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News Scan: Dec 16, 2008

Sanger Institute Returns Five SOLiDs to Life Technologies as BIG Picks up Eight
The Wellcome Trust Sanger Institute has returned five SOLiD sequencing systems that Applied Biosystems had placed at the institute a year ago, In Sequence has learned. The systems were returned to Life Technologies, the new firm formed by the recent merger of ABI and Invitrogen.
Separately, Life Technologies said this week that the Beijing Institute of Genomics of the Chinese Academy of Sciences has acquired eight SOLiD next-generation sequencing systems.
Jason Liu, senior director of SOLiD Commercial Operations at Life Technologies, told In Sequence last week that the instruments returned by the Sanger Institute were “sales demonstration units” that ABI had placed at the institute for a scientific collaboration on small cell lung cancer in December 2007.
In May of this year, ABI said that scientists were using the five instruments to sequence the genomes of a small cell lung cancer cell line and a non-cancerous cell line to comprehensively cover genomic variations in both cell lines.
The return of its SOLiD sequencers comes about a month after the Sanger Institute said that it had purchased 11 additional Illumina Genome Analyzer sequencers, adding to 26 Illumina units already on site (see In Sequence 11/18/2008).
At the time, Julian Parkhill, director of sequencing at the Sanger Institute, told In Sequence that it was easier and less costly to add Illumina sequencers to the institute’s existing pipeline, and that the decision was not a verdict on the merit of the SOLiD or the Genome Analyzer.
"The Sanger Institute looked carefully at all available machines for its recent sequencing expansion and how they might fit with its pipelines for sequence production," Parkhill told In Sequence via e-mail this week. "For these purposes, the Institute sought the minimal additional commitment in molecular biology and informatics over its existing large-scale capillary platforms."
He added that the institute will continue to review next-gen sequencing platforms.
During a conference call in October, an ABI official revealed that the company has been using the placement of SOLiD instruments with potential customers as a sales strategy (see In Sequence 10/28/2008).
The SOLiD units returned from the Sanger Institute “will be re-deployed into other strategic accounts within the European region,” according to Liu.
BIG previously had one SOLiD system in house. It plans to use the nine sequencers to explore mutation profiling of cancer genes, investigate genetic variation in model organisms, analyze microbes metagenomically, and discover and characterize novel microRNAs.
“By expanding our fleet of SOLiD Systems, we will benefit from the throughput, flexibility and sensitivity of these systems, which we expect will contribute greatly to major genomic initiatives, such as resequencing to identify pathogen genomics and genetics, cancer genetics, and to conduct individual research programs within the Institute,” Chung-I Wu, director of BIG, said in a statement.
The researchers also plan to use the SOLiD system, combined with the new SOLiD small RNA expression analysis kit, to investigate the role of coding and non-coding transcripts, in an effort to develop RNA expression profiles in stem cells.

Helicos to Place Single-Molecule Sequencer at Broad Institute at No Cost
Helicos BioSciences said this week in a filing with the US Securities and Exchange Commission that it is preparing to place a Helicos Genetic Analysis System at the Broad Institute.
The company said that it is providing the system to the Broad at no cost and that it expects to install it in early 2009.
Helicos said that it has recently improved its single-molecule sequencing chemistry and other aspects of the system so that it now generates approximately 100 megabases to 140 megabases per hour — an improvement over the 50 megabases per hour that the company reported in its third-quarter earnings statement.
The company said that the system provides median read lengths of 33 bases and has an approximate total error rate of 5 percent, including a substitution error rate of 0.5 percent.
Earlier this year, Helicos placed its sequencing system at Stanford University and genomic services firm Expression Analysis, but the company has not disclosed the financial terms for either of those agreements.

VisiGen to Continue as Life Technologies Subsidiary
The University of Houston said last week that VisiGen Biotechnologies, following its acquisition by Invitrogen (now Life Technologies), will operate as a wholly owned subsidiary and retain its name.
VisiGen President and CEO Susan Hardin, a former biology and biochemistry professor at UH, will continue as VisiGen’s research director.
The University of Houston holds an equity share in VisiGen, a spin-off of the university, and said it will receive nearly $500,000 from the initial installment of the deal, noting that the deal is the largest acquisition of a UH spin-off to date.
"In addition to the earliest experiments with this DNA sequencing technology being done on the UH campus before VisiGen moved to its own facilities, a collateral benefit of this spin-off to our university is that it provided a place for the training and employment of our graduates, with about half of VisiGen's employees being UH alumni," said John Bear, dean of UH's College of Natural Sciences and Mathematics, in a statement.
According to the university, VisiGen “achieved proof of concept” for its technology. The acquisition “will provide the catalyst needed to bring it to market through the development of critical technologies made possible with the new resources available to its researchers.”
Invitrogen merged with Applied Biosystems last month to form Life Technologies.

