GenomeSweep

Back in 2004, Life Science Insights surveyed a group of genome experts for opinions on the date when cheap human genome sequencing would be available.  Here is a summary of what they said:

Forty percent of the genome experts interviewed by LSI believe that the $1000 genome will not be reached within ten years.  This compares to a mere 17% who believe it will be here in five years. Ten percent of respondents said that scientists would not even reach the $100,000 genome within ten years. Clearly, there is disagreement over how fast these technologies are developing.

Predictions are fun to watch play out over time, particularly when expert opinions vary wildly.  Remember GeneSweep?  The experts in this contest made predictions about the number of genes in the human genome.  They ranged from 25,000 - 300,000.  Here is a snapshot of the distribution of bets, dating from March 2003:

Genesweep

With such wildly different opinions about the future of personal genomics, perhaps a Long Bet is in order.  GenomeSweep anyone?

Zachary Zimmerman, The Promise of the $1000 Human Genome (PDF). Life Science Insights, October 2004.

GeneSweep History from Cold Spring Harbor.

Internet Archive snapshot of GeneSweep page from March 2003.

In case you’re wondering, the winner of GeneSweep was Lee Rowen from the Institute for Systems Biology in Seattle.  Her prediction was 25,947 genes.

Making the Genome Usable

One can make a profession of figuring out how to make a piece of technology easy to use.  In the computing industry, we call this work "usability" or "human-computer interaction" or "interaction design".  Making the human genome easy to use is one of the challenges that lie ahead for the field of personal genomics. 

This is the first post on this blog with the tag "usability" and I’m using this occasion to celebrate what appears to be the first AJAX-driven genome browser, GBrowse (a prototype).  AJAX is a group of web technologies (named by the geeks at Adaptive Path) featured in many of the hot, new web applications like Google Maps. 

Will the genomics industry follow the example of the computing industry and have entire professions and degrees grow-up around making the human genome usable?

Genome X Prize

The X Prize now has named Laurence Kedes of UCLA to lead the Genome X Prize.  Genome sequencing remains far too expensive, but is dropping quickly.  From their webpage:

The cost of DNA sequencing is decreasing by half every two years. Today it
  would cost $20 million and take six months to decode one entire human genome.

Who’s counting?

ANTONIO REGALADO. Prize for DNA Decoding Aims to Fuel Innovation. WSJ Jan 27, 2006.

Genome X Prize

Flockhart on the ascent of PGx

MIT Technology Review interviewed David Flockhart of IUPUI recently.  Here is a snip about the adoption of PGx testing:

TR: But the FDA has already approved a number of genetic tests to guide prescriptions. Aren’t doctors using them?

DF:
No…A major problem is
going to be educating physicians who are, as yet, relatively uneducated
about the availa­bility of genetic tests to guide some of their
prescribing decisions.

TR: How long will that take?

DF:
…The movement of these tests into the clinic will happen
gradually with fits and starts….Demand will kick in within a year or
two, as patients realize the power of these tests. That will be the
biggest driver…

Erika Jonietz. Getting Personal about Drugs. Genetic tests are poised to revolutionize prescription writing. MIT Technology Review. March/April 2006.

David Flockhart’s website at IUPUI.

Viruses in the Genome

Carl Zimmer has an excellent post on viruses in the human genome.  Here is the juicy snip:

The human genome carries full-fledged retroviruses, as well as
viruses in various state of decay. Scientists have identified 98,000 of
these viruses, along with about 150,000 fragments of defunct viruses.
All told, they make up 8 percent of the human genome. In many cases,
the virus genes have disappeared altogether, leaving behind flanking
repeats, which have been duplicated to millions of copies that take up
about 40 percent of the genome. As a point of comparison, our "own"
genes–in other words, those that encode proteins that make up our
bodies and allow our bodies live–make up only about one percent of the
genome.

Some of these endogenous retroviruses are only found in some people
and not others. They must have invaded someone’s genome and then spread
to his or her descendants, but have not yet spread throug our entire
species. Others appear to be ubiquitous–meaning that they are ancient
passengers that had already spread throughout an ancestral population.

Read the whole piece.

Carl Zimmer, The Sixty-Million Year Virus. The Loom, March 13, 2006.

Norbert Bannert, and Reinhard Kurth. Retroelements and the human genome: new perspectives on an old relation. PNAS. October 5, 2004. vol. 101 (Suppl. 2) 14572-14579. [A nice open-access review article on human endogenous retroviruses (HERVS)]

Video Editorial on Personal Genomics

""Personalized genomics" — sequencing an individual’s genome so that
genetic vulnerabilities can be identified early — is a pipe dream
today: It would cost $10-$20 million per person. However, these new
sequencing technologies make it plausible that personalized genomics
will be feasible in the next few decades"

The statement "plausible that…[it] will be feasible in the next few decades" seems a wee bit on the conservative side of technological forecasts I’d say.

Anthony Komaroff. "Personalized Genomics" Gets Closer. Medscape. Feb 24, 2006.

Genetics of Caffeine Metabolism and MI, Gulp

An article published in JAMA last week showed that coffee drinkers that are slow metabolizers of caffeine are at greater risk of heart attack.  [Gulp] Caffeine is metaboized via an enzyme (CYP1A2) that lives in the liver.  Genetic polymorphisms of this enzyme are common.  Some people metabolize caffeine more quickly or slowly than others, related to which version of the CYP1A2 gene they have. [Gulp]

The slow metabolizer variant (CYP1A2*1F, nomenclature here) is quite common, at least in Costa Rica where the study was undertaken–54% of the population were carriers of *1F allele. [Gulp]

Caffeine_genetics_heart_attack_gulp_1

Figure: The cup of coffee
I’m currently drinking is
approximately the size
of a small dog.

Cornelis MC, El-Sohemy A, Kabagambe EK, Campos H. Coffee, CYP1A2 genotype, and risk of myocardial infarction. JAMA. 2006 Mar 8;295(10):1135-41.

Medscape CME (bug-me-not username/password)

University of Toronto Department of Nutritional Sciences

Caffeine at Flickr, (circumstantial favorite)