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Scientists Compare Genome Analyzer, SOLiD

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In an effort to determine which second-generation sequencing platform to get for their institution, researchers at Columbia University compared the ability of the Illumina Genome Analyzer and Applied Biosystems SOLiD sequencers to accurately detect mutations in a mutant strain of C. elegans.

In their study, which was based on data generated last spring and published in PLoS One in late 2008, the scientists found that when using similar coverage and mapping criteria, the SOLiD platform led to fewer false-positive variants than the GA, while the GA determined fewer false-negative variants.

The scientists acknowledge that their comparison is merely a "snapshot" taken during "a technological tornado," and that the results are likely already outdated.

Based on their results, and in order to serve the needs of a variety of users, the Columbia researchers chose to acquire both an Illumina GA and an ABI SOLiD.

The study started last spring "with a basic dilemma that many institutions face: we had a budget to get a sequencer, and it spurred discussions among the faculty regarding what technology we should pursue, and whether we should pursue only one technology or both," says Itsik Pe'er, a professor of computer science at Columbia University and an author of the study. "There are trade-offs in terms of keeping diversity versus maintaining different pipelines."

At the time, Columbia had already ordered a 454 Genome Sequencer, so the decision was between an Illumina Genome Analyzer or an ABI SOLiD.

In their analysis, the researchers focused on a 4-megabase region, an area to which they had previously mapped the mutation causing the phenotype of the mutant C. elegans strain. Both platforms detected the variant that gives rise to the mutant phenotype of the C. elegans strains.
The Illumina platform called more small insertions and deletions in the region than the SOLiD, though the researchers did not validate all of these indels.

Julia Karow

Datapoint

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DNAVision's AgriFood subsidiary, which offers biosafety level 3 laboratory services, will provide new services including next-generation sequencing after it moves to a new facility.

Sequencing Notes

There's been all sorts of news out of Helicos BioSciences recently. The company announced that it had signed a definitive agreement with institutional and current investors to raise about $18.6 million through a private placement of its shares; net proceeds were expected to be about $17.9 million. Not long after, Helicos disclosed that it would pay down $10 million of its $20 million loan from GE Capital by the end of 2008. Finally, the company said it was planning to place a sequencing system with the Broad Institute at no cost early this year.

The J. Craig Venter Institute will use a sample prep system from Pressure BioSciences for a research project that's part of the NIH-funded Human Microbiome Project.

Funded Grants

$2,023,275/FY 2008
Targeted 2nd generation sequencing in phenotyped Framingham & PGP populations
Grantee: George Church, Harvard University
Began: Sep. 30, 2008; Ends: Jun. 30, 2010
According to the abstract, Church and his team aim to "develop, demonstrate, and validate a pipeline for high-throughput, low-cost targeted resequencing of all human exons based on next-generation sequencing techniques" with the goal of using sequencing "to characterize genotypes and genetic variation in genome-wide medical targets."

$406,968/FY 2008
SCODA DNA extraction to normalize species representation
Grantee: Andre Marziali, Boreal Genomics
Began: Sep. 26, 2008; Ends: Jul. 31, 2010
With this funding, Marziali will "apply our SCODA technology for concentrating and purifying nucleic acids to perform integrated extraction and fragment length selection in a single automated step, in order to reduce the time and labor required to produce clone libraries from contaminated samples."

The Scan

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A computational approach presented in PLOS Computational Biology produced fewer false-positive species identifications in simulated and authentic metagenomic sequences.

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