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USPTO, Affymetrix, Illumina, DiaGenic, Harvard Medical School, Michael J. Fox Foundation, Progenika, Personalized Medicine Coalition, Golden Helix, Progeny Software, GeneGo, Cytoscape

Analyst Warns that USPTO Patent Re-exams May Delay Affy v. Illumina Case
The recent decision of the US Patent and Trademark Office to re-examine four Affymetrix patents central to ongoing litigation between Affy and Illumina could delay the resolution of the case by up to a year, according to an analyst that covers both companies.
Garp Research and Securities’ Alistair Mackay wrote a report published in Barron’s last week that the second phase of the case against Illumina, as well as additional cases filed last fall in the US and in Europe, could be slowed by the reexaminations.
Affy filed an initial patent-infringement suit against Illumina in 2004. The second part of the proceedings is scheduled to commence next month. In October Affy filed more suits against Illumina in both the US and in Europe (see BAN 10/30/2007).


“We believe that this development is likely to delay the 2004 case before Judge Farnan’s [US District Court] in Delaware for up to one year,” he wrote. “The Feb. 11, 2008, starting date for the Part Two jury trial is now in question.”
In regard to the suits filed in October, Mackay added that “as there is overlap between the contested US patents and the three European ones, we believe that these cases may also be slowed.”
Mackay could not be reached to comment on his report by press time. As of Jan. 2, no documents requesting a delay of trial had been filed by attorneys connected to the case. Attorneys representing Illumina and Affymetrix could not be reached to comment on the possibility of a delay of trial by press time.
Illumina said last month that the USPTO will re-examine four patents that are part of an intellectual property infringement suit filed by Affymetrix against Illumina.
Illumina said the USPTO will re-examine patents No. 5,545,531, entitled “Methods for making a device for concurrently processing multiple biological chip assay,” and No. 5,795,716, entitled “Computer-aided visualization and analysis system for sequence evaluation.” The first patent was initially assigned to Affymax, which spun out Affymetrix, while the second patent is assigned to Mark Chee.
The other two patents being re-examined are No. 6,355,432, entitled “Products for detecting nucleic acids,” and No. 6,646,243, entitled “Nucleic acid reading and analysis system.”
In March, a jury sided with Affy in the first phase of the litigation. It found that Illumina's arrays, assays, scanners, software, and related products infringe “one or more claims” of all five of the patents Affy mentioned in the suit (see BAN 3/20/2007).


The jury awarded damages of $16.7 million commensurate with a loyalty rate of 15 percent for the period 2002 through 2005.
The next phase of that case will focus on the validity of Affymetrix's patents and is scheduled to begin on Feb. 11. The following phase is expected to occur in May or June 2008 and will determine whether Illumina's infringement was willful (see BAN 8/14/2008).

DiaGenic, Harvard Med to Use Michael J. Fox Funds for Parkinson’s Dx Research
DiaGenic and researchers at Harvard Medical School will use funding from the Michael J. Fox Foundation to develop a blood-based test for early detection of Parkinson’s disease.
DiaGenic will work with Clemens Scherzer, an assistant professor of neurology at Brigham and Women’s Hospital and Harvard Medical School, who has led the MJFF-funded Harvard PD Biomarker Study for three years.
The study partners will identify and validate gene expression signatures for Parkinson’s using peripheral blood samples that have already been collected for the Harvard study. Signatures will be incorporated into a test to run on a standard platform that will be combined with DiaGenics’ analysis software.
The grant will cover the initial funding for the study, the company said, but the amount of the gift was not disclosed. 
Scherzer said in a statement that he is “optimistic that the use of peripheral gene expression will prove valuable for the early detection of neurological disorders.”

Progenika Joins Personalized Medicine Coalition
Progenika has joined the Personalized Medicine Coalition, a group that aims to promote policies that will benefit medicine aimed at diagnosing and treating disease and illness based on an individual’s unique genetic requirements.
Progenika, a US-based subsidiary of the European molecular diagnostics company Progenika Biopharma, is developing and marketing array-based DNA tests designed to predict drug response and to help diagnose and predict disease.

Golden Helix and Progeny Software to Integrate Genetic Data-Handling Software
Golden Helix and Progeny Software said last month that they will partner to develop an integrated software platform for analyzing, storing, and managing genotype and copy number variation data.
The companies will integrate Progeny’s LAB data management platform and Golden Helix’s SNP & Variation Suite. The combined products will allow users to store, manage, and analyze data with one interface.
"The growing size and complexity of genetic studies continues to create computational challenges in terms of storing and analyzing data,” Golden Helix CEO Christophe Lambert said in a statement. “Yet, the most arduous process is often the constant formatting, reformatting, and transfer of data among packages.”
As part of the agreement, Golden Helix has extended an exclusive distribution agreement with Progeny Europe covering Western Europe. 

GeneGo Integrates MetaCore, MetaDrug with Open Source Cytoscape Platform
GeneGo said last month it has integrated two of its data analysis software offerings with Cytoscape, an open source pathway-visualization package developed by the Institute for Systems Biology and other academic partners.
GeneGo said it is integrating its MetaCore 4.5 software, used in target selection and validation for toxicology, and MetaDrug 4.5, which is used to study the toxicity and biological effects of novel small-molecule compounds.
The company said plug-ins are available for network and molecular profiling analyses, new layouts, additional file format support and connection.
GeneGo first mentioned its plans to integrate its software with Cytoscape in July, when ISB licensed its MetaCore and 1-2-3 Workflow software.

The Scan

New Study Highlights Role of Genetics in ADHD

Researchers report in Nature Genetics on differences in genetic architecture between ADHD affecting children versus ADHD that persists into adulthood or is diagnosed in adults.

Study Highlights Pitfall of Large Gene Panels in Clinical Genomic Analysis

An analysis in Genetics in Medicine finds that as gene panels get larger, there is an increased chance of uncovering benign candidate variants.

Single-Cell Atlas of Drosophila Embryogenesis

A new paper in Science presents a single-cell atlas of fruit fly embryonic development over time.

Phage Cocktail Holds Promise for IBD

Researchers uncovered a combination phage therapy that targets Klebsiella pneumonia strains among individuals experiencing inflammatory bowel disease flare ups, as they report in Cell.