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Illumina, Affymetrix, Keygene, University Medical Center Utrecht, NIH, NCI, National Research Council, New England Journal of Medicine

Illumina to Pay Affy $90M to Settle Patent Suits, Cease Litigation
Illumina said last week that it will pay Affymetrix $90 million to settle all ongoing patent lawsuits between the two companies, and that both firms have agreed to a covenant not to sue for use of current and future products.
The agreement ends patent litigation between the companies in the US, Germany, and the UK dating back to 2004.
Last March, a jury sided with Affy in the first phase of the litigation, finding that Illumina's products infringed “one or more claims” of Affy’s patents and awarding total damages of more than $16.7 million for the period of 2002-2005 and a royalty of 15 percent.
Last fall, Affy filed another round of suits, in which it claimed, among other allegations, that Illumina’s Genome Analyzer infringes two of its US patents (see In Sequence 10/30/2007).
The next phase of the case, which was to focus on the validity of Affymetrix's patents, was supposed to begin on Feb. 11, 2008.
The terms of the settlement announced last week call for Illumina to make the one-time payment of $90 million, without admitting liability.
Illumina said the settlement dismisses all litigation and that it will pay Affymetrix when the courts formally dismiss the suits.
The agreement formally dismisses with prejudice Illumina’s counterclaims and grants Illumina, its customers, and affiliates a perpetual covenant not to sue for “making, using, or selling any of Illumina’s current products, evolutions of those products and services related thereto,” Illumina said.
Affy also agreed to extend the covenant not to sue to cover the making, using, or selling of Illumina products based on future technology developments.
The deal covers all fields except for photolithography, a field in which Illumina does not operate.
The suits were filed in the United States District Court for the District of Delaware; in Regional Court in Dusseldorf, Germany, and in the High Court of Justice, Chancery Division Patents Court in London.

KeyGene to Use 454 GS-FLX in Bacterial, Viral Sequencing Services Deal with UMC Utrecht
Keygene will provide genomic sequencing services for University Medical Center Utrecht using its 454 GS-FLX system, the Dutch company said this week.
Under the agreement, Keygene will provide sequencing services for bacterial and viral sequencing projects as well as for other “more complex” studies, as well as its own Seqtag DNA sample identification tags.
Keygene’s manager of business development, Mark van Haaren, said the contract will allow the company to “improve our sequencing capabilities, and the close interaction with the UMC Utrecht scientists will allow us to develop and implement new sequencing applications.”
The company also said the agreement allows it to test out new research applications on the GS-FLX.

NCI to Grant About $11M for Cancer Molecular Analysis Technologies
The National Institutes of Health said last week it will support a number of new grants to develop new cancer-related molecular technologies under the National Cancer Institute’s Innovative Molecular Analysis Technologies Program.
Applications for these grants are due on March 11, May 29, and Sept. 24, 2008.
NCI will grant a total of $3 million to between 10 and 15 applicants for cancer molecular analysis tools. Applicants can request up to $500,000 over a three-year period. These grants would support tools that could be used to develop profiling technologies for DNA, RNA, proteins, and other biomolecules, including “technologies for the massively parallel analysis of the expression of genes that would overcome limitations of the existing multiplexed gene expression technologies.” More information can be found here.
NCI will grant a total of $1.5 million to fund between 10 and 15 grants for research that will evaluate the performance of new molecular analysis technologies and will focus on the application, rather than development, of these technologies. Further information is available here.
NCI also will use $1.5 million to support four or five grants for evaluating the performance of new molecular analysis technologies and developing applications for a cancer-relevant biological system. Applicants may apply for up to three years of funding. The research should focus on applications for the tools or methods and could include in vitro, in vivo, or in situ technologies. For more information, click here.
Another NCI grant will offer up to $500,000 in fiscal 2009 for up to five programs to develop or study the application of technologies for sample preparation, purification, processing, and handling. Applicants may apply for funding over two years. The technologies involved could include tools, techniques, tools, instruments and devices, but not software or informatics solutions. Click here for more information.
The NCI also will grant around $500,000 in the coming year for up to three other grants for maximizing the quality and utility of biospecimens for molecular analyses of cancer cells. This FOA also will support development of methods and tools to assess sample quality and to preserve sample integrity and to establish criteria for verifying and assessing quality control. More information is available here.
The NCI plans to support between three and five Phase I and Phase II SBIR grants seeking to develop and eventually commercialize molecular analysis technologies with around $1.3 million. Applicants may seek up to $100,000 a year for a total of two years for Phase I programs, while Phase II applicants can request up to $750,000 per year up to three years. For more information, click here.
Another program will use the STTR grant mechanism to fund Phases I, II, or III and Phase I and II Fast-Track applications with a total of $1.3 million for molecular analysis technologies. The NCI will support between three and five small businesses with up to $100,000 per year for up to two years for Phase I research, and a total of $750,000 for up to three years for Phase II research. Click here for more information
A related program will grant up to nearly $1.3 million for between three and five SBIR grants with budgets up to $100,000 per year for up to two years. This grant will also will be aimed at supporting research into technologies to be used in the preparation, purification, processing, and handling of cancer-relevant samples. More information is available here.
The NCI also will support cancer-related sample technology development with approximately $1.3 million over one year for between three and five Phase I and Phase II SBIR technology development programs. Click here for additional information.

