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BC Cancer Agency's GSC Installs 8 More SOLiDs for Cancer Genome Projects; Also Plans Illumina Expansion

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By Julia Karow

This story has been updated to reflect that the GSC purchased a total of 10 SOLiD systems, including two it received last summer for evaluation, and to add comments from Life Technologies.

The Genome Sciences Centre of the British Columbia Cancer Agency in Vancouver has installed eight additional Applied Biosystems SOLiD 3 Plus instruments, adding to its existing fleet of 14 Illumina Genome Analyzers IIx, two SOLiD 3 Plus, and eight 3730 Sanger sequencers.

According to a Life Technologies spokesperson, the center purchased a total of 10 SOLiD systems, including the two it already had on site for evaluation since last summer.

Marco Marra, director of the GSC, told In Sequence last week that the center plans to use the 10 SOLiD units initially primarily in whole-genome cancer sequencing of breast and ovarian tumors. Over the next 12 months, the GSC also plans to expand its Illumina sequencing capacity.

Last year, Marra and colleagues Sam Aparicio and David Huntsman published two studies on sequencing breast and ovarian cancer genomes, respectively (IS 6/16/2009 and 10/13/2009), and "we will be building on those early interactions," Marra said.

In particular, the scientists are planning to sequence approximately 100 tumor samples, as well as matched normal DNA, over the next year or so, with breast and ovarian cancer being the "lead candidates" for the tumor type. Life Technologies will provide technical and bioinformatics support to make sure the project proceeds on time as part of the instrument deal, according to Jay Therrien, head of global SOLiD sales at Life Tech.

The GSC has been a longstanding customer of Illumina and received one of the first commercial Solexa sequencers in late 2006, before the company was acquired by Illumina in early 2007 (IS 7/3/2007). Last summer, the center gained its first hands-on experience with the SOLiD system, when it installed two of the instruments (IS 6/30/2010).

"We have been very pleased with the performance of the machine, especially recently, and we see definite roles for it in our expanded plans for whole-genome sequencing," Marra said.

In its most recent tests, he said, the researchers "have seen extremely good SNP calling with the SOLiD platform, and certainly, the [operating] costs are more than competitive. We think it's got all the right ingredients to help us in our ambition to sequence cancer genomes."

In addition, he said, he and his colleagues have been "extremely impressed" by the service and support provided by Life Technologies for the instruments, and both the performance and the service "played a significant role in our decision to beef up our SOLiD platform."

According to Therrien, the SOLiD technology "has matured significantly over the last six months," both in terms of data accuracy and sequencing cost reductions. He said the $6,000 and $3,000 reagent costs that Life Tech has cited for human genome sequencing on the SOLiD 4 and 4hq platforms, respectively, "are valid," adding that "we commit to those contractually."

Over the last few months, he said, "probably the biggest market segment for us has been cancer research centers," and more of these centers are adopting the SOLiD platform, though he could not provide specifics at this time.

But the GSC also plans to install additional Illumina sequencers over the next year or so, though Marra said it is premature to reveal details yet. "We haven't bailed out on Illumina," he said.

The GSC will continue to use its Illumina instruments — currently all GAIIx, though Marra said the center would like to exchange them for HiSeq 2000 soon — for a variety of applications and sequencing library types, whereas the SOLiD platforms — currently version 3 Plus, with plans to upgrade to version 4hq by the end of the year — will initially take their place in whole-genome cancer sequencing. The center has not yet gained much experience with other library types on the SOLiD platform, he said.

Marra said he recognizes that maintaining pipelines for two different sequencing platforms is a challenge — one of the reasons the Wellcome Trust Sanger Institute cited when it returned five SOLiD instruments in late 2008 in favor of increasing its fleet of Illumina instruments (IS 12/15/08). "How well we actually manage to do it, I suppose, only time will tell," according to Marra.

However, he said, "the benefits that we see before us as a consequence of having the SOLiD outweigh the potential downside."

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