Jul 24, 2012
Whole Genome Sequencing Study Provides Key Insight Into Human Evolution and Origin of Short Stature
New data published in journal Cell shows Complete Genomics’ sequencing data enabled the discovery of 5 million new genetic variants and, likely, a new hominin ancestor
MOUNTAIN VIEW, Calif. – July 26, 2012 – Complete Genomics, Inc. (NASDAQ: GNOM) today announced that its high-accuracy, whole-genome sequencing service has been used to study human evolution in three African populations. The findings, to be published online today, will be highlighted on the cover of the Aug. 3 issue of the journal Cell.
The research team, led by Sarah Tishkoff, Ph.D., of the University of Pennsylvania, discovered 13.4 million genetic variants; at the time they were discovered, 5 million of them were new, having never been previously reported.
Only 72,000 of these genetic variants were found in the coding region of the genome; the remainder were in the non-coding regions, underscoring whole human genome sequencing’s power to enable major discoveries that would be missed using exome sequencing.
“It’s extremely important that we explore both coding and non-coding regions of the genome in biomedical research to make sure we have the complete picture,” said Tishkoff, a Penn Integrates Knowledge professor with appointments in the School of Arts and Sciences biology department and the Perelman School of Medicine genetics department. “The non-coding regions can determine whether and how a gene is expressed, and thus provide vital information about disease susceptibility, as well as normal human variation.”
“It was immensely exciting to discover millions of new genetic variants in our species, and interpreting all this diversity is a fun challenge,” added Joseph Lachance, the study’s first author, a postdoctoral researcher in the departments of biology and genetics at the University of Pennsylvania.
Complete Genomics sequenced the whole genomes of 15 African men, five each from three hunter-gatherer populations – the Hadza and Sandawe of Tanzania and the Western Pygmies of Cameroon – at more than 60x coverage. These populations were chosen because they are significantly different in appearance, language and local environments, and are not well represented in other genomic datasets.
Tishkoff’s team also identified partial sequences in each of the three populations that appear to have come from a hominin lineage other than Homo sapiens. While there is no reference genome available for this alternate hominin, the researchers believe it could be a sibling species to the Neanderthal.
“We are excited to see our whole genome sequencing service starting to answer some of the big questions about the origins of the human race,” said Dr. Clifford Reid, chairman, president and CEO of Complete Genomics. “We are just beginning to witness the positive impact that highly accurate, population-scale genomic data will have on our quest for scientific discovery.”
In addition, the researchers sought to determine why Pygmies are universally short in stature, with men only 1.5 meters (4 foot 11 inches) tall on average, by pinpointing variants that were common in the Pygmies of Cameroon but rare or absent in the other two groups. They found several candidate genes that act on the pituitary gland, which controls childhood growth and sexual development, among other functions. “This is a unique haplotype which could shed light on novel mechanisms of regulation of pituitary development and pituitary gene expression,” Tishkoff added.
The researchers also identified differences between the three populations in genes governing immune system function and smell and taste, suggesting that these were evolutionary adaptations in response to their different local pathogens and other environmental conditions.
About Complete Genomics
Through its pioneering sequencing-as-a-service model, Complete Genomics provides the most accurate whole human genomes available today. The ease of use and power of Complete’s advanced informatics and analysis systems provide genomic information needed to better understand the prevention, diagnosis, and treatment of diseases. Additional information can be found at http://www.completegenomics.com.
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