Bushman and Bantu genomes sequenced

Archbishop Tutu's personal genome sequenced in a study to shed light on human genetic variation and effect on human health

This image shows a group of hunters from the Ju/'hoansi tribe in the Namibian Bush. The indigenous hunter-gatherers of southern Africa, often referred to as Bushmen, represent the oldest known lineage of modern man. By sequencing the genomes of four Bushmen and one Bantu representative from Southern Africa, researchers show that Bushmen have more genetic differences between each other than for example, do a European and Asian. The inclusion in current databases of the Bushman and Bantu genomes sequenced by Stephan Schuster et al. will ensure the inclusion of Southern Africans in medical-research efforts. Photo Credit: Stephan C. Schuster, Penn State University


Human genomes from Southern African Bushmen and Bantu individuals have been sequenced by a team of scientists seeking a greater understanding of human genetic variation and its effect on human health. The study's findings were published in the journal Nature on 18 February 2010.

"We sequenced the personal genomes of four Bushmen participants who are tribal leaders from their communities and are at least 80 years of age, and from one Bantu participant who is in his late 70s," said Stephan Schuster, a professor at Penn State and a co-leader of the project. The Nature paper reveals the identities of each of these five participants. The other co-leader, Vanessa Hayes of the University of New South Wales, who also is a group leader at Children's Cancer Institute Australia, added, "The Bantu participant is Archbishop Desmond Tutu, who, through his Tswana and Nguni ancestry, is an ideal representative for most Southern Africans."

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. The study also reveals striking levels of genetic differences among the individual study participants. Webb Miller, professor of biology and computer science at Penn State, who performed the comparative analysis of the genomes, underscores the genetic uniqueness of the Bushmen by saying, "On average, there are more genetic differences between any two Bushmen in our study than between a European and an Asian. To know how genes affect health, we need to see the full range of human genetic variation, and Southern Africa is the place to look."

This study used three new sequencing technologies, which deliver DNA sequences with unprecedented economy and speed. Tim Harkins, who led the study's industry partners, said, "This project provides a unique opportunity to compare the strengths of current sequencing technologies, and it demonstrates that their combination results in data that is more accurate than from projects using only one of these methods." As sequencing technologies evolve, the number of genomic studies is growing exponentially. "Human genomics is becoming a realistic and powerful medical resource that will gain momentum in 2010," Schuster said.

A nearly life-long medical history accompanies each of the study's five personal genomes, facilitating the identification of genetic differences that may have contributed to particular health conditions. The researchers expect that these genomes will enable more accurate identification of diseases caused by rare genetic variants in Southern Africans and also in the global human population. To date, a genome-wide approach to identifying genetic disease susceptibility has disproportionally benefited the Western World in comparison to the African continent but "As a result of this project," Hayes said, "Southern Africans will immediately be included in genome-wide disease association studies, increasing our ability to examine regionally significant diseases."


This image shows Stephan Schuster, of Penn State University, and Vanessa Hayes, of the University of New South Wales, preparing genetic samples in their field laboratory in Namibia. Photo credit: Stephan Schuster, Penn State

Because the research team has made the the five genomes sequenced in its study freely available, the scientists expect that Southern Africans will be better represented in future studies of how genetic variation influences the effectiveness of drugs - a research field known as pharmocogenomics, which relies on human genome sequences and is considered by many to be the future of drug design. "To make our results easier to use than earlier genome sequences, we have established freely available Internet servers at Penn State," Miller said. Inclusion in pharmocogenomic studies is expected to benefit Southern Africans, who often have been poorly represented in pharmaceutical trails and who suffer from population-based differences in the effectiveness of drugs, such as anti-viral treatments for HIV/AIDS. The new data also is expected to help Southern African scientist and Southern African entrepreneurs to develop appropriate treatments when world-wide approaches fail locally.

The Bushmen that participated in this study are the first people whose genomes have been sequenced that still practice a hunter/gatherer lifestyle, enabling scientists to correlate the unique physiology of Bushmen with the genetic variants detected in this study. "The availability of Bushman and Southern African Bantu genomes permits researchers to examine one of the few remaining instances in the world of coexisting foraging and farming groups," said Schuster. The study identified several genetic adaptations in the Bushmen that make them ill-suited to certain perils of an agricultural lifestyle, including high-fat diets and exposure to malaria. - PSU


February 2010