The first individual genome ever sequenced -- a complete DNA blueprint of celebrity scientist Venter -- has revealed genetic variation among humans far richer than previously imagined.
Researchers at the J. Craig Venter Institute (JCVI), along with collaborators at The Hospital for Sick Children in Toronto and the University of California San Diego (UCSD), have published a genome sequence of an individual, Craig Venter, that covers both sets of chromosomes that were inherited from each parent.
Two other versions of the human genome currently exist—one published in 2001 by J. Craig Venter, Ph.D., and colleagues at Celera Genomics, and another at the same time by a consortium of government-funded researchers. These genomes were not of any single individual, but, rather, were a melding of DNA from various people. In the case of Celera, it was a consensus assembly from five individuals, while the government-funded version was a haploid genome based on sequencing from a limited number of individuals. Both versions greatly underestimated human genetic diversity.
This new genome, known as the “HuRef” version, represents the first time a true diploid genome from one individual—Dr. Venter—has been published. The research is available in the latest issue of the open-access journal PLoS Biology.
Researchers at the JCVI have been sequencing and analyzing this version of Dr. Venter’s genome since 2003. Building on reanalyzed data from Dr. Venter’s genome that constituted 60% of the previously published Celera genome, the team had the goal of constructing a true reference human genome based on one individual. Using whole genome shotgun sequencing and highly accurate long reads from Sanger dideoxy automated DNA sequencing, the team produced additional data making the final 32 million sequences.
From the combined data set of more than 20 billion base pairs, the researchers were able to assemble the human genome with an overall length of 2.810 billion base pairs. The genome was covered 7.5 times, ensuring that each set of contributing chromosomes was covered over 3.2 times for greater than 96% coverage of the two parental genomes. The team at JCVI compared and contrasted the new HuRef diploid genome sequence to earlier versions of published human genomes and found that the HuRef version improved upon both these early versions by providing more and correctly oriented base pairs.
Since the HuRef genome is diploid, each of the parental chromosomes could be directly compared to each other. One of the most surprising and important findings from this research was the high degree of genetic variation that was found between two chromosomes within a single individual.
Source: Public Library of Science
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