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Applied Biosystems; Celera; Wellcome Trust; European Bioinformatics Institute; CLC Bio; RainDance Technologies France SARL; Ben and Catherine Ivy Foundation; Translational Genomics Research Institute; Stanford University; HHS Secretary’s Advisory Committe

Newly Split Celera and ABI Settle on Terms for Sharing Tech and IP, Divvy Up Dx Market
Applied Biosystems and Celera may have split into two independently operated companies on July 1, but they will continue to share certain instruments, technologies, and intellectual property, according to documents filed with the US Securities and Exchange Commission last week.
According to the terms of an operating agreement disclosed last week, ABI will continue to partner on certain technology-development projects and will maintain some co-marketing arrangements with Celera, but will be restricted in its ability to sell some of its tools in the diagnostic market.
The agreement gives Celera “continued access” to ABI’s capillary electrophoresis sequencers and associated consumables and permits Celera to continue development of “a new FDA-compliant diagnostic instrument based on [ABI’s] CE technology.”
Kathy Ordoñez, previously president of Celera and now CEO of the independent firm, disclosed in January that Celera was developing a diagnostic version of ABI’s sequencer, but the company has not divulged further details on its development plans since that time.
According to last week’s SEC filing, Celera will pay the costs of developing the new diagnostic instrument, including any “incremental costs” incurred by ABI.
In addition, the operating agreement permits ABI to sell its CE sequencers to “any end-user for any purpose,” as well as under original equipment manufacturer agreements, “except that it will not be able to OEM the CE sequencers for commercialization of human diagnostic tests for specified conditions for a period of three years after the date of the separation outside of Asia, Africa, the Middle East and South America.”
ABI also agreed that it will not commercialize these diagnostic tests anywhere in the world, or enter into an agreement with a third party to co-promote or co-market CE sequencers to be used with these tests outside of Asia, Africa, the Middle East, and South America for the same three-year period.
The operating agreement places “no restrictions” on the development or commercialization of next-generation sequencing instruments for either ABI or Celera.
In addition, ABI will be the “preferred supplier of Celera’s next-generation real-time instrument,” the filing stated. If Celera and ABI are unable to agree on terms for this instrument, “Celera will be given access to [ABI’s] intellectual property to the extent necessary to make or to have a next generation real-time system made for Celera by a third party.”
ABI is also permitted to sell real-time instruments to any end-user for any purpose, except for “restrictions” covered by an existing supply agreement between ABI and Abbott relating to Abbott’s m2000 system. With the exception of this supply arrangement, ABI “will not OEM real-time instruments to any third party for use in the human in vitro diagnostics, or HIVD, field unless the third party has obtained a license to [ABI’s] real-time intellectual property in the HIVD field.”
However, the agreement states that ABI's OEM real-time customers cannot commercialize human diagnostic tests for “specified conditions” on these instruments for three years after the date of the separation.
The agreement also covers reagents. Specifically, ABI agreed that it will not “knowingly commercialize” sequence-specific primers and probes for incorporation by a third-party product manufacturer into human diagnostic products, or to a clinical laboratory for performing ‘‘home-brew’’ human diagnostic testing for the specified conditions for three years after the date of the separation. This restriction does not apply to Asia, Africa, the Middle East, or South America.
ABI also agreed not to commercialize analyte-specific reagents or human diagnostic kits for testing the same specified conditions for a period of three years after the date of the separation.
ABI and Celera also agreed to “work together” in licensing “specified intellectual property” of ABI to third parties in the human in vitro diagnostics field. “Revenues from these licenses will be shared equally between [ABI] and Celera,” the filing stated.
However, Celera will not commercialize products in forensics and applied markets that incorporate ABI’s intellectual property, unless it obtains a license to that IP “on standard third-party terms.”
The filing noted that the three-year time restrictions described in the agreement do not apply to the commercialization of “a competing product acquired as part of an acquisition” by ABI, nor would it prohibit an acquiror of ABI “from continuing to commercialize a competing product following an acquisition.”
ABI is in the process of being acquired by Invitrogen in a $6.7 billion deal that is expected to close in the fall. The combined company will retain the Applied Biosystems name but will be based at Invitrogen’s headquarters in Carlsbad, Calif.

