Tuesday, September 4, 2007

DNA squencing and microarrays (movie link)

It's announced today that Craig Venter has just published his own personal genetic code in the journal PLoS Biology at a cost of $10 million dollars ($60 million in contribution to previous efforts). Venter's gene map provides new insight into our genetic destiny. What the paper confirms is that individuals' genomes have much more variation than what was originally determined by the the human genome project. According to the paper, there are millions of gene variants between individuals, with the bulk of variants (78%) being SNPs....no surprise to the microarray community.

Venter says it's just the beginning of a new era of personal genomics. "For the first time, we can answer almost any question of what's genetic, what's the environment. Our genes can tell us probabilities of what might happen and give us a chance to do something about it." The quote sounds good in the media coverage, but those of us in the industry know that statement is simply not true. Did anyone watch the Nova television documentary, "Cracking the Code of Life"? Using genetic based tests for health related "probabilities" has been true for many years.


See CNN video news coverage here:
http://www.cnn.com/2007/HEALTH/09/04/dna.venter/#cnnSTCVideo

What I thought was great about the paper and media coverage...

*High density SNP microarrays were used to validate the SNP sequencing data.
The CGH microarrays detected an additional 62 copy number variable regions that the sequencing data did not get. This blends two of the most powerful technologies we have (sequencing and microarray). I dislike the naive division between scientists who believe sequencing is going to replace all microarray and visa versa. It's clear these two technologies are complimentary and will be used in conjunction with one another for many years to come. Peer reviewed publications show very high frequencies of copy number length polymorphisms (see Jan. '06 Nat Genet.) confound sequencing, fundamental genome assembly and annotation errors (Cytogenet Genome Res. 2006;112:1-5).

*The importance of SNPs, SNP discovery and SNP screening platforms come into the forefront. We have now even more confirming data that SNPs represent the largest portion of genetic diversity between humans. As has been discussed in previous posts to this blog, ex-situ microarrays are very useful tools in screening individuals for known SNPs in a cost effective and high throughput manner.

*The other nice thing is that it puts genetic testing in the main stream news again and points out the inevitable, DNA testing simply does not scare people any more. Venter has been so bold to call the fear of knowing one's own genetic code "irrational". The unknown is scary to many of us, but events like this one shows that the controversy of making individuals genetic information public just isn't so controversial any more. James Watson has already done it and more people are volunteering see; Personal Genome Project. Craig Venter is considered by many to be an egomaniac. Much of what is says is done to promote his own agenda and media circus (the announcement of the paper comes out at the same time as his autobiography) but at the end of the day I would have to say he's done a good thing.