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NIST, Applera, Bio-Rad, MJ Research, Stratagene, FDA, Epidauros Biotechnologie, Roche Molecular Systems, Third Wave, Caltech


NIST to Spend $6.3 Million to Improve Microarray Research

The National Institute of Standards and Technology will spend $6.25 million to develop a program aimed at identifying and addressing challenges in gene-expression measurement, validation, and quality control, NIST announced last week.

Over the next 5 years, the Metrology for Gene Expression Program will try to “improve the quality, reliability and comparability of gene expression measurements with microarrays,” NIST said in a statement.

To these ends, the group will work with microarray tool vendors and users in order to “evaluate sources of error and variability in measurement.” From this, the group hopes to “develop reference data, reference materials and measurement methods to enable quality assurance for the chemistry, detection methods and information processing used in microarray analysis.”

To illustrate one challenge in standardizing gene-expression data, the NIST said that one experiment using three different microarray platforms to measure the same sample found that “under the most stringent criteria the three agreed on only four out of 275 genes identified.”

“Enormous quantities of gene-sequence data are pouring out of labs thanks to dramatic gains in DNA sequencing technology, but that’s only a start,” NIST said. “The real question is how genetic information translates into biological activity.”

The External RNA Control Consortium, a group of almost 50 organizations from industry, academic labs, federal agencies and other key stakeholders, helped “inspire” the group, it said.

NIST has been working on the development of gene expression standards for at least a couple of years.

Calls seeking additional information about the program were not returned to BioArray News.

Applera Gets RT-PCR Patent; Files Suit Against Competitors

Last week, Applera was granted a patent on its real-time PCR instrumentation. That same day, the company sued Bio-Rad, Bio-Rad subsidiary MJ Research, and Stratagene for allegedly infringing the patent.

The patent, US No. 6,814,934, “Instrument for monitoring nucleic acid amplification,” was awarded Nov. 9. In a complaint filed with the District Court in Connect-icut on that day and obtained by BioArray News sister publication GenomeWeb News, Applera alleges that MJ Research’s Opticon, Opticon 2, and Chromo 4 systems; Bio-Rad’s iCycler iQ and MyiQ instruments; and Stratagene’s Mx4000 and Mx3000P instruments infringe the ‘934 patent.

The complaint seeks a permanent injunction against all three parties from infringing the patent and “an order that Bio-Rad, MJ Research, and Stratagene destroy their inventory of infringing instruments.” In addition, the suit seeks “compensatory damages in the form of lost profits, but not less than a reasonable royalty” resulting from the infringement.

In a statement issued today, Stratagene said that it is “in the process of evaluating the allegations set forth therein and the prosecution history for the ‘934 patent.”

The company noted that it is “a long-term licensee of Applied Biosystems, an operating group of Applera, for the manufacture, use and sale of thermal cyclers for use in PCR.”

Stratagene CEO Joseph Sorge said, “We hope to preserve our cooperative business relationship with both Applied Biosystems and Applera as we formulate an appropriate response and course of action.”

Bio-Rad officials could not be reached for comment.

In June, ABI successfully obtained injunctions against Bio-Rad, MJ Research, and MJ Research distributor Biozym in Germany, prohibiting these companies from manufacturing and selling thermal cyclers for real-time PCR.

FDA to Issue Final Guidance Document on Pharmacogenomics Data

The US Food and Drug Administration will issue the final guidance document for pharmacogenomic data submissions before the end of the year, according to Larry Lesko, director of the FDA’s Office of Clinical Pharmacology and Biopharmaceuticals.

The document will be “out by January 2005,” Lesko said during a lunchtime keynote address titled “How is the FDA Preparing for the Increasing Application of Pharmacogenomics in Drug Development?”Lesko was speaking last week at Scientific American’s Targeted Medicine conference in New York.

Organizational difficulties related to the recent presidential election and the requirement that “three people have to sign off” on the guidance in each of the FDA’s related centers contributed to the delay, he said. The guidance will appear on a special FDA website upon release, along with a companion Manual of Policies and Procedures and “frequently asked questions” documents, said Lesko. He did not disclose the website address.

Following an invited session on pharmacogenetics held Oct. 29 at the 54th annual American Society of Human Genetics meeting in Toronto, Lesko told BioArray News’ sister publication GenomeWeb News that the guideline’s release was not delayed because of revisions to the document itself. “It’s been done for about four weeks,” said Lesko. “There is no scientific reason it’s not going out.” He said then that the guidance would be issued as soon as final legal and other reviews of the document were completed.

