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454 Collaborating With Pharmas for HIV Diagnostic Applications; Rival Solexa Unmoved

454 Life Sciences "is starting a number of collaborations" with undisclosed pharmaceutical companies to determine whether its newly launched sequencing technology could be used to identify drug-resistant strains of HIV, according to founder Jonathan Rothberg.

Speaking at the Genomes, Medicine and the Environment Conference this week, Rothberg also said his company's GS 20 instrument is "well on track" to being able to sequence a mammalian genome at 8X coverage for less than $100,000 by the end of 2006. It costs around $1 million to attain this kind of coverage using existing Sanger-style techniques, he said.

Rothberg has in the past said 454 plans to meet the $100,000 genome goal by the end of the year, but hasn't publicly defined the coverage he could generate until now.

That 454 is talking with drug makers on what are essentially molecular diagnostics applications is noteworthy because Roche, its marketing and commercialization partner, has allied itself with the company because it was able to obtain the option to use its platform if and when it can develop a diagnostic application.

Roche must "move out of PCR — it has finite applications, and molecular testing is evolving into miniaturization, into more sequencing, more patterns, more of that type of thing that PCR can't do," Shara Rosen, an analyst with Kalorama Information, an industry consultancy based in New York, told Pharmacogenomics Reporter in May.

Highlighting the sensitivity of the GS 20, Rothberg said it can now produce 20 million-40 million base pairs of "Phred 20 or above sequence," and said that 454 collaborators have used the instrument to sequence "well over 100" de novo genomes. He also said that the next-generation instrument can sequence more than 100 million "Phred 20 or better bases ... routinely."

But John West, CEO of rival Solexa, discounted 454's diagnostic stance and said focusing attention on downstream applications that are several years away should take a back seat to the research community, which is his immediate core market.

"Our focus has been, 'How do we get to the whole human genome?'" West told Pharmacogenomics Reporter's sister publication GenomeWeb News this week. It could take years for a company to win regulatory approval for an HIV strain-typing test — even one that has the backing of the world's largest molecular diagnostics company, and even for such a small virus as HIV.

"The real market in the real term is the research market," West said. He added that Solexa has in he past collaborated with drug makers for similar applications for Lynx's MPSS platform, and said he hopes to collaborate eventually with pharmas with the company's sequence-by-synthesis instrument. Solexa merged with Lynxin March.

West reiterated the company's goal of launching the platform by the end of the year and to begin generated revenue from it, first as a service, by the middle of 2006.


NIH, Advocacy Groups Award $10.8M to Fund Autism Genetics Research

Five institutes from the National Institutes of Health and three non-profit autism advocacy groups together have awarded five grants worth $10.8 million to three research groups studying the genetics of autism susceptibility, the NIH said this week.

The grants, to be awarded over the next five years, have been funded by the NIH's National Institute of Child Health and Human Development, National Institute on Deafness and Other Communication Disorders, National Institute of Environmental Health Sciences, National Institute Mental Health, and National Institute of Neurological Disorders and Stroke.

Voluntary organizations contributing funds are Cure Autism Now, National Alliance for Autism Research, and the Southwest Autism Research and Resource Center.

The grants have been awarded to three teams of investigators from the following institutions:

  • A collaboration between Rutgers University, the University of Medicine and Dentistry of New Jersey, and the Robert Wood Johnson Medical School, led by Linda Brzustowicz, James Millonig, and Veronica Vieland, respectively, for a project entitled "Identification and Functional Assessment of Autism Susceptibility Genes."
  • Cold Spring Harbor Laboratory, led by Jonathan Sebat, for a project entitled "Determining the Genetic Basis of Autism by High-Resolution Analysis of Copy Number."
  • Emory University, led by Michael Zwick, for a project entitled "Identifying Autism Susceptibility Genes by High-Throughput Chip Resequencing."

The NIH did not detail specific amounts awarded to each group.


Bio Research Says FDA Asks for Additional Data on Pharmacogenomic Technology

Bio Research Support said this week that the US Food and Drug Administration has asked the company for additional data on the TranscriptPanel, a proprietary method of applying commercially available genomics tools to accelerate drug-gene interaction studies.

