Tuesday, September 04, 2007

Venter's Genome

This research article in PLoS Biology describes the genomic DNA sequence from both chromosomes of a single individual- J. Craig Venter. Here is the abstract:

We have generated an independently assembled diploid human genomic DNA sequence from both chromosomes of a single individual (J. Craig Venter). Our approach, based on whole-genome shotgun sequencing and using enhanced genome assembly strategies and software, generated an assembled genome over half of which is represented in large diploid segments (>200 kilobases), enabling study of the diploid genome. Comparison with previous reference human genome sequences, which were composites comprising multiple humans, revealed that the majority of genomic alterations are the well-studied class of variants based on single nucleotides (SNPs). However, the results also reveal that lesser-studied genomic variants, insertions and deletions, while comprising a minority (22%) of genomic variation events, actually account for almost 74% of variant nucleotides. Inclusion of insertion and deletion genetic variation into our estimates of interchromosomal difference reveals that only 99.5% similarity exists between the two chromosomal copies of an individual and that genetic variation between two individuals is as much as five times higher than previously estimated. The existence of a well-characterized diploid human genome sequence provides a starting point for future individual genome comparisons and enables the emerging era of individualized genomic information.

Today's Globe and Mail also has this story here. Here are some excerpts:

Now researchers from Canada, the United States and Spain have decoded all 46 of the chromosomes belonging to J. Craig Venter, the 60-year-old upstart American biologist whose company, Celera Genomics, compiled the private version of the human genome seven years ago. And the results indicate that those first celebrated DNA maps seriously underestimated the genetic diversity of humans - by a factor of at least five.

The new work suggests that the genetic code in the chromosomes we carry can vary widely, not only between any two strangers waiting at a bus stop, but between brothers and sisters.

"The biggest single surprise is how much we missed the boat with the human genome seven years ago, and how different we really are," Dr. Venter said in an interview. "The overwhelming message back then was that we are all like identical clones of each other. ... It's comforting to know we are more unique than that."

....Most experts predict that routinely reading individual genomes will become a reality within five years as the technology to unravel the six billion chemical units that make up DNA gets faster and cheaper.

Kathy Siminovitch, director of genomic medicine at Toronto's Mount Sinai Hospital and the Samuel Lunenfeld Research Institute, noted that the first Human Genome Project rang in at roughly $1-billion (U.S). But with the new generation of "ultra-fast" DNA sequencing machines that have hit the market within the past two years, she said the bill is expected to drop to less than $100,000 by year's end.

Connecticut biotech firm 454 Life Sciences, for instance, has been using the technology to decode the full genome of James Watson, the Nobel laureate who co-discovered the structure of DNA in 1953. That publication is expected later this year.

"It seems like it is possible to think that a $1,000 genome could be within reach," said Dr. Siminovitch, who is buying an ultra-fast sequencer for the University Health Network. "When we see how much variation there is in [Dr. Venter's] DNA, then chances are there is this much variation in all DNA. ... This publication [of the Venter genome] will drive the momentum to get the price down and to be able to do this on lots of people."

The prospect of a $1000 genome is a really exciting one.