The Jan. 1 due date follows a string of at least three previous, revised deadlines. Pharmacogenomics Reporter, also a BioArray News sister publication, reported in June that Lesko expected the completed guidance by the end of the summer. The regulatory agency had originally planned it to release by June 30.

“We’re in the final stages, and hope to release it [to FDA lawyers] by the end of July,” Lesko said in June. “It has been reviewed, vetted, and discussed.”

FDA to Release Theranostics Draft Guidance in Early 2005

The US Food and Drug Administration will release a draft of its diagnostic-therapeutic companion product guideline for public comment in February, said Larry Lesko, director of the FDA’s Office of Clinical Pharmacology and Biopharmaceuticals at Scientific American’s Targeted Medicine conference, held in New York last week.

No due date has yet been set for the final companion-product document, said Lesko.

According to BioArray News’ sister publication Pharmacogenomics Reporter, the “theranostics” draft guidance was originally slated for release by the end of the year.

Roche Licenses Polymorphism for Inclusion in CYP450 Test

Epidauros Biotechnologie has licensed a genetic polymorphism to Roche Molecular Systems to include in its AmpliChip CYP450 test, the Bernried, Germany-based company said last week.

Under the non-exclusive license, Roche can use a polymorphism of the promoter region of the CYP2D6 gene in discovery, production, and commercialization of the AmpliChip.

Roche will make an upfront payment to Epidauros and pay the company royalties on sales of the AmpliChip CYP450 test, which is currently available in the European Union. Roche has said in the past that it intends to file the product for approval in the United States.

Third Wave predicts ‘05 Molecular Dx Revenues of $23 Million-$26 Million

Third Wave Technologies expects revenues from clinical molecular diagnostic products to expand to between $23 million and $26 million in 2005, the com-pany said last week.

Third Wave said the revenue will be “driven chiefly by the company’s core genetics, cystic fibrosis, and HCV genotyping reagents.”

The company also held a conference call to detail expansion of its molecular diagnostic product development efforts to move the company past the core SNP detection technology products market it serves with its Invader-brand chemistry.

Third Wave generated $36.3 million in 2003. The company does not break down revenues for its molec-ular diagnostics business.

Separately, Third Wave was added to the Nasdaq Biotechnology Index as part of the exchange's semi-annual listing update, the exchange said last week.

Caltech To Use Grant Funds for Systems Biology Research

Caltech said today that a portion of a recently awarded $25.4 million grant will help fund systems biology research.

The grant, awarded by the Gordon and Betty Moore Foundation, will enable Caltech faculty to create “new nanoscale technologies to aid the emerging field commonly referred to as systems biology,” the school said in a statement.

Caltech defines systems biology as a methodology that uses, among other components, “specific gene expression as well as ... proteins expressed by genes. In many cases, systems biology depends on advances in genomics, which in turn is based upon large-scale assays of biological activity at much smaller scales.

“Nanobiotechnology promises to provide new means for such studies, ultimately at the level of individual cells and molecules,” Caltech said.

Caltech said it will use the money for “architectural modification and creation of new laboratories, professional and administrative staff, facilities operations and service contracts, state-of-the-art research equipment, and a networking/communication program to link Caltech researchers with their peers worldwide.”

The Gordon and Betty Moore Foundation focuses on “environmental conservation, science, higher education, and the San Francisco Bay Area,” the school said. The gift is part of a $300 million commitment the foundation made to Caltech in 2001.

The Scan

Study Reveals New Details About Genetics of Major Cause of Female Infertility

Researchers in Nature Medicine conducted a whole-exome sequencing study of mote than a thousand patients with premature ovarian insufficiency.

Circulating Tumor DNA Shows Potential as Biomarker in Rare Childhood Cancer

A study in the Journal of Clinical Oncology has found that circulating tumor DNA levels in rhabdomyosarcoma may serve as a biomarker for prognosis.

Study Recommends Cancer Screening for Dogs Beginning Age Seven, Depending on Breed

PetDx researchers report in PLOS One that annual cancer screening for dogs should begin by age seven.

White-Tailed Deer Harbor SARS-CoV-2 Variants No Longer Infecting Humans, Study Finds

A new study in PNAS has found that white-tailed deer could act as a reservoir of SARS-CoV-2 variants no longer found among humans.