Wellcome Trust Awards EBI $10M to Manage Trace Sequence Archive
The UK’s Wellcome Trust has awarded the European Bioinformatics Institute €6.3 million ($10 million) through 2012 to manage an international archive of raw DNA sequence data, EBI said this week.
EBI, an outpost of the European Molecular Biology Laboratory located on the Wellcome Trust Genome Campus in Hinxton, UK, will maintain the resource, called the Trace Archive, in collaboration with the National Center for Biotechnology Information in the US. EBI is taking over from the Wellcome Trust Sanger Institute, which has maintained the archive in Europe up until now.
The Trace Archive, available here, currently contains almost 1.8 billion traces from 1,262 species, which is the equivalent of 100 terabytes of data.
The resource will enable researchers to reanalyze DNA sequence rather than resequencing samples — an option that can be up to 1,000 times cheaper than regenerating sequence, EBI said.
The Trace Archive is a collaborative effort between Ewan Birney and Paul Flicek at the EBI. Flicek, head of the Vertebrate Genomics Team, said in a statement that the EBI’s “first task is to incorporate the novel types of data generated by new sequencing technologies, for example, short reads.”
EBI said that the amount of data in the archive is expected to double over the next four years.

Denmark's CLC Bio Moves to New Headquarters
Danish bioinformatics firm CLC Bio said last week that it has moved its headquarters to a new building in the Katrinebjerg neighborhood of Aarhus, Denmark.
Thomas Knudsen, CEO of CLC Bio, said in a statement that the company had “outgrown” its previous location at the Aarhus Science Park.
The company was founded in January 2005, and now has nearly 50 employees, with offices in Aarhus; Boston; Nottingham, UK; Rio de Janeiro, Brazil; and New Delhi and Hyderabad, India.
The company said it is currently working on establishing another new office in Asia later this year, but did not provide further details on the intended location.

RainDance Technologies Forms French Subsidiary for Euro Partnering
RainDance Technologies has formed a subsidiary in France that will focus on developing research partnerships in Europe, the company said last week.
The new company, RainDance Technologies France SARL, will be based in Strasbourg at the Louis Pasteur University’s Institute of Science and Supramolecular Engineering. Andrew Griffiths, a RainDance founder, is director of the institute’s Chemical Biology Laboratory.
The subsidiary is expected to start operations at the beginning of September, RainDance said.
RainDance was founded in 2004 and is based in Lexington, Mass. It is developing an analytical platform that produces picoliter-volume droplets that can contain a single molecule, reaction, or cell, and are each the “functional equivalent of an individual test tube,” the company said.
The company plans to focus its initial application on human genome resequencing research.
The new subsidiary is expected to help RainDance develop collaborations with European groups studying genomics, molecular biology, and drug discovery, RainDance CEO, Chris McNary, said in a statement.

TGen to Lead New Brain Cancer Consortium with PGx Focus
The Ben and Catherine Ivy Foundation said last week that it has awarded $3 million to the Translational Genomics Research Institute to lead a new research consortium that will apply genomics tools to the study of brain cancer.
The consortium, called the Ivy Genomics-Based Medicine, or Ivy GBM, Project, involves nine US research institutions who will study whether genetic differences in individual brain tumors can help predict the most effective treatment option for each patient.
This project will categorize tumors by molecular profiling and test each tumor against a range of treatments to match differences in response with the profiles.
“Currently, all patients get basically the same treatment without taking into account the genetic profile of their tumor,” said Catherine Ivy, Founder of the Ivy Foundation, in a statement.
“The end goal of this research initiative is to identify how tumors with different genetic features respond to a set of treatment regimens and ultimately, it is hoped, provide physicians with the tools they need to offer brain tumor patients the most effective treatment options based on the specific genetic profile of their tumor,” she said.
Michael Berens, head of the brain tumor research lab at TGen, will manage the project, which will take place in two stages and span four to five years.
In stage I of the project, which is expected to last 18 months, project partners will develop models for predicting treatment response based on the genetic profile of patients’ tumors.
If stage I is successful, the project will proceed to the second phase, a clinical trial for patients with recurrent glioblastoma multiforme.
In addition to Berens and TGen, Ivy GBM Project participants include Antonio Chiocca and Sean Lawler of Ohio State University; Howard Colman of MD Anderson Cancer Center; G. Yancey Gillespie of the University of Alabama at Birmingham; C. David James of the University of California, San Francisco; Tom Mikkelsen of Henry Ford Hospital; Jann Sarkaria of the Mayo Clinic; Andrew Sloan of Case Western Reserve University School of Medicine; and Craig Webb of the Van Andel Research Institute.

