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FDA, CombiMatrix, Qiagen, Ambry Genetics, Roche, Gene Logic, Eli Lilly, Orchid Cellmark, National Cancer Institute, National Human Genome Research Institute, Illumina

FDA Says CombiMatrix’s CGAT Not Regulated Under IVDMIA …
The US Food and Drug Administration has notified CombiMatrix that its microarray-based diagnostic service for identifying genetic disorders does not fall under its recent guidance covering in vitro diagnostic multivariate index assays, and therefore will not be subject to some new regulations.
In a letter from the FDA’s Office of In Vitro Diagnostic Device Evaluation and Safety, director Steven Gutman wrote that CombiMatrix’s Constitutional Genetic Array Test does not meet the definition of an IVDMIA.
In a copy of the OIVD letter provided by CombiMatrix, Gutman wrote, “We do not believe that your device, as described, meets the definition of an IVDMIA as defined in the Draft Guidance document on IVDMIAs.”
The FDA released the IVDMIA draft guidance, which outlines the regulatory rules for companies and labs that manufacture these tests on Sept. 6.
CombiMatrix said the letter followed a September meeting to discuss CGAT with OIVD officials at the company’s lab, after which the agency decided the test did not require FDA oversight. This opinion has freed the company to pursue marketing its CGAT without regulatory considerations.
CombiMatrix said the OIVD opinion presently applies only to the CGAT, but asserted that its strategy will be to develop a series of array-based molecular diagnostic services as laboratory-developed tests, and potentially to seek FDA approval to sell some tests to other labs.

… But Says Six of Qiagen's Artus Dxs Require Approval for Sale in US
The US Food and Drug Administration has sent a letter to Qiagen warning it that certain of its molecular diagnostics currently manufactured in Hamburg, Germany, do not have regulatory approval for sale in the US.
In an Oct. 2 letter to Qiagen CEO Peer Schatz, the FDA said six diagnostic products manufactured at the Hamburg site are improperly marketed and require regulatory review by the agency.
On its web site, Qiagen stresses that the products — tests for herpes virus, lyme disease, parvovirus, Chlamydia, and malaria — are designed for use in CLIA labs and therefore do not require FDA oversight.
The FDA, on the other hand, claims that because the tests are packaged with instructions they are subject to agency review.
The products cited by the FDA letter include the artus CMV PCR, C. Trachomatis PCR, C. Trachomatis Plus PCR, Parvo B19 PCR, Borrelia PCR, and Malaria PCR analyte specific reagents.
According to a Qiagen spokesman, only two of the assays have been sold in the US, and their sales are “very immaterial.” He said the assays are based on older designs from artus, a molecular diagnostics manufacturer that Qiagen acquired last year for around $40 million.
The spokesman said that as part of the integration of artus, Qiagen “has already completed or initiated ensuring compliance” of the ASRs.
In its letter, available here, the FDA said it “has concluded that you market these products as ASRs for sale directly to clinical laboratories and not as components intended to be included as part of a finished, packaged, and labeled device as defined in 21 CFR 820.3(c).
“Our review has determined that these reagents are medical devices as defined by section 201(h) of the Federal Food, Drug, and Cosmetic Act (Act), 21 U.S.C. § 321(h), because they are intended for use in the diagnosis of disease or other conditions, or in the cure, mitigation, treatment, or prevention of disease, or are intended to affect the structure or function of the body,” the agency concluded.
The FDA goes on to say that the products “are not ASRs under 21 C.F.R. 864.4020 and require FDA pre-market review prior to being marketed.”
The agency also noted that the tests “are also misbranded under section 502(o) the Act, 21 U.S.C. 352(o), because you did not notify the agency of your intent to introduce these devices into commercial distribution, as required by section 510(k) of the Act, 21 U.S.C. 360(k).
“You should take prompt action to correct the violation(s) addressed in this letter,” the FDA concluded in the letter. “Failure to promptly correct these violation(s) may result in regulatory action, which may include detaining your devices without physical examination upon entry into the United States until the corrections are completed.
The Qiagen spokesman also stressed that the FDA’s letter implied “no issue with product quality,” and the ASRs manufactured at the Hamburg facility were produced using a complaint quality system.

Ambry Genetics Settles Roche PCR Infringement Claim
Roche Diagnostics has agreed to a settlement offer from Ambry Genetics after Roche sued the company for allegedly infringing certain of its PCR and related technology patent, Roche said this week.
Under the settlement, Roche will drop its suit against the Ambry in return for payment of past royalties of an undisclosed amount in the field of human in vitro diagnostics.
Ambry Genetics, based in Aliso Viejo, Calif., specializes in genetic testing in the areas of cystic fibrosis, chronic and hereditary pancreatitis, alpha-1-antitrypsin, and other pulmonary diseases.

