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Affymetrix, Roche, Johnson & Johnson, FDA, GeneScan, MWG Biotech, Whatman, Illumina, Genelabs, Lynx Therapeutics


Affymetrix, Roche Get FDA Clearance for Microarray-based Dx Products

In a significant step for microarray-based diagnostics, and for the pharmacogenomics sector, the US Food and Drug Administration has cleared Roche’s AmpliChip CYP450 DNA chip and Affymetrix’s GeneChip 3000Dx chip reader as an in vitro diagnostic.

The approval, announced in an FDA statement on Dec. 23, marks the first time that a DNA chip reader has won FDA clearance for IVD use. The agency also said the clearance may open the door for additional micro-array-based molecular diagnostics to be sold nationwide.

The chip and its reader were approved for sale in the European Union in September.

“The FDA’s decision is another milestone demonstrating Affymetrix’s commitment to clinical diagnostic products,” Stephen Fodor, chairman and CEO of Affymetrix, said in a statement.

“Physicians can use the genetic information from this test to prevent harmful drug interactions and to assure drugs are used optimally, which in some cases will enable patients to avoid less effective or potentially harmful treatment choices,” Lester Crawford, acting FDA commissioner, said in the agency’s statement.

The FDA said that the AmpliChip “is the first DNA microarray test to be cleared by the FDA and its clearance paves the way for similar microarray-based diagnostic tests to be developed in the future.”

Affymetrix Inks Diagnostics Collaboration with J&J Unit; Amends Terms of Gene Logic Deal

The recent US Food and Drug Administration approval of the AmpliChip is already paying dividends for Affymetrix.

The Santa Clara, Calif.-based microarray giant last week announced that it had given a Johnson & Johnson company “long-term and comprehensive” access to its GeneChip technology to create and market in vitro diagnostics for certain undisclosed cancers.

The agreement gives Veridex non-exclusive rights to Affy’s arrays and instruments. Financial terms of the agreement were not disclosed.

Two weeks ago, the FDA cleared Roche’s long-awaited AmpliChip CYP450 DNA chip and Affy’s GeneChip 3000Dx chip reader as an in vitro diagnostic. The approval, announced in an FDA statement on Dec. 23, marks the first time that a DNA chip reader has won FDA clearance for IVD use. The agency also said the clearance may open the door for additional molecular diagnostics based on microarrays to be sold nationwide.

The chip and its reader were approved for sale in the European Union in September.

Also, Gene Logic last week announced amendments to its 2002 microarray supply agreement with Affymetrix. In an SEC filing, Gene Logic said that it will pay Affymetrix a mere $500,000 in annual subscription fees in 2005, instead of the $4 million that it paid in prior years.

Gene Logic also said it will purchase at least $500,000 worth of Affymetrix products and services in December, and at least another $9.5 million in 2005. The companies will also establish pricing for probe array products for the period between July 1, 2003, and Dec. 31, 2005.

The original contract, signed in 1999 but revised in January 2002, sets the terms for supplying Gene Logic and its subsidiaries with DNA probe arrays from Affymetrix for developing database products and serv-ices. That agreement, disclosed in a 2002 SEC filing by Gene Logic, did not provide any financial details.

FDA Publishes PGx Guidance in Federal Register; Final Version Due in Early 2005

The US Food and Drug Administration has published in the Federal Register its draft Guidance for Industry on Pharmacogenomics Data Submissions, and now expects to release the final guidance “early next year,” according to an FDA spokesperson.

The widely anticipated document, the approval of which has been delayed numerous times since it was released as a draft in November 2003, is designed to encourage drug makers to use pharmacogenomics technologies in their drug-discovery efforts and submit some of their findings as a way to help the FDA broaden its knowledge of the technologies.

Published in the Federal Register on Dec. 27, the guidance may therefore be a catalyst for greater use of gene-expression and SNP-genotyping technologies, and might embolden makers of these tools to develop new versions.

As BioArray News’ sister publication GenomeWeb News reported last month, an FDA official said the agency would issue the final guidance document before the end of the year. The document will be “out by January 2005,” said Larry Lesko, director of the FDA’s Office of Clinical Pharmacology and Biopharmaceuticals.

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.

The Jan. 1 due date follows a string of at least three previous, revised deadlines. Pharmacogenomics Reporter, 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 to release it by June 30.

GeneScan Buys Stake In MWG

GeneScan Europe has acquired 25.1 percent of MWG Biotech pursuant to a stock-purchase agreement with two major shareholders announced last month.