Researchers Propose Guidelines on the Use of Race and Ethnicity in Genomics Studies
An interdisciplinary group of researchers from Stanford University proposed ten principles this week that it hopes will limit the misuse of racial and ethnic categories in future genetic research.
In an open letter published this week in Genome Biology, the researchers noted that the rise in human genetic variation research in recent years has “rekindled debates about the connection between genetic traits and human ‘racial’ difference.”
As a result, they write in the paper, the research community is “divided on the question of whether racial categorization is an appropriate means of organizing potentially useful genetic data or a pernicious reification of historically destructive typologies.”
In an effort to explore these issues, faculty from the humanities, social and life sciences, law and medical schools at Stanford began meeting in 2003 for a series of discussions and workshops. The guidelines published this week grew out of those discussions and are intended “to promote interdisciplinary dialog on these important concerns and to encourage responsible practices,” the authors write.
Among the principles outlined in the paper is a declaration that the group does not believe that there is a scientific basis “for any claim that the pattern of human genetic variation supports hierarchically organized categories of race and ethnicity.”
The authors also note that “racial and ethnic categories are created and maintained within sociopolitical contexts and have shifted in meaning over time.”
The group also cautions against making the “naive leap” to a genetic explanation for differences in complex traits, “especially for human behavioral traits such as IQ scores, tendency towards violence, and degree of athleticism.”
In addition, they “discourage the use of race as a proxy for biological similarity and support efforts to minimize the use of the categories of race and ethnicity in clinical medicine, maintaining focus on the individual rather than the group.”
The authors also call for improved education and outreach regarding human genetic variation, and recommend that researchers, journalists, “and others engaged in the translation of research results” collaborate on efforts to “avoid overstatement of the contribution of genetic variation to phenotypic variation.”
The researchers said they hope that scientific data about human genetic variation “might undermine spurious popular beliefs about the existence of biologically distinct human races and beliefs that support racist ideologies.”

SACGHS To Draft Report on Genetics Education By Next Summer; Leavitt Calls DTC Testing Debate a 'Good Struggle'
The HHS Secretary’s Advisory Committee on Genetics, Health and Society plans to release a draft report covering its recommendations on genetics education by next summer, a SACGHS official said last week.
During a session on personalized genomics during a SACGHS meeting Washington DC, SACGHS member Barbara Burns-McGrath said that the committee expects to prepare a draft report that will cover its priorities and recommendations concerning genetics education by the summer of 2009, and a final report by 2010.
Department of Health and Human Services Secretary Michael Leavitt, who unexpectedly dropped in on the meeting last week, told attendees that consumer genomics “is an area of particular interest to me.”
Leavitt offered encouragement to meeting attendees who had gathered to hash out a range of complex issues, such as the scientific validity of these tests and the regulatory status of the field.
“We’re struggling with so many different issues and trying to find a balance, and [trying to find] that place between fostering innovation and at the same time giving people that sense of confidence” that products and services are safe, Leavitt told the group.
He added that this debate is a “good struggle” and a necessary one.
“It’s evident to me that at some point [direct-to-consumer genetic testing] is going to be very common, and if we don’t have the ability to manage this information in a standardized way, and we don’t have the capacity to protect the privacy of those [who take these tests], then there will be a great opportunity cost,” Leavitt explained.
“I believe that if people are given information that is high quality and that is consistent, then they will use it in a way that will drive their own interests, and in doing so, will drive the quality up and the costs, ultimately, down,” he said.
Leavitt also made it clear that he does not view consumers as being unable to comprehend the subtleties involved in interpreting genetic information, particularly in terms of utilizing knowledge about disease risk.
“I think that it’s often the case that consumers are underestimated in terms of their capacity to sort through this, and there’s often a sense of well-intended protection that we want to provide that sometimes can strain the process,” he said.
Leavitt added that he tries to look at the issue through a broad scope. “It’s the tension of those on both sides of the debate that ultimately will bring improvement,” he said.
Muin Khoury, director of the Center for Human Genomics at the US Centers for Disease Control and Prevention, told the committee that the discussions last week “should not go unnoticed,” and urged SACGHS to act quickly.
Raising the question of whether the group was just “buying time between now and December,” when another administration will run HHS, he warned that this would amount to “missed opportunities for coordinated action.”
Khoury advocated drafting a letter for Secretary Leavitt that would offer advice on some of the issues the committee views as most important or pressing.
SACGHS is not the only group planning to issue a set of recommendations regarding consumer genomics. The Personalized Medicine Coalition, an industry advocacy group, spoke last week with several DTC genomics companies, including Navigenics, DeCode, and 23andMe, about strategies they could take to show both compliance and to begin to assuage concerns about their business.
Amy Miller, public policy director at PMC, said the group may continue to work with the companies to develop “basic guidelines for how these companies should act.”
Miller said PMC is considering several sets of guidelines, including a set for companies, one for consumers who are considering DTC genetic services, and another for physicians educating them about what the services do.
Miller described the meetings between the committee and industry as “the beginning of a conversation” about how consumer genomics can work in all the US without running afoul of regulatory bodies.
— By Matt Jones, originally published on GenomeWeb Daily News

