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Research Team Publishes World’s First Southern African Genome and Multiple Exomes

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The Penn State-led team has used 454 Sequencing Systems and NimbleGen Sequence Capture arrays to build the first complete genome and exome sequences from the indigenous hunter-gatherer people of southern Africa, the oldest known human lineage.

In a study published online in Nature, a team of researchers from Penn State University and the University New South Wales present the complete genome sequences of an indigenous hunter-gatherer from the Kalahari Desert and a Bantu from southern Africa, along with three additional whole exome sequences of Kalahari hunter-gatherers.

The four hunter-gatherer participants were chosen for their linguistic group, geographical location and Y-chromosome haplotype while the Bantu individual is the revered Archbishop Desmond Tutu of South Africa. The landmark study represents the first of its kind to analyze whole genome and exome sequence data from this genetically distinct population, which is thought to be the oldest known lineage of modern day humans.

The findings, which include over 13,000 novel SNPs, provide new insights into human population diversity and may enable the future development of drugs that benefit this ethnic group.

Interestingly, the approach for generating and analyzing the Kalahari hunter-gatherer whole genome sequence presented in the paper is unique to other recently published Asian, Yoruban, and European individual genomes. “We recognized that the genomes of the southern African participants in this study would diverge more from the human reference genome than other publically available genome sequences,” explained Stephan C. Schuster, lead author and Professor of Biochemistry and Molecular Biology at Penn State University. “As a result, the goal was to generate data of sufficient quality for de novo genome assembly rather than simply mapping against the human reference.”

In order to generate the massive amounts of high-quality data required for de novo assembly of a human genome, the researchers turned to the GS FLX System with long-read GS FLX Titanium Series chemistry.

The study results were consistent with the belief that southern Africans are among the most divergent of all human populations. The researchers identified more SNPs in their genomes than in other individual human genomes sequenced to date, as well as thousands of novel SNPs.

“These results will be a rich resource for future work, providing many new candidate functional sites that have not been included in whole-genome association studies,” said Vanessa Hayes, a project co-leader and Group Leader Cancer Genetics at the Children’s Cancer Institute Australia for Medical Research at the University of New South Wales. “Ultimately, we hope that these sequences will serve as an important cultural and genetic archive of this indigenous population, one of the last remaining hunter-gather societies.”