Gene Logic to Reposition Drugs for Eli Lilly
Gene Logic last week said it will try to discover new development paths for drug candidates discontinued in clinical trials by Eli Lilly.
The candidates were discontinued for reasons other than safety, Gene Logic said.
Under the deal, Gene Logic has the option to receive an exclusive license to any drug candidate Eli Lilly decides not to pursue. Eli Lilly would receive success-based milestone and royalty payments on those candidates.
The milestone payments and royalties under the agreement are similar to those in development-stage in-licensing deals, Gene Logic said. The payments are discounted because Eli Lilly originated the compound.
Gene Logic has similar agreements withPfizer, Roche, and Organon.
Additional details were not disclosed.

Orchid Cellmark Extends UK Scrapie Genotyping Contract
Orchid Cellmark this week said it has renewed an ongoing contract with the UK to continue offering genotyping services to sheep farmers in an effort to combat scrapie.
The company reported that the contract, awarded under the National Scrapie Plan for Great Britain, is worth more than $3.5 million per year.
The UK government extended the contract through 2007 and 2008, Orchid said.
Orchid will use its DNA testing services to help sheep farmers breed sheep that are less genetically susceptible to the disease. The UK plan hopes to use genetic analysis to completely eradicate the disease.

Cancer Genome Atlas Pilot Project Outlines Research for Participating Labs
The National Cancer Institute and the National Human Genome Research Institute this week disclosed additional information about the Cancer Genome Atlas Pilot Project.
According to the organizers, awards have been made to seven institutions in five states to establish Cancer Genome Characterization Centers. These centers, which will work as a network, will be charged to use genome-analysis technologies “to identify major changes in the genomes of the cancers chosen for TCGA pilot program.”
The Broad Institute of MIT and Harvard will use the Affymetrix platform to identify changes in expression and copy number alterations that occur in cancer; Harvard Medical School and Brigham and Women's Hospital will use the Agilent platform to characterize tumor samples for alterations in chromosome segments copy number. This center will also develop new technologies to analyze expression profiles.
Lawrence Berkeley National Laboratory, Berkeley, Calif., will use the Affymetrix Exon 1.0 array platform to identify changes in the transcription profiles that occur in cancer; Memorial Sloan-Kettering Cancer Center in New York will use Agilent arrays to characterize chromosome segment gains and losses. This center will also develop new approaches to detect novel genetic rearrangements.
The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University, a joint project with the University of Southern California/Norris Comprehensive Cancer Center, will detect changes in methylation profiles associated with transcribed genes in cancer samples.
Stanford University School of Medicine will use high-throughput whole-genome genotyping technology to identify chromosome segments copy number variation found in cancer; and the University of North Carolina Lineberger Comprehensive Cancer Center in Chapel Hill, NC, will use an Agilent array platform to identify changes in the transcription profiles that occur in cancer.
Additionally, SRA International of Fairfax, Va., will develop the Data Coordinating Center, which will track data produced by components of TCGA, “ensuring that this data meets quality standards set for the project, and make TCGA data publicly accessible through databases supported by NCI's Cancer Biomedical Informatics Grid and the National Library of Medicine's National Center for Biotechnology Information.
The DCC will also establish public data resources that scientists can use in their research.

Genotype Product Deals Drive 174-Percent Growth in Illumina's Q3 Revenues
Illumina this week reported a 174-percent increase in total revenue for the third quarter of 2006, as compared with the same period last year.
Citing heightened demand for its BeadChip product line, the company reported total revenue of $53.5 million for the quarter ending Oct. 1, compared with $19.5 million in the third quarter of 2005. 
Revenues from product sales nearly tripled to $46.9 million from $16.3 million in the prior-year period.
The company cited recent genotyping deals with GlaxoSmithKline, Duke University, Massachusetts General Hospital, and Harvard Medical School as examples of demand for its products.
Illumina reported net income of $16.2 million for the quarter, including total non-cash stock compensation expense of $3.8 million, compared to a net loss of $1.5 million in the third quarter of 2005.
R&D spending rose to $7.7 million from $7 million in the prior-year period.

Illumina ended the third quarter with cash and short-term investments worth $169.9 million, of which $44.2 million was in cash and cash equivalents.

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