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Agencourt Bioscience, National Cancer Institute, Applied Biosystems, Covaris, ZS Genetics, Sequenom, National Center for Genome Resources, Illumina, Franek Technologies, Helicos, Personalized Medicine Coalition

Agencourt to Sequence Cancer Samples for NCI Researchers
Agencourt Bioscience has won a contract from the National Cancer Institute to provide sequencing services for cancer research, the Beckman Coulter subsidiary said this week.
Under the agreement, which initially runs for one year with an option to renew for a second year, NCI research collaborators may request sequencing services for specific genes “at any time.”
Researchers will send Agencourt cancer samples and controls along with lists of genes or genome regions to be sequenced.
The goal is to provide NCI research collaborators “with a consistent, cost-effective, high-throughput sequencing resource,” according to Agencourt.
The sequencing services are performed “at this time by Sanger sequencing,” an Agencourt spokeswoman told In Sequence by e-mail. Projects will be similar in nature to the cancer sequencing projects that Agencourt has been conducting for Johns Hopkins University (see In Sequence 11/6/2007)  “but probably not as large,” she said.
Sequence trace data will be submitted to the National Center for Biotechnology information, and base calls will be placed in a database managed by the NCI. Agencourt will also develop a web site for project collaborators that will allow them to query the NCBI Trace database for additional metadata and relate these data to other experimental results and clinical data.
The contract has received an undisclosed amount of funding from the NCI. 

Covaris to Provide Sample-Prep Instrument, TriLink Reagents for ABI’s SOLiD
Applied Biosystems will sell Covaris’ sample preparation instrument to support its SOLiD sequencer, Covaris said this week.
Under the agreement, ABI will distribute and support the Covaris S2 sample-prep system. Covaris said the technology handles beads and generates both fragment and mate-pair libraries.
Jim Laugharn, president and CEO of Woburn, Mass.-based Covaris, said in a statement that the firm’s instrument “can be used for both high-intensity shearing of genomic DNA with one sample and for controlled, gentle mixing of enzymatic reaction beads in the next sample.”
Separately, TriLink Biotechnologies said last week that it is supplying reagents for ABI’s SOLiD system. As part of the agreement, TriLink is providing custom dye-labeled oligonucloetides.
TriLink, based in San Diego, manufactures custom oligonucleotides, modified nucleoside triphosphates, and synthesis reagents for the research, diagnostic and OEM markets.

ZS Genetics Receives Three Patents for EM Sequencing Platform
ZS Genetics has received three US patents related to its electron microscopy-based sequencing technology, the North Reading, Mass.-based company said this week.
The firm received patents No. 7,291,467, “Systems and methods of analyzing nucleic acid polymers and related components,” and 7,291,468, “Systems and methods of analyzing nucleic acid polymers and related components,” on Nov. 6; and patent No. 7,288,379, “Systems and methods of analyzing nucleic acid polymers and related components,” on Oct. 30.
According to the company, the patents’ claims cover methods for sequencing nucleic acids; for detecting, identifying and quantifying nucleic acids; and for computerized systems for genetic analyses.
ZS Genetics is developing a DNA sequencing platform that is based on taking detailed images of individual DNA or RNA molecules by electron microscopy (see In Sequence 2/20/2007).

Sequenom Added to Nasdaq Biotechnology Index
Following its semi-annual re-ranking, the Nasdaq Biotechnology Index has added Sequenom to the firms it covers.
Sequenom’s shares will start trading as part of the index on Monday, Nov. 19.
The firm’s shares have more than doubled since mid-September, following Sequenom’s announcement that it had licensed technology from Harvard University that it will use to develop a nanopore-based sequencing platform.
Sequenom was one of eight new firms added the Biotech Index, but it was the only non-therapeutics company added. The other seven firms are Beijing Med-Pharm, Cadence Pharmaceuticals, Eurand, Halozyme Therapeutics, Obagi Medical Products, Orexigen Therapeutics, and Theravance.
Index criteria include listing on the Nasdaq Global Market or Nasdaq Global Select Market, and meeting minimum requirements for market value, average daily share volume, and seasoning as a public company.

NCGR to Run Two Illumina Genome Analyzers In New Sequencing Center
The National Center for Genome Resources in Santa Fe, NM, said last week it plans to officially launch its New Mexico Genome Sequencing Center on Nov. 19.
The NMGSC, the product of a partnership between the NCGR and the New Mexico Institute of Mining and Technology, will use two Illumina Genome Analyzers in studies of an undisclosed assortment of diseases and crops.
NCGR President Stephen Kingsmore said the center, which will be able to generate about 400 megabases a day, will allow state researchers to study the molecular causes of diseases.
“We also are sequencing a variety of crops, which will allow us to develop new uses for those crops and breed improved crops that can withstand severe weather or disease,” Kingsmore added.
Part of the financial backing for the new center came from the New Mexico state government, NCGR said in January, when it secured $600,000 to buy its first sequencer.

Franek ‘Recommended’ Backup Power Provider for ABI and Illumina Next-Gen Sequencers
Franek Technologies said last week that both Applied Biosystems and Illumina have chosen it as their “recommended source” for providing their next-generation sequencing systems with battery backup power.
The company, which provides certified category III-3 laboratory battery backup power protection systems, “is now written into the site prep documents for both ABI's SOLiD System DNA Analyzer and Illumina's Genome Analysis System for all model 1206 configurations for North American and international installations,” Franek said in a press release.

Helicos Joins Personalized Medicine Coalition
Helicos BioSciences has joined the Personalized Medicine Coalition, the company said last week.
“Living in an era where patients will have the opportunity to have their genome sequenced, it’s essential for us to join the discussion on how society will deal with this scientific breakthrough,” Patrice Milos, Helicos’ vice president and chief scientific officer, said in a statement.
Founded in 2004, the PMC is an advocacy group aimed at “advancing the understanding and adoption of personalized medicine.”

The Scan

Y Chromosome Study Reveals Details on Timing of Human Settlement in Americas

A Y chromosome-based analysis suggests South America may have first been settled more than 18,000 years ago, according to a new PLOS One study.

New Insights Into TP53-Driven Cancer

Researchers examine in Nature how TP53 mutations arise and spark tumor development.

Mapping Single-Cell Genomic, Transcriptomic Landscapes of Colorectal Cancer

In Genome Medicine, researchers present a map of single-cell genomic and transcriptomic landscapes of primary and metastatic colorectal cancer.

Expanded Genetic Testing Uncovers Hereditary Cancer Risk in Significant Subset of Cancer Patients

In Genome Medicine, researchers found pathogenic or likely pathogenic hereditary cancer risk variants in close to 17 percent of the 17,523 patients profiled with expanded germline genetic testing.