According to Jim Novakoff, president of Bio Research Support, the company submitted data derived from the technology to the FDA under the voluntary genomic data submissions program the agency initiated earlier this year. Novakoff said the company provided data on the drug Benadryl in order to demonstrate how the TranscriptPanel technology worked and to obtain approval to incorporate data from the technology in new drug application submissions.

"What we want to be able to do is incorporate [the TranscriptPanel] into clinical trials," he said. As an example, he said that drug-discovery firms could use the technology to increase the speed and lower the costs of toxicology studies for potential drugs. "The FDA has to be comfortable with the results we're giving before they'll allow us to work with them and pharma companies."

Novakoff said that Bio Research conducted a study wherein Benadryl was administered to 25-year-old, healthy males.

"We were able to figure out how [the drug] worked, why it was effective in suppressing immune response, why it was effective in helping with Parkinson's [disease], and ... we were able to identify which variant of Parkinson's it would be helpful for and which it would not," Novakoff told PGx Reporter's sister publication GenomeWeb News.

He added that the company was also able to identify other indications for which Benadryl might be effective in treating, including cancer.

The work was done in collaboration with General Electric Healthcare, which provided CodeLink chips; Genus BioSystems, which conducted wet lab work; and GeneGo, which supplied its MetaCore data analysis platform, Novakoff said. Warner-Lambert, which makes Benadryl, was not involved, he noted.

"We submitted [these data] to the FDA and asked what they thought," Novakoff said. "They said, 'So far, so good, but you need to do a whole lot more.'"

He said that the FDA has asked for a variety of additional information, including how Bio Research plans to "deal with tracking two medications or more in each patient simultaneously."

He noted that the data already submitted to the FDA was obtained through a study administering Benadryl to people not taking any medications. The FDA asked, "What happens if you add Benadryl to the cocktail of medicines someone is already taking?" Novakoff said.

He said he expects Bio Research to be able to generate the data requested by the FDA within about six months.


New US Legislation Could Be Boon for Forensic DNA Testing Shops

DNA-based forensic testing companies would benefit from a new federal bill that seeks to allow law-enforcement officials to obtain DNA from arrested suspects and illegal immigrants and upload the data into a federal DNA database.

The bill has passed the US House of Representatives and Senate and will have to be signed by President Bush in order to become law.

Currently, only convicted felons can be included in the federal DNA database, called the Combined DNA Index System, or CODIS. Five states authorize DNA testing of many arrested suspects, but the states are prohibited from uploading the DNA profiles into CODIS.

If the new legislation is passed, states will be allowed to upload DNA profiles from arrested suspects into the CODIS database. This could potentially result in millions of individuals being added to the database in coming years, according to forensics company Orchid Cellmark.

In addition, the new legislation will authorize the US Department of Justice to collect arrestee samples from all federal and military offenders. This could potentially involve an estimated 250,000 new DNA profiles annually.

The new legislation will also allow DNA samples to be taken from immigrants trying to cross the US border illegally. This could potentially affect 300,000 individuals each year.

Under the provisions of the bill, federal DNA grant money authorized under the 2005 President's DNA Testing Initiative, or Justice for All Act, can be used for forensic DNA testing of arrestees.

The bill, which is part of the Violence Against Women Act of 2005, or Senate Bill 1197, is now being finalized by Congress. Once finalized, it will be presented to President Bush for his signature.

If passed, the bill is expected to increase the use of forensic DNA testing, which would benefit forensic DNA testing companies such as Orchid, Cluefinders, and DNA Diagnostics.

More information about the bill can be found on the Library of Congress website.


Proteomic, Genomic, Bioinformatic Research Could Benefit From NIH's New $41.5M Clinical and Translational Research RFAs

The US National Institutes of Health last week issued a request for applications for $41.5 million in grants to support the creation of centers, departments, or institutes within academic health centers to encourage the combination of clinical and translational science.

The grants may help genomics, proteomics, and bioinformatics research through their focus on topics such as the development of biomarkers for research purposes; clinical informatics for longitudinal studies; development of research devices and methods that could be used in patients' homes; and predictive toxicology in human populations.

The grants will also support biomedical informatics as "the cornerstone of communication within the [new research centers], and with all collaborating organizations," the NIH said.

The Institutional Clinical and Translational Science Awards will issue four to seven grants totaling $30 million to fund the creation of these organizations, and it will issue 50 one-time grants totaling $11.5 million to help academic centers prepare a future CTSA application.

