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Illumina Wins This Round on Points

By Kevin Davies

January 20, 2009 | First Base | In August 2005, on the eve of the publication of the first commercial next-generation sequencing technology, 454 Life Sciences founder and Chairman Jonathan Rothberg preemptively declared: “We won the race. Everyone may not be happy with that, but we are.”

Three years on, the publication of not one but three complete human genomes in the same issue of Nature last November effectively marks the end of the latest chapter in the sequencing saga. These included the first African genome, led by David Bentley and colleagues at Illumina UK; the first Asian genome, produced by Jun Wang and colleagues at the Beijing Genomics Institute (BGI) in Shenzen, China; and the first cancer genome, that of a deceased leukemia patient, produced by Elaine Mardis, Rick Wilson, and colleagues at the Washington University School of Medicine Genome Center in St Louis.

The common thread in those publications was the platform—Illumina’s Genome Analyzer (GA), which bought British company Solexa in 2006 for a cool $600 million. Steady advances in read length, throughput, and accuracy gave Illumina the edge over its rivals. “We won,” says John Milton, the former Solexa head of chemistry now with Oxford Nanopore Technologies, even while acknowledging that Applied Biosystems’ (AB) SOLiD instrument might be of higher quality. Clive Brown, Solexa’s former head of bioinformatics also now at Oxford Nanopore, agrees. “We won. Enough of the boxes were ticked in terms of efficiency and performance and it’s won. It’s clearly well ahead of everyone else.” Howard Hughes Medical Institute investigator Tim Harris, an authority in single-molecule biology who left Helicos last April, confirms, “The Illumina guys have clearly won this round, there’s no doubt.”

Illumina marked the genome milestones with a press conference at the American Society of Human Genetics (ASHG) convention in Philadelphia last November. The company’s CIO, Scott Kahn, said the simultaneous publications made a statement regarding how far sequencing technology has come. “No one in this room would have thought that in a single publication in Nature, there’d be effectively four genomes published.” (Kahn counted both the tumor and normal genomes in the Wash U. study.)

Illumina also announced the sale of 11 more GA instruments to the Wellcome Trust Sanger Institute, bringing their tally up to 36. It’s not that the GA instruments have dramatically (or even incrementally) greater throughput or accuracy than SOLiD, but the Sanger Institute already has the workflow, informatics pipeline, and trained personnel in place for that platform.

Of course, AB—now Life Technologies following the merger with Invitrogen—isn’t taking this lying down. Kevin McKernan (see “The Drive for the $1000 Genome,” Bio•IT World, May 2007) anticipates the SOLiD version 3.0 will reach a human genome cost of around $10,000 early this year, though how quickly those prices can be translated into the field remains to be seen. An AB salesperson at ASHG said that the three major advantages of its 3.0 SOLiD system were flexibility, accuracy, and throughput. AB recently announced it was placing six SOLiD instruments with the Broad, and eight more to the BGI.

What Happens Next?

Now, all eyes are on what’s next for next-gen sequencing. British hopes have shifted from Cambridge to Oxford, where Oxford Nanopore Technologies is making impressive strides on both the chemistry and engineering fronts, details of which should be forthcoming later this year.

Six thousand miles away, Complete Genomics will soon present details of its first assembled human genome and start taking orders for its $5,000 genome service. (CEO Clifford Reid will keynote the 2009 Bio•IT World Expo—see p. 11). Pacific Biosciences recently published the first examples of its real-time single-molecule sequencing technology. Helicos recently laid off one third of its workforce, but hopes for stronger sales under new CEO Ronald Lowy, who takes over from Steve Lombardi. With many other companies lying in wait, 2009 should see plenty more fascinating twists and turns.

This article also appeared in the Jan-Feb 2009 issue of Bio-IT World Magazine.

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