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Caltech, Massey University, Otago University, Friedrich Loeffler Institute, Illumina, Affymetrix, Codon, Duke, MIT, Blue Heron, Van Andel Institute, Spectrum Health

Caltech’s Beckman Institute Closes Sequencing Facility
The California Institute of Technology’s Beckman Institute closed its sequencing service facility on March 1, In Sequence has learned.
In a letter to users announcing the closure, BI professors Judy Campbell and Barbara Wold explained that the facility was not able to compete with “commercial DNA sequencing services with 24-48 hour turn-around times, favorable pricing structures, and high reliability.”
Campbell and Wold note in their letter that “several major Caltech DNA user labs have migrated their sequencing business to these commercial sources over the past two years, and others let us know they are likely to do so.”
While acknowledging that it was a “difficult decision” to close the facility, Campbell and Wold explained that “the commercial services benefit from economies of scale and robustness of performance they get from having multiple machines and large staffs. This mandated that we change with the times.”
The BI facility had one 48-well ABI 3730 and its cost per sample was $10. BI now recommends that Caltech researchers use sequencing services from Santa Monica-based Laragen, which charges $7 per sample, or the City of Hope DNA sequencing lab in Duarte, Calif., which charges $6 per sample.

New Zealand Universities Partner to Purchase Sequencing Equipment
New Zealand’s Massey University and Otago University said earlier this month that they plan to jointly buy NZ$2 million ($1.4 million) worth of next-generation sequencers.
The universities did not disclose what technology they intend to purchase, but noted in a press release that it will “produce DNA sequences 1,000 times faster than existing technologies.”
Otago's Department of Anatomy and Structural Biology and the Allan Wilson Centre for Molecular Ecology and Evolution at Massey's Palmerston North campus will purchase the sequencers, which will be linked to a shared genetics database.
They plan to make the technology available through a nationwide high-speed internet network for research and education.
"Purchasing these sequencers will be a first step in forming a New Zealand Genomics Consortium to provide New Zealand scientists with access to large, expensive equipment," said Tony Reeve, director of Otago's Cancer Genetics Laboratory, in a statement.

German Animal Health Research Center Installs 454 GS 20
Roche Applied Science said this week that Germany’s Friedrich Loeffler Institute on Riems Island, the Federal Research Institute for Animal Health, has installed the Genome Sequencer 20 system manufactured by 454 Life Sciences and distributed by Roche.
The institute will use the system for virus identification and research. Roche said that the system can analyze sixteen influenza virus genomes in a single work step.

Jury Says Illumina Infringed Five Affy Patents, Orders $16.7M Royalty Payment; Illumina to Appeal
A jury has found Illumina guilty of infringing five Affymetrix patents and has required it to pay Affy $16.7 million in royalties, according to a verdict filed last week in a US District Court in Delaware.
Illumina plans to appeal. In a statement, Illumina CEO Jay Flatley said that the verdict was made "without consideration of the validity and enforceability of any of the patents asserted by Affymetrix" and is therefore "preliminary."
Flatley added that the case will now proceed to another phase, during which Illumina intends to prove that Affy's claims are "invalid and unenforceable." In the meantime, he said, "we will continue to sell the products that are the subject of this suit and no damages will be payable to Affymetrix until all appropriate appeals have been taken."
Affymetrix sued Illumina in July 2004 for allegedly infringing six patents, but the company later dropped one patent from the case. Affy sought lost profits, royalties, damages for willfulness, and a permanent injunction that would prohibit Illumina from using the patented technology.
The jury on March 12 found that Illumina had infringed 11 of 12 claims but did not find that Affymetrix was entitled to the damages it sought. Instead it decided that Illumina must pay Affy a 15-percent royalty rate, which amounted to $16.7 million for sales through the end of 2005.
Flatley said that this amount is "less than half" the total amount of damages that Affy sought in the trial.

Codon, Duke, MIT Sue Blue Heron for Infringing IP to Synthesize DNA
Codon Devices, Duke University, and the Massachusetts Institute of Technology have sued Blue Heron Biotechnology for allegedly infringing five US patents that Codon has licensed exclusively from the universities.
The suit, filed in a US District Court in Delaware, claims that Blue Heron is infringing four Duke patents used to map gene mutations, manipulate genes, and fractionate DNA molecules.
The claimants also say Blue Heron is infringing an MIT patent used to screen for genetic variation.
The plaintiffs claim that Blue Heron, by using its GeneMaker platform to hybridize and synthesize oligonucleotides and build genes from duplexes, is infringing these patents, some of them willfully.
In the complaint, Codon, Duke, and MIT seek damages and a permanent injunction that would bar Blue Heron from using the IP.
The patents, which cover DNA error correction technologies, include US Patent Nos. 5,459,039; 5,556,750; 5,679,522; 5,702,894; and 5,750,335, all of which are exclusively licensed to Codon Devices, Codon said in a statement.
In a statement on its website, Blue Heron said “there is no basis for the allegations of patent infringement.”
CSO John Mulligan said Blue Heron “has always maintained the highest levels of integrity in matters of intellectual property,” and said the company “intends to vigorously defend against these baseless claims of patent infringement.”
The company said it expects the lawsuit to have “no material impact” on its business.

Van Andel Institute, Spectrum Health Create Lab to Study Genomics, Proteomics of Disease; Next-Gen Sequencing Under Consideration
The Van Andel Institute and Spectrum Health have created the Center for Molecular Medicine, a lab that will study genomics and proteomics for application in cancer, heart disease, mental illness, and other diseases, Spectrum Health said last week.
Spectrum, a non-profit group that operates seven hospitals in Western Michigan, said the CMM, located in Grand Rapids, has $6 million in funding.
The CMM will use Van Andel’s infrastructure and employees along with Spectrum’s clinical lab and research resources.
Van Andel CEO and Chairman David Van Andel said Spectrum has “a large patient population which allows us to apply what we're learning directly into the clinical setting."
The CMM will focus on multiplex protein detection and gene-expression profiling. A Van Andel spokesman told In Sequence that the center is “currently in the process of evaluating 454 sequencing technology,” but added that it “has not set a timeframe on any decisions.”

The Scan

Myotonic Dystrophy Repeat Detected in Family Genome Sequencing Analysis

While sequencing individuals from a multi-generation family, researchers identified a myotonic dystrophy type 2-related short tandem repeat in the European Journal of Human Genetics.

TB Resistance Insights Gleaned From Genome Sequence, Antimicrobial Response Assays

Researchers in PLOS Biology explore M. tuberculosis resistance with a combination of sequencing and assays looking at the minimum inhibitory concentrations of 13 drugs.

Mendelian Disease Genes Prioritized Using Tissue-Specific Expression Clues

Mendelian gene candidates could be flagged for further functional analyses based on tissue-specific transcriptome and proteome profiles, a new Journal of Human Genetics paper says.

Single-Cell Sequencing Points to Embryo Mosaicism

Mosaicism may affect preimplantation genetic tests for aneuploidy, a single-cell sequencing-based analysis of almost three dozen embryos in PLOS Genetics finds.