NRC Calls for More Sequencing, 'Omics' Tool Development for Plant Genomics Initiative
A federal cross-agency effort to plumb the secrets of plant life through genomics research should expand its sequencing capabilities and focus on developing new tools for epigenomics, transcriptomics, proteomics, metabolomics, and other so-called “omics” disciplines, according to a report published last week by the National Research Council.
The report, prepared by a committee of 12 experts in plant genetics and other fields, reviews the accomplishments of the decade-old National Plant Genome Research Initiative and recommends a number of future research directions and objectives.
Among those recommendations is a call to “expand plant genome sequencing, plant-associated microbial sequencing, plant-associated metagenome sequencing, and associated high-quality annotation.”
In order to meet this demand, the NRC report, available here, recommends that the NPGI expand its existing relationship with the DOE’s Joint Genome Institute and “empower” researchers “to access and utilize next-generation sequencing technologies for a broad spectrum of genomics and metagenomics discovery.”
NPGI was launched in 1998 as a way to coordinate research funding from multiple federal agencies. It is managed by the Interagency Working Group on Plant Genomics, which includes representatives from the National Science Foundation, the National Institutes of Health, the US Department of Energy, the US Department of Agriculture, the US Agency for International Development, the US Forest Service, and the Office of Management and Budget.
According to the report, the NPGI has awarded a total of 392 grants over the last 10 years totaling $774 million.
The NPGI has provided “a huge bang for the buck” over the last ten years, Jeff Dangl, a professor of plant genetics at the University of North Carolina at Chapel Hill and chair of the review committee, told In Sequence’s sister publication GenomeWeb Daily News.
When it comes to pitching the government for more funding, Dangl said, greater knowledge of the “three Fs” — food, fiber, and fuel — will be the centerpiece of plant biologists’ arguments. Dangl said that the challenge now is to “generate the three Fs in an environmentally sustainable way, and plant biology plays a huge role in that.”
Dangl said that in addition to the need for more sequencing and “omics” tools, there also is a need for greater emphasis on bioinformatics in the plant community.
“What we found is the same challenge in all of genomics,” he said. “How do you generate interoperable databases for different kinds of data? We can have really good ones for grasses, [but] how well does it talk to a tomato database? Or what can these say about the ripening of strawberries?”
According to the report, the NPGI’s centerpieces to date have been the sequencing of the Arabidopsis and rice genomes — projects that have led to a number of important discoveries.
— Abridged version of an article by Matt Jones, GenomeWeb Daily News staff reporter

NEJM Editorial Warns of Downside to ‘Premature’ Consumer Genomics Market
Testing services from companies like 23andMe, Navigenics, Knome, and DeCode Genetics are “premature attempts at popularizing genetic testing,” according to an opinion article in last week’s New England Journal of Medicine.
According to the article, these consumer-oriented tests “neglect key aspects of the established multifaceted evaluation of genetic tests for clinical applications” and could confound treatment or complicate doctor-patient relations.
While all of these companies claim that their tests should not be used as the basis for medical decisions, some physicians are concerned that customers for these tests will nevertheless begin seeking medical direction based on their results, according to the NEJM article.
The authors of the op-ed include Muin Khoury, director of the National Office of Public Health Genomics at the US Centers for Disease Control and Prevention; David Hunter, a professor of epidemiology and nutrition at the Brigham and Women’s Hospital at Harvard Medical School; and Jeffrey Drazen, an environmental health professor at Harvard who also serves as NEJM’s Editor-in-Chief.
The article, “Letting the Genome out of the Bottle Will We Get Our Wish?”, makes the case that the medical field and the public will not be ready to deal with the implications of consumer genomics until more translational medicine connects information from the vast amount of genome-wide association data to personal genomes in meaningful ways.
Khoury told In Sequence’s sister publication GenomeWeb Daily News last week that the field as it stands now should be considered “recreational genomics.”
“People think it’s like a big social genomic party, but it’s much more profound than that, [and] could have profound effects,” he said.
Khoury and his co-authors note in the article that there are three important issues that consumer genomic testing needs to address before it can become part of medical care: analytic validity, clinical validity, and clinical utility.
Khoury said that a personal genomic profile currently “doesn’t mean that much more than an alphabet soup.”
“If you’re willing to pay a thousand bucks for that and get a printout, that’s your choice,” he said, adding that some consumers may not know what they’re getting into, or how this market might develop.
“The bottom line here is that people are beginning to be concerned that there may be more harm than benefit,” Khoury explained. “And that’s why there have been calls for regulation” such as the Genetic Information and Nondiscrimination Act, which President George W. Bush has said he would sign but which has yet to make it to his desk.
Khoury and his co-authors said more translational research is needed that would connect genomic data to diseases and “show the meanings of these variants” before personal consumer genome profiles will be more useful in mainstream medicine
— Abridged version of an article by Matt Jones, GenomeWeb Daily News staff reporter

The Scan

Germline-Targeting HIV Vaccine Shows Promise in Phase I Trial

A National Institutes of Health-led team reports in Science that a broadly neutralizing antibody HIV vaccine induced bnAb precursors in 97 percent of those given the vaccine.

Study Uncovers Genetic Mutation in Childhood Glaucoma

A study in the Journal of Clinical Investigation ties a heterozygous missense variant in thrombospondin 1 to childhood glaucoma.

Gene Co-Expression Database for Humans, Model Organisms Gets Update

GeneFriends has been updated to include gene and transcript co-expression networks based on RNA-seq data from 46,475 human and 34,322 mouse samples, a new paper in Nucleic Acids Research says.

New Study Investigates Genomics of Fanconi Anemia Repair Pathway in Cancer

A Rockefeller University team reports in Nature that FA repair deficiency leads to structural variants that can contribute to genomic instability.