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UCSD, Venter’s TCAG Pen Pharmacogenomics Collab

The University of California, San Diego and Craig Venter’s nascent Center for the Advancement of Genomics intend to use large-scale genome analysis to predict the occurrence and outcome of disease, with an initial focus on hypertension and cardiovascular disease.

In the hypertension study, UCSD will send DNA samples from a group of patients to TCAG for sequencing and SNP analysis. While TCAG conducts the sequencing, UCSD researchers will simultaneously run phenotyping tests.

UCSD actually began the hypertension study two years ago with a $2.9 million, four-year grant from the National Heart, Lung and Blood Institute as part of the NIH Pharmacogenomics network. Preliminary results will be announced next month at the American Society for Human Genetics meeting in San Francisco.

Asked what SNP-genotyping technologies TCAG researchers will use, or how many patients or samples will be tested, Heather Kowalski, a spokeswoman for the nonprofit, said its scientific teams involved in the collaboration “are meeting to hammer out these issues.”

Floundering, Lynx Closes $3M In Private Stock Placement

Lynx Therapeutics has completed a $3 million private financing round of common stock and warrants for common stock. The financing, made to certain undisclosed institutional investors, comprised the sale of 744,000 newly issued common shares at approximately $4.03 per share, and the issuance of warrants to buy 186,000 shares of common stock for around $9.91 per share.

“We will continue to consider various other financing options,” Kevin Corcoran, Lynx’s president and CEO, said in a statement.

In August, Lynx, of Hayward, Calif., reported $3 million in cash and cash equivalents, including restricted cash, and said it is “considering various other options, including additional equity financing.” Also that month, the company retained the Washington, DC-based investment bank Friedman, Billings, and Ramsey as a financial advisor.

In May, Lynx was delisted from the Nasdaq exchange and began trading on the Nasdaq SmallCap Market exchange. The company, which had been floundering financially since late last year, was ordered by the Nasdaq to transfer its common stock to the smaller market because Lynx’ market cap falls below the Nasdaq’s minimum requirement.

Pyrosequencing to Lay off 30 More In Cost-Savings Program

Pyrosequencing will lay off 30 staffers, on top of 40 sacked in August, as part of a new belt-tightening program that is expected to save the company between SEK45 million and SEK 55 million ($6 million to $7 million) annually.

The new corporate structure will be effective from Oct. 1 when Hans Johansson starts as president. Johansson was previously president of Personal Chemistry, which Pyrosequencing acquired last month.

In August, Pyrosequencing reduced its staff by around 40 people. After the new round of cutbacks, the workforce of the new company will be approximately 150 employees, with 85 based in Uppsala, the company said. Pyrosequencing also has facilities in Boston, Mass.; Cambridge, UK; and Constance, Germany.

Agencourt to Offer Discounted Sequencing Services to Invitrogen’s SAGE Customers

Agencourt Bioscience will become the preferred provider of gene sequencing services to customers of Invitrogen’s Serial Analysis of Gene Expression technology.

Terms of the deal call for Invitrogen’s I-SAGE kits to include discounted sequencing services from Agencourt.

Transgenomic Extends Licensing Deal with Geron

Transgenomic will provide an additional supply of modified nucleic acid building-block compounds to Geron, which will use the technology to synthesize one of its thiophosphoramidate-based telomerase inhibitor cancer drugs.

Transgenomic CEO Collin D’Silva said the extended non-exclusive licensing agreement will enable Transgenomic to manufacture phosphoramidate-based oligonucleotides and the chemical building blocks required for their synthesis “for use in diagnostic and therapeutic applications by other biotechnology, pharmaceutical and diagnostics companies to the mutual benefit of both Transgenomic and Geron.”

Geron said it will use the technology to help develop its cancer drug GRN163L, formerly known as GRN719.

PathBLAST Reveals Conserved Protein-Interaction Networks

Whitehead Institute scientists published a study in the Proceedings of the National Academy of Sciences this week in which they used a protein interaction network mapping program called PathBLAST to compare the interaction networks predicted by the entire genomes of S. cerevisiae (yeast) and the bacterium H. pylori.

PathBLAST, developed by Whitehead fellows Trey Ideker and Brent Stockwell, uses algorithms to represent chemical structures.

The study showed that both organisms had two similar pathways — one for catalyzing DNA replication and one involved in protein degradation — and that in both organisms these two pathways were integrated as a single network.

Impath Files for Chapter 11 Protection, Seeks $15 Million Bailout from Banks

Impath has applied for Chapter 11 bankruptcy protection in the US Bankruptcy Court for the Southern District of New York as the company develops a plan to reorganize.

As part of the bankruptcy process, Impath, which is believed to have snubbed an offer from rival Quest Diagnostics to acquire it, will ask the court to allow it to continue paying employees and maintain cash management programs, among other short-term goals [see 9/4/03 SNPtech Reporter].

The distressed diagnostics-services company has also asked the court to approve a $15 million Debtor-in-Possession financing facility. If approved, up to $3 million of this money will be available immediately on an interim basis, pending final approval of the full $15 million financing facility, to supplement Impath’s existing capital.

The bankruptcy filing will allow Impath “to conduct business as usual so that we may maintain the quality and availability of our products and services,” Carter Eckert, chairman and CEO, said in a statement this week. He added that all of the company’s facilities are “fully operational.”

US Genomics Wins $500K SBIR Grant to Develop Its Gene-Mapping Technology

US Genomics has received a $500,000 phase II SBIR grant from the National Science Foundation to develop its DNA-analysis and genomic-mapping technologies.

The grant is a follow-on to a phase I SBIR grant that helped the young company develop gene maps based on analyses of individual DNA molecules.

US Genomics said that the second grant will help optimize its nanofluidics; develop fluorescence-detection strategies; and design easier methods to prepare and isolate samples.

AstraZeneca Nabs Gene-Expression Patents from Discovery Partners

AstraZeneca has obtained worldwide, non-exclusive rights to patents held by Discovery Partners International for an in vitro gene expression-profiling technology.

Specifically, the patent portfolio covers the use of in vitro gene expression profiling as a response to drug-induced stresses for indicating toxicity of chemical compounds.

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The Scan

UK Funds to Stay Ahead of Variants

The UK has announced a further £29.3 million to stay on top of SARS-CoV-2 variants, the Guardian reports.

Push for Access

In a letter, researchers in India seek easier access to COVID-19 data, Science reports.

Not as Cold

Late-stage trial results are expected soon for an RNA-based vaccine that could help meet global demand as it does not require very cold storage, the New York Times writes.

Genome Research Papers on Microbes' Effects on Host Transfer RNA, Honeybee Evolution, Single-Cell Histones

In Genome Research this week: influence of microbes on transfer RNA patterns, evolutionary relationships of honeybees, and more.