The research bodies created by the grants should facilitate faculty "to conduct original research, develop graduate and postgraduate training curricula," and lead integrative programs, the NIH said.


Despite Verdict, Stratagene Still Free to Sell Competent-Cell Products — for the Moment

Stratagene is free to sell its competent-cell products until a district court addresses the suit between it and Invitrogen again, according to an Invitrogen official.

Invitrogen said that a US appeals court ruled in its favor in a four-year-old patent-infringement suit against Stratagene. The appeal overturned a 2002 decision by a federal district court in Texas and ruled that Stratagene infringes a patent involving a process for developing competent-cell products.

The ruling that "substantially all" of the chemically competent cell products sold by Stratagene infringe Invitrogen's patent means that the suit will be remanded to the US District Court for the Western District of Texas, which will resolve remaining issues, such as possible damages injunctions, and any of Stratagene's remaining defenses.

"They also will address some of the invalidity defenses Stratagene had raised, and found that, based on the defenses, that our patent was valid," Alan Hammond, chief intellectual-property counsel of Invitrogen, told Pharmacogenomics Reporter's sister publication GenomeWeb News.

"We've asked for damages and injunctions in the district court," said Hammond. He estimated that the district court would be likely to address the suit within three to six months. When the court would resolve the matter is less clear, he said.

According to Hammond, along with documents Stratagene filed with US Securities and Exchange Commission, Invitrogen originally sued Stratagene over the competent-cell patent in March, 2001. A November, 2001, summary judgment by the US District Court for the Western District of Texas initially found no infringement of Invitrogen's competent-cell patent No. 4,981,797, a decision that was reversed by the Federal Circuit Court of Appeals in May, 2003.

After that point, the case was sent back to the district court, which found Invitrogen's '797 patent invalid in January, 2004. The current finding by the Federal Circuit Court of Appeals, triggered by an Invitrogen appeal, holds that Stratagene indeed infringed Invitrogen's '797 patent.

"The appeals court has made a final hearing on [the lawsuit], and unless they try to have some sort of re-hearing, it will go back to the district court," said Hammond. Otherwise, the issue of whether infringement took place has been resolved, he said.


Investment Bank Downgrades ABI for 'Modest' Revenue Projections

An investment bank last week cut its outlook for Applied Biosystems for having "modest" revenue projections and other reasons, according to CBSMarketwatch.

J.P. Morgan cut ABI's shares to "underweight" from "neutral," citing valuation and the lack of catalysts, CBSMarketwatch said.

The news service said the J.P. Morgan broker "told clients its concerns include the modest top-line growth projections, a lack of near-term uses of cash and the absence of visible near-term catalysts."


BioMérieux and ExonHit Extend Alliance to Develop Microarrays for Early Cancer Detection

BioMérieux and ExonHit have extended their collaboration for six years to develop microarray-based diagnostics for early cancer detection, the firms said last week.

The alliance began in 2003 with the aim of developing diagnostics for breast cancer. It has now been enlarged to other types of cancers, including colon, prostate, and lung.

The objective of the collaboration is to develop microarrays that can detect genomic cancer markers in blood or tumor samples. The chips would be based on ExonHit's gene-expression patents and bioMérieux's diagnostics experience.

Terms of the agreement call for ExonHit to grants bioMérieux an exclusive license to use its technology and methods in the field of blood diagnostics, gene profiling, and microarray design.

In exchange, bioMérieux will fund ExonHit's R&D costs for each cancer studied. There will be a minimum of five research programs. ExonHit will also receive milestone payments for each key milestone that is reached as well as royalties on future product sales, the partners said.

Financial details were not disclosed.

Filed under

The Scan

Billions for Antivirals

The US is putting $3.2 billion toward a program to develop antivirals to treat COVID-19 in its early stages, the Wall Street Journal reports.

NFT of the Web

Tim Berners-Lee, who developed the World Wide Web, is auctioning its original source code as a non-fungible token, Reuters reports.

23andMe on the Nasdaq

23andMe's shares rose more than 20 percent following its merger with a special purpose acquisition company, as GenomeWeb has reported.

Science Papers Present GWAS of Brain Structure, System for Controlled Gene Transfer

In Science this week: genome-wide association study ties variants to white matter stricture in the brain, and more.