science 2008-2009: 11: genomics, cheap and personal

Sequencing genomes has become remarkably cheaper and quicker. The Human Genome Project took thirteen years, the involvement of nearly three thousand scientists across sixteen institutions in six countries, and a small matter of $2.7 billion, to produce a sequence in 2003. In 2008, a handful of scientists took just over four months, spending less than $1.5 million, to provide a sequence of the DNA of James Watson. The trend is expected to continue, perhaps reaching rates of a billion kilobases per day per machine after 2010. The X Prize Foundation has offered a $10 million prize for the first successful attempt to sequence 100 human genomes in ten days at under $10,000 per genome.

After his sequence had been read, James Watson was counselled by a team of experts who explained what teh implications were of the twenty detected mutations associated with increased disease risk. “It was so profound”, one expert told Nature, in a plea for further research, “how little we were actually able to say”.

That doesn’t bode well for personal genomics. As sequencing becomes cheaper, we may all become Jim Watsons. Indeed, direct-to-consumer whole-genome testing went on sale in 2007. Three companies were pioneers: 23andMe and Navigenics in California, and deCode in Iceland. On payment, these companies would cross check your DNA against a million single-point genetic polymorphisms. Critics complained that the clinical usefulness of this information was unclear, and led to unnecessarily frightened customers, and demanded regulation or restriction. Furthermore, the information meant very little unless it was placed in the context of family histories and other facts. The companies replied that individuals had the right to their own genetic knowledge. Furthermore, 23andMe’s technological and financial links to Google, which was launching its Google Health, a facility for recording personal medical histories, points to how genetic information might be interpreted in the future.

Cheaper sequencing has also aided the phylogenetic investigations of the tree of life. Draft sequences for more and more organisms were published in the 2000s. In addition to a host of micro-organisms, notable sequences published (reading like an alternative Chinese calendar) were: the model fly Drosophila melanogaster (2000), the model plant Arabidopsis thaliana (2000), rice (2002), the mouse (2002), the malaria mosquito Anopheles gambiae (2002), the model organism Neurospora crassa (2003), the wilk worm (2004), the rat (2004), the chicken (2004), the chimpanzee (2005), the dog (2005), a sea urchin (2006), the cat (2007), the horse (2007), the grape vine (2007), platypus (2008), corn (2008), sorghum (2009) and the cow (2009). Nor did organisms have to be living to give up genetic secrets. Almost complete sequences of the mammoth (2008) and the Neanderthal (2009) were salvaged from fossils.

Each of these genomes is useful within some working world. Of course the availability of a complete sequence of the human genome was of specific interest to medical researchers, including cancer scientists.