Lenetix May Offer DeCode Tests in New York, California, Maryland
DeCode Genetics has entered into a partnership with a laboratory services firm that may help it circumvent regulations in several states that have barred unlicensed firms from selling genetic tests, company officials said earlier this month.
“We have established a relationship with a commercial laboratory in New York, who is working through the validation of our test,” Clyde Shores, DeCode’s VP of diagnostic marketing and sales, told investors during the company’s annual research and development update this month.
The firm, Lenetix, has licenses in New York, California, and Maryland, “and if we sublicense our testing to them, then they would be able to begin marketing our tests to each of those states,” Shores said.
In the recent regulatory battle between California state health officials and direct-to-consumer personal genomics companies, DeCode Genetics has tried to set itself apart from competitors by claiming that it does not market its DeCodeMe personal genomics service to the general public and is awaiting a state license before offering its tests in the state.
In fact, as reported by In Sequence’s sister publication Pharmacogenomics Reporter, the company has stated that it is not offering DeCodeMe services to residents of New York and Maryland, where it also does not have a license.
It appears that the partnership with Lenetix may allow the company to sell its tests in these states while it awaits the appropriate licensing, or potentially, in case it does not receive a license at all.
“This is a strategy to expedite the commercialization of our tests in each of those states in the case that we don’t receive state approval sooner,” Shores said.
DeCode Chief Scientific Officer Jeffrey Gulcher had earlier criticized competitors Navigenics and 23andMe for trying to claim compliance with state laws by outsourcing the genotyping for their services to state-licensed clinical laboratories.
“Regarding the California state license for diagnostics, it is important to point out that we do our own genotyping internally and therefore have not assumed, as some others have, that subcontracting to a licensed laboratory for the genotyping automatically achieves compliance,” DeCode co-founder Jeff Gulcher told Pharmacogenomics Reporter previously.
Gulcher was referring to Navigenics’ and 23andMe’s response to the California Department of Public Health’s warning letters for allegedly marketing genetic tests without a state license and directly to consumers. DeCode, Navigenics, 23andMe were among 13 companies to receive cease-and-desist letter from CDPH.
23andMe claims compliance with California’s laws, citing the fact that Illumina, the company that performs the genotyping for its service, is licensed in the state. Furthermore, the company says it employs a California-licensed physician to order the tests.
Navigenics has also maintained that it is in compliance because the genome scans that are part of its service are performed by Affymetrix, which is CLIA-certified in California, and the tests are ordered and reviewed by a California-licensed physician. Navigenics also said it encourages its customers to use its genetic counselors to better understand the test results.
Although the DeCodeMe service uses the Illumina 1M beadchip to analyze consumers’ DNA, the company has tried to set itself apart from competitors by the fact that it conducts its own genotyping.
“In many ways, 23andMe and Navigenics are only marketing organizations, somewhat akin to the dotcom companies, because they don’t do their own genotyping; they don’t control the quality of what they do,” Decode CEO Kari Stefansson said during this month’s R&D presentation.
“At DeCode, and for DeCodeMe, we do all the genotyping ourselves. … We are responsible for the quality of the tests, which ultimately makes us responsible for our reputation as a diagnostics company,” he said.
While Navigenics and 23andMe have continued to market their tests in California despite CDPH’s warning letters, DeCode has denied that it markets its products in the state. Furthermore, DeCode maintains that once it receives the appropriate licensing, it will only market its tests to doctors.
There is no reason to assume that even if DeCode provides its tests through Lenetix that will change its plan to only market to physicians in these states.
On its website, Lenetix describes itself as an “international laboratory resource providing rapid genetic screening and diagnostic testing for healthcare providers such as obstetricians, gynecologists, family practitioners, nurse midwives, laboratories and diagnostic facilities worldwide including their patients.”

The Scan

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