Tag Archives: medicine

Paul Nurse: Family Trees Can Be Dangerous

One of the points that I have always made about the advent of personal genomics was that we are going to find out some family secrets that have been under wraps for a very long time. This may not always be a bad thing. But there are going to be some cases where the participants may not be quite so prepared to handle the information. Here Paul Nurse tells a tale of ancestry and genetics that illustrates some of that complexity. It’s only 10 minutes–and it’s quite funny. Have a look.

Direct to the YouTube in case you want that: http://youtu.be/X9Jktke38I8

Tip of the Week: PSI Structural Genomics Knowledgebase

Last January I did a tip that featured the monthly Structural Genomics Update, which is essentially a newsletter and article collection from PSI Structural Genomics Knowledgebase (SGKB). However, the update is just one aspect of what SGKB offers. In today’s tip I want to feature the wonderfully efficient ways that Structural Genomics Knowledgebase provides you with to learn about the proteins that you are interested in. What I tried to stress in this tip is the different emphasis that Structural Genomics has compared to the RCSB PDB. The RCSB PDB is a GREAT resource, which we also have free tutorial on, but it was created by and for structural biologists. Its displays feature angstroms, angles, conformers and more.

Me, I’m a Molecular Biologist by training & I think about proteins in terms of genomes, pathways, medical relevance, molecular functions, and the like. The SGKB thinks like me, and even organizes information and links into those sorts of categories. I really like how it presents protein information to me, and in the process how it eases me into thinking about the more ‘hard core’ structural details that I see in PDB. The tip is just a teaser taste of the SGKB – if I peak your interest, please do check out OpenHelix’s full, free introductory tutorial on the PSI-SGKB (sponsored by PSI SGKB) as well as the site itself. You never know, you might just learn to love a crystal! :^)

Personal Genomics, tipping points and a personal perspective

ResearchBlogging.org Please indulge a long post from a personal perspective, what genomics is about to do for _me_. This is information that many, if not all, of our readers already know. I’ve been researching and working in either experimental biology or genomics for over 20 years. Ever since the beginning of the Human Genome Project , which coincidently started the same year I started my Ph.D. program, into my postdoctoral research at EMBL and now my work at OpenHelix, I’ve known that someday personal genomics was going to impact me, and millions of others, in a big way. Yet, it has always felt that it was one of those things that would be a decision I and we as a society didn’t have to make until we turned that corner that seemed always “just ahead.”

But now I think we’ve turned a corner. It feels, to mix metaphors, that we’ve hit a tipping point. The Human genome project, the mapping and sequencing of the/a human genome from 1990 to 2003, cost approximately 2,700,000,000 dollars (that’s 2.7 billion, I wanted to get all the zeros in). Celera did the genome for 300,000,000. The cost of sequencing an entire human genome has been plummeting ever since. In 2007, the cost of sequencing the genome of James Watson (co-discoverer of DNA) was about 2,000,000. The today cost is about 10,000. Complete Genomics and other companies are on the march to quickly reducing the cost of sequencing a genome under 1,000.

Let me graph the last 8 years for you, mind you, this is starting from the 300,000,000 number, not the 2.7billion, because that graph would be a straight line down.

So, within a year, the cost of sequencing your, my, genome will reach 1,000. If not less. We’ve seen this coming for years now, and it’s upon us. But what does it mean?  A lot of data. But data means nothing without context and analysis. Sequencing my genome would be a waste of 1,000 dollars if I gleaned nothing from it.

Yet, even that seems to have turned the corner from a few tidbits of genetic information to a steady steam and the beginning of a flood.

You know you’ve turned a corner when a genomics testing company begins to offer genetic tests to the mass market through Walgreens. There’s enough context in that data to make money from it, or so they hope. You can be sure the corner is safely behind you when the FDA tells Pathway Genomics and Walgreens that they will need to hold off while they make sense of the regulatory implications. Genomic ancestry test are are also gaining is usability… and scrutiny.

It was the recent Lancet paper on the clinical analysis that seemed to be a tipping point, not for me or those in the field. Genomics has been on my radar since 1988, but for society. I blogged about the paper and it’s use of genomics resources such as GVS, dbSNP and others. In the paper, the researchers did a thorough clinical assessment of an individual’s genome. We’ve brought down the cost of sequencing, now we are learning how much it’s going to take to assess that data from a medical point of view, and importantly, what we can learn from it.

What can we learn from it? I read this paper again from a personal perspective now. Could I learn something from sequencing and analyzing my genome, and if so what. My answer came to this: yes, I could learn something and in fact enough that I’m not convinced that as soon as that sequencing gets down to a 1,000 or lower (and is a high quality sequence :), I’m going to do it.

There are three things I see from this paper that one could learn from assessing their genome: prevention, early detection and therapy. I believe the former will be, for most people, something they already know and their genome sequence will tell them nothing new. The other two could be a wealth of information they will want, even need, to know. You’ll notice I left off ‘cure.’ I saw nothing in this paper, and nothing on the near horizon, that suggests to me that our genome sequence data will help with curing anything. Perhaps, just not much. Yet, the possibilities of early detection of disease and personalized drug treatment are tantalizing. Continue reading

How much rat poison indeed…

It is somewhat serenditous in that I just completed the first draft of a tutorial that uses several genomic resources to look at the CYP2C9 gene variations and wafarin dosage, but a recent report in the NEJM looks at wafarin dosage from a combined clinical and pharmacogenetic data standpoint. As Daniel MacArthur at Genetic Future says,

“the real clinical benefits of widespread genetic screening will come first in pharmacogenomics – these results provide a neat demonstration of this process in action.”

And he also points to a nice tool the authors created for determining dosage based on CYP2C9 genotype and other indications. A taste of things to come.