Tuesday, September 04, 2007

Craig Venter's Genome

The genomic pioneer bares his genetic code to the world.

By Emily Singer

Personal genomes: Genomics pioneer Craig Venter (above) has sequenced his entire genome and released it to the world. Credit: J. Craig Venter Institute

Five years ago, Craig Venter let out a big secret. As president of Celera Genomics, Venter had led the race between his company and a government-funded project to decode the human genome. After leaving Celera in 2002, Venter announced that much of the genome that had been sequenced there was his own. Now Venter and colleagues at the J. Craig Venter Institute have finished the job, filling in the gaps from the initial sequence to publish the first personal genome.

His newly released genome, published today in the journal PLoS Biology, differs from both of the previous versions of the human genome (one from Celera, the other from the Human Genome Project) in that it details all of the DNA inherited from both mother and father. Known as a diploid genome, this allows scientists to better estimate the variability in the genetic code. (In a genome sequence generated from a conglomerate of different individuals, some variations are lost in the averaging.) Within the genome of 2.810 billion base pairs, scientists found 4.1 million variations among the chromosomes; 1.2 million of these were previously unknown. Of the variations, 3.2 million were single nucleotide polymorphisms, or SNPs, the most well-characterized type of variation, while nearly one million were other kinds of variants, including insertions, deletions, and duplications.

Venter's genome will join that of another genomic pioneer, James Watson, codiscoverer of the structure of DNA. (See "The $2 Million Genome.") Announced in June, Watson's genome was sequenced by 454, a company based in Branford, CT, that's developing next-generation sequencing technologies. (For more on 454's technology, see "Sequencing in a Flash.")

Venter's and Watson's genomes are likely just the first in an upcoming wave of personal genomes, a crucial step in the advent of personalized medicine: the ability to tailor medical treatments to an individual's genetic profile. (See "The X Prize's New Frontier: Genomics.") Venter has already explored some of his genome, discovering that he carries genetic variations that put him at increased risk for Alzheimer's disease, heart disease, and macular degeneration. He says that he's been religiously taking statins, cholesterol-lowering drugs, ever since.

Venter talks with Technology Review about what lies ahead for his genome.

Technology Review: Why did you decide to embark on this project?

Craig Venter: The genome we published at Celera was a composite of five people. To put it together, it became clear that we had to make some informatics compromises--we had to leave out some of the genetic variation. We knew the only way to truly understand the genome would be to have the genome of one individual. Rather than starting from scratch, we decided to take what we had from the Celera genome and add more sequence. The goal was to get an accurate reference sequence from a single individual.

TR: How does your genome sequence add to what we know from the Human Genome Project?

CV: The government labs sequenced and assembled a composite haploid genome from several individuals [meaning it included a DNA sequence from only one of each chromosome pair]. There was the assumption back then that having half of the genome was all that was needed to understand human complexity. But it's become clear that we need to see the composite of the sets of chromosomes from both the mother and father to see the variation in the genome.

This genome has all the insertions and deletions and copy-number differences. That gives us a very different view.