March 14, 2006 | Last month marked the fifth anniversary of the first publications of the draft sequence of the human genome. For all their well-publicized differences, the respective project leaders, Francis Collins and J. Craig Venter, share one deep-rooted interest: slashing the cost of genome sequencing. For Collins, improvements in sequencing capability will make ambitious projects such as The Cancer Genome Atlas (see Feb. 2006 Bio•IT World, p. 20) feasible.
For Venter, improving sequencing technology will speed the analysis of environmental genomics data that his nautical expedition is doing so much to stimulate. But Venter is actively encouraging this technological breakthrough. A few years ago, his foundation established a $500,000 prize to reward the group or individual that most helps cross the “$1,000 genome” threshold. Despite tremendous progress, Venter felt that a bigger incentive was necessary.
Enter Google, specifically co-founder Larry Page, who last year invited Venter to join the Board of the X Prize Foundation. The original X Prize, worth $10 million, was awarded to Burt Rutan and SpaceShipOne. The X Prize Foundation now intends to offer a $5 million to $20 million prize to the first team that develops the technology capable of cracking the genome of 100 people in a few weeks for about the price of a plasma television.
Chances are this prize won’t be awarded for several years, although companies such as Solexa, 454, and Helicos BioSciences have given notice they are in the running. Solexa’s John West and 454’s Jonathan Rothberg say that their new commercially available instruments can sequence (or resequence) a human genome for about $100,000 within three months — at least on paper.
Another likely contender is Harvard Medical School geneticist George Church. Church and colleagues are doing for affordable genome sequencing technology what Stanford University’s Pat Brown did for microarray analysis a decade ago — bringing it to the masses. Church detailed his approach in Science last year, providing a relatively affordable system for “sequence by synthesis” DNA sequencing. Another fascinating approach, being developed in conjunction with Agilent, involves passing a DNA molecule through a narrow protein pore and reading off the sequence identity by measuring telltale shifts in conductivity.
But Church’s interest goes beyond mere technology. Writing in January’s Scientific American and interviewed in Technology Review, Church unveiled plans for what he calls the Personal Genome Project (PGP). Church believes the next stage of the genome project will see sequence data married with medical information to better understand health risks before the onset of symptoms. “The “$1,000 genome” has become shorthand for the promise of DNA-sequencing capability made so affordable that individuals might think the once-in-a-lifetime expenditure to have a full personal genome sequence read to a disk for doctors to reference is worthwhile,” writes Church. But for that to occur, there need to be wholesale changes in attitudes, education, and legislation, with issues including insurance, genetic discrimination, electronic medical records, and physician education looming large.
Following a yearlong debate with Harvard’s Institutional Review Board, Church was finally granted permission to launch the PGP pilot program. As a prelude to gathering and posting personal genomic and other “omics” data, Church has already released some of his medical data. Following a tip from a West Coast hematologist, Church changed his medication and halved his cholesterol level. “In the future this kind of experience would not rely on transcontinental serendipity but could spawn a new industry of third-party genomic software tools,” says Church.
Church’s goal is to recruit a diverse band of volunteers — not just tenured professors — who will publicly share medical and genomic data. Aside from stimulating advances in sequence analysis, Church hopes the PGP will spur software development to help physicians interpret PGP data. “Your doctor could use software to scan through your genome and pick out all the alarm signals,” says Church.
The vision of doctors conducting whole-genome scans from a blood sample, giving their patients a souvenir copy of their DNA on DVD, may have moved a step closer. After all, as Church points out, if people are crazy enough to pay $35,000 to clone their cat, there will surely be a market for personal genomes in the $10 to $20,000 range.
Church, Rothberg, and West speak at Bio•IT World’s Life Sciences Expo on April 4.