Specific details of the sale, which included 8,656,500 shares of MWG, were not disclosed.

GeneScan also has purchased about €2 million in MWG convertible bonds from the shareholders.

MWG Biotech said separately that it has sold convertible bonds totaling €6.5 million. Proceeds of the sale will be used to support MWG’s ongoing restructuring, the company noted.

In November, the company said it expected to raise €10 million through the sale of its convertible bonds.

Whatman Plans to Lay Off 160 Employees As Part of S&S Integration

Whatman announced last week that a review of its business operations following the Dec. 1 acquisition of Schleicher & Schuell has been completed, and that the company has decided to cut approximately 160 jobs.

This reduction will reduce Whatman’s headcount to about 1,000, and result in a one-time charge of £11.4 million, the company said. Whatman announced in early November that it would acquire Schleicher & Schuell for €50.2 million.

Whatman also said that its US manufacturing operations will be focused in Stanford, Maine. Its US sales and administrative operations and global business development activities, will be based in Florham Park, NJ.

Additionally, former Schleicher & Schuell head office functions will be integrated into Whatman and streamlined, while the sales and business development activities of the two companies will be combined and optimized.

Whatman said that it is working to narrow the product offerings of the companies from 21,000 to 7,000, an effort that will cost about £800,000. An additional £2.4 million charge unrelated to the Schleicher & Schuell acquisition also will be recorded in 2004.

In total, Whatman expects to record a charge of £14.6 million in 2004, of which the pre-tax cash cost is £13.8 million.

Illumina, Affy Get NIH Grants

Illumina has won around $1.5 million through a pair of recent grants from the US National Institutes of Health, according to the NIH.

The grants, which the NIH said are effective as of Dec. 26, but Illumina had not previously disclosed, include $506,021 for a high-throughput methylation-profiling system; $194,951 for research into allelic expression-monitoring by array-based genotyping; $603,106 to develop a protease substrate array; and $169,877 to develop an allergy peptide array.

Meanwhile, Affymetrix has received roughly $2.5 million through a pair of recent grants from the NIH as well.

The grants, which the NIH said are effective as of Dec. 26, but Affy had not previously disclosed, include $366,248 for research entitled “DAS2: A Distributed Genome Annotation Sequence;” and $2,100,004 for research into pathogen and genetic-element detection using microarrays.

Genelabs Gets $1.25 Million from Affy In Amended Licensing Deal

Genelabs Technologies has received $1.25 million from Affymetrix after amending a non-exclusive license to Genelabs’ Linker-Aided DNA-amplification technology, Genelabs said last week.

Affy licensed the technology, called LADA, from Genelabs in December 2002. According to the company, the amendment converts the license to a “fully paid up non-exclusive license” and eliminates royalties and fees that were payable under the original agreement.

The license relates to inventions covered under US patent number 6,107,023, entitled, “DNA Amplification and Subtraction Techniques,” as well as certain international patents. The patent claims “a method of amplifying nucleic acids by attaching DNA linkers of a known sequence to the ends of unknown DNA sequences which are targeted for amplification,” Genelabs said.

Lynx Gets $3 Million Bridge Loan

Lynx Therapeutics has obtained a $3 million bridge loan from Silicon Valley Bank, the company said last week.

The financing, which is secured by Lynx’s assets, will keep the company going as it prepares to be acquired by Solexa. The loan will support Lynx’s operations until the company completes an equity financing sometime this year, acting CEO Mary Schramke said in a statement.

The acquisition by Solexa is expected to close in the first quarter of 2005.



The Scan

Positive Framing of Genetic Studies Can Spark Mistrust Among Underrepresented Groups

Researchers in Human Genetics and Genomics Advances report that how researchers describe genomic studies may alienate potential participants.

Small Study of Gene Editing to Treat Sickle Cell Disease

In a Novartis-sponsored study in the New England Journal of Medicine, researchers found that a CRISPR-Cas9-based treatment targeting promoters of genes encoding fetal hemoglobin could reduce disease symptoms.

Gut Microbiome Changes Appear in Infants Before They Develop Eczema, Study Finds

Researchers report in mSystems that infants experienced an enrichment in Clostridium sensu stricto 1 and Finegoldia and a depletion of Bacteroides before developing eczema.

Acute Myeloid Leukemia Treatment Specificity Enhanced With Stem Cell Editing

A study in Nature suggests epitope editing in donor stem cells prior to bone marrow transplants can stave off toxicity when targeting acute myeloid leukemia with immunotherapy.