ goal: “To define the extent of human diversity that exists globally so we can have a true picture of variation that human genomes have and to help make sense of that variation by linking genotype to phenotype.” Phenotype cannot only mean disease conditions (associated with genes) but also evolved behaviors. For example, how the Bushmen are able to go for a week without water in the desert climate is a phenotype that may be encoded in their genes. Understanding the genetic basis for disease and behavior in different populations will certainly be a challenge, but clearly Vanessa is a person who thrives when presented with challenges.
Vanessa’s limited spare time revolves around her family, including two children — each born on different continents — who keep her busy with the latest goal to teach mom how to surf! A keen soccer player in Australia, she has turned to a new adventure since her move to San Diego, kickboxing. She says she doesn’t get much sleep, particularly little in the past three years, but at least now she’s working mostly on U.S. time rather than two opposite time zones.
If she had time for another career, “it is hard to think of another career as I am doing exactly what I love, combining my passion for the rich-diversity of people from Southern Africa (and globally) from whom we have so much to learn, with the speed and dynamics of everyday life of 21st century science. What better place to combine these two worlds than here at JCVI.” Vanessa hopes via her new position to understand and educate others about the breadth of human genetic diversity existing in populations worldwide.