Life Technologies Confirms Closure of ABI's Connecticut Corporate Offices
Life Technologies, the recently merged combination of Invitrogen and Applied Biosystems, confirmed with In Sequence’s sister publication GenomeWeb Daily News last week that it will close ABI’s corporate offices in Norwalk, Conn., as part of efforts to eliminate redundant operations.
The firm will shutter the facility in July 2009, and corporate functions at that site will be transitioned to other locations, according to a Life Technologies spokesperson. The firm did not disclose how many positions would be eliminated as part of the closure, but several local media outlets in Connecticut reported that around 100 jobs will be lost as a result. Life Technologies also has not disclosed how many jobs would be transferred to other offices.
In advance of the completion of the merger, Invitrogen said in October that it expects $80 million in synergies, mostly from cost savings, in the first year after closing the deal. Part of those synergies were expected to come from corporate overhead reductions, “which unfortunately does include the elimination of redundant positions between the two companies,” the spokesperson said in an e-mail last week.

2009 MicroScale Bioseparations Meeting to Include Next-Gen Sequencing
The 2009 MicroScale Bioseparations meeting will include a session on next-generation sequencing technologies.
Talks will focus “on the role or non-role of electrophoresis in future genome sequencing,” according to Annelise Barron, a professor of bioengineering at Stanford University who organizes the all-day session with Kevin Ulmer, CSO of Genome Corp.
The meeting will take place in Boston Feb.1-5, 2009, with the session on next-gen sequencing scheduled for Feb. 4. More information can be found here.

Life Technologies, Illumina Added to Nasdaq-100 Index
Life Technologies and Illumina are among the firms that have been added to the Nasdaq-100 Index.
Both firms will be added to the index effective Dec. 22.
The Nasdaq-100 was established in January 1985 and represents the largest non-financial domestic and international securities listed on the Nasdaq based on market capitalization.
Life Technologies, formed by the recent merger of Invitrogen and Applied Biosystems, has a market cap of around $3.8 billion. Illumina’s market cap is roughly $2.7 billion.

Leerink Swann Cautiously Optimistic About Next-Gen Sequencing in ‘09
Citing a survey that said that university-based researchers are seeing reductions in their budgets, investment bank Leerink Swann said it was cautiously optimistic about the adoption of next-gen sequencing next year.
The investment bank said that a survey of 117 university-based life science researchers found that 68 percent of them are seeing reductions in their budgets. “While improved NIH funding looks to be a silver lining, we are particularly cautious on capital equipment trends,” Leerink Swann analyst Isaac Ro wrote in the report.
Among the researchers surveyed, 45 percent said that DNA sequencing products were a high priority, which benefits firms such as Illumina, said Leerink Swann. The bank also cautioned that “high price tag” of the next-generation sequencing instruments “could pose a barrier for some new customers.”

“Unfortunately, tighter budgets mean that certain research tools, even those that add value, will go by the wayside,” according to the report. “Not surprisingly, capital equipment was most often cited as the first thing to go. While we believe transformative technologies such as [next-generation sequencing] and genotyping arrays will continue to see good adoption, we believe basic lab equipment and high-end instrumentation will be challenged in the current environment.”

The Scan

Enzyme Involved in Lipid Metabolism Linked to Mutational Signatures

In Nature Genetics, a Wellcome Sanger Institute-led team found that APOBEC1 may contribute to the development of the SBS2 and SBS13 mutational signatures in the small intestine.

Family Genetic Risk Score Linked to Diagnostic Trajectory in Psychiatric Disorders

Researchers in JAMA Psychiatry find ties between high or low family genetic risk scores and diagnostic stability or change in four major psychiatric disorders over time.

Study Questions Existence of Fetal Microbiome

A study appearing in Nature this week suggests that the reported fetal microbiome might be the result of sample contamination.

Fruit Fly Study Explores Gut Microbiome Effects on Circadian Rhythm

With gut microbiome and gene expression experiments, researchers in PNAS see signs that the microbiome contributes to circadian rhythm synchronicity and stability in fruit flies.