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Interpreting the Genome

By Kevin Davies

September 27, 2011 | First Base | Twelve months ago, we published a special issue of Bio•IT World dedicated to “The Road to the $1,000 Genome.” While we didn’t expect to reach that momentous if somewhat arbitrary threshold so soon, there’s no doubt we’re getting very close. This past summer, Illumina announced yet another drop in its personal genome sequencing service, dropping the introductory individual price below $10,000. For academic and pharma customers seeking whole genome sequencing services, the cost per genome is now as low as $4,000, competition being driven by the emergence of many new service providers, and even one or two sequencing service brokers, such as Denmark’s BlueSEQ, offering to find the right sequence and analysis partner for a client’s needs.

As the cost of whole-genome sequencing halves every five months or so, the focus inevitably shifts to the cost of analyzing and interpreting the genome. The task of analyzing the flood of next-generation sequencing (NGS) data is likened by the Broad Institute’s Matthew Trunnell to driving in a snowstorm. “If we just waited for the roads to be ploughed, it would be really easy, but we have to white-knuckle it now,” rather than wait however long for the perfect platform, with negligible errors, long read lengths, and high throughput. Perhaps seeking inspiration from a well-known ‘next-generation’ expert, the Broad’s upstream NGS pipeline is humorously named Picard, which feeds into a disease-specific pipeline appropriately dubbed Firehose. Agility is at a premium, says Trunnell, but NGS is still posing tough questions for the IT crowd five years later. “It’s new to us,” says Trunnell. “We’re not high-energy physics!”

In our 2011 genome informatics special issue, we offer a collection of features, profiles, and interviews around the latest trends in NGS and genome informatics. Perhaps the most gratifying story in genome interpretation this year is the work of Elizabeth Worthey and colleagues at the Medical College of Wisconsin (page 19). Worthey, whom I had the pleasure of interviewing this summer in Copenhagen, played a pivotal role in the much publicized case of Nicholas Volker, a sick Wisconsin boy whose genome was sequenced (almost as a last resort), resulting in a positive diagnosis and therapy. The Volker case highlights the vast potential of clinical genome sequencing, even though—as Worthey readily admits—the gratifying outcome in that case is by no means guaranteed.

Our cover image depicts Chris Toumazou, the founder and CEO of a relatively small British company, DNA Electronics, which has been licensing its intellectual property to some of the biggest names in the business, including Ion Torrent Systems and Roche. Toumazou has a distinguished record in medical devices, and his latest gizmo, the ‘SNP-Dr,’ which instantly calls to mind Mr Spock’s tricorder, shows the potential of real-time genomic diagnostics (page 27).

Several articles look at new software initiatives from the commercial and academic fields. Managing editor Allison Proffitt interviewed many leading genome informatics companies for their latest tools and trends, including Knome, Real Time Genomics, Partek, and DNASTAR (page 35). On the open-source front, we meet the two founders of Galaxy, an increasingly popular platform for easy and efficient access to a variety of genome informatics tools (page 44).

On page 24, Richard Resnick, CEO of GenomeQuest, discusses his company’s ambitions in the genome analysis realm. As one might expect of someone who took his bioinformatics training from Broad Institute director Eric Lander, Resnick is a knowledgeable and refreshingly candid spokesperson for the genome informatics industry.

Challenges and Opportunities

Speaking of candid, I was struck by the open attitude of BGI founder Huanming Yang, who gave us an exclusive interview during a visit to Boston earlier this year (page 31). Yang has worked wonders, building BGI into the world’s largest genome sequencing center, providing services for a large number of academic and pharma clients. But as in any arena, reaching the pinnacle is one thing, staying there is quite another, and Yang does not sugarcoat BGI’s challenges in the next few years.

One of the first NGS platforms featured in Bio•IT World was in 2007, when Kevin McKernan took us through the basics of SOLiD sequencing, now part of Life Technologies. McKernan spent his final 12 months at Life Technologies leading the R&D team of newly acquired Ion Torrent Systems, before stepping down this summer. His new venture, Medicinal Genomics, has sequenced and released data from the cannabis genome. This may sound like some fancy new recreational genomics start-up, but as McKernan explains (page 40), the goal is to better understand the potent anti-cancer properties of some of the plant’s active compounds.

Our digital edition carries two bonus articles in this report: a story about VAAST (page 48), a promising algorithm for the detection of pathogenic mutations amidst an ocean of exome or whole-genome data, which is available to academic users now and will be part of a commercial package by San Francisco-based Omicia shortly. And we talk to Laurie Goodman, the editorial director of GigaScience, a new peer-reviewed open-access journal published by BGI, devoted to big data in genomics and life sciences (page 46).

This article also appeared in the 2011 September-October issue of Bio-IT World magazine.
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