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Gene Express, AbaStar, Castle Biosciences, University of Texas MD Anderson Cancer Center, National Cancer Institute, Institute for Systems Biology, Complete Genomics, Johns Hopkins, Rosetta Genomics

Gene Express, AbaStar to Collaborate on MDx Tests for Neurological Disorders
Gene Express this week said that it has signed a definitive agreement to collaborate with AbaStar MDx on the development of biomarker tests for neurological and psychological disorders.

Under the agreement, AbaStar has licensed Gene Express’ SEM Center and StaRT-PCR technology. It will combine the PCR technology with its own RNA biomarker signatures to develop diagnostic tests that run from a blood sample and provide results in a day.

“StaRT-PCR uses known quantities of Internal Standard for each gene to provide quantitative results and standardized PCR gene expression data,” said AbaStar President and CEO Terry Osborn. “Thus during the product development process the diseased patient and normal subject gene expression data can be put into a standardized database that can be leveraged for use with future clinical trials to refine the molecular signatures and for future products.”

The firms expect to collaborate over the next several years on developing and commercializing the tests. They said that they will create several hundred gene standards, screen gene expression profiles, and create validated standardized mixtures of internal standards for clinical trial use.

The partners estimated that the overall value of the pact could potentially exceed $100 million.


Castle Biosciences Signs Option Deal for MD Anderson Brain Cancer Test
Houston-based startup Castle Biosciences has signed an option agreement to license a biomarker-based brain cancer test from the University of Texas MD Anderson Cancer Center.
The firm said that the test, which was developed and validated at MD Anderson in collaboration with other US institutions, could potentially predict a patient’s likelihood to respond to standard treatment based on the cancer’s genetic footprint. It said that it would provide more details on the test in the near future.
Further details of the agreement were not disclosed.

NCI-Led Trial to Test EGFR as Marker for Lung Cancer Drug Response
The National Cancer Institute said last week that it is starting an initiative to validate if a biomarker can predict the clinical benefit of a chemotherapy drug for non-small cell lung cancer in certain patients.  
The study, called Marker Validation for Erlotinib in Lung Cancer, or MARVEL, will seek to find out if there is value in choosing patients for treatment with the drug based on the presence or absence of EGFR activation.
EGFR can be higher in some lung cancers due to the presence of extra copies of its coding gene, which can activate tumor growth. A drug that blocked that activation “could have a significant impact on lung cancer treatment,” NCI said.
MARVEL is a four-year, phase III study that will be run by the North Central Cancer Treatment Group and will include other NCI-sponsored clinical trial groups. It also will establish whether erlotinib delivers “a meaningful benefit” over the standard chemotherapy the patients received.
Under the program, researchers will test around 1,200 lung cancer patients for EGFR, and then randomly assign treatment with either erlotinib or pemetrexed after the patients have received their standard chemotherapy.
Erlotinib, sold under the brand name Tarceva by Genentech, specifically targets EGFR. Pemetrexed, which is called Alimta and is sold by Eli Lilly, blocks tumor cell growth by another mechanism.
The MARVEL program will test if erlotinib will be superior in patients with EGFR-positive lung cancer, and if pemetrexed would be better for treating patients with EGFR-negative lung cancer, as earlier studies have suggested. MARVEL researchers also will incorporate genetic studies for both drugs that will be useful in further identifying patients with different sensitivity and toxicity profiles to those therapies.
"Because lung cancer is such a lethal disease and because it is particularly difficult to treat, especially if diagnosed in its later stages, the MARVEL trial is of major importance because it could define, based on a single test, the best therapy for this disease,” NCI Director John Niederhuber said in a statement. “The future of moving highly targeted agents from the lab to the clinic will be heavily dependent on biomarkers for patient selection," he added.
The MARVEL study is the outcome of the Oncology Biomarkers Qualification Initiative, which was developed formed in 2006 between NCI, the US Food and Drug Administration, the Centers for Medicare and Medicaid Services.
The trial also will include collaborative work from the Cancer and Leukemia Group B, the Eastern Cooperative Oncology Group, the Southwest Oncology Group, and the National Institute of Canada Clinical Trials Group, as well as industry partners.

Complete Genomics, ISB To Collaborate on Genome Studies; Firm Targets $5K Genome for 2009
The Institute for Systems Biology and third-generation sequencing company Complete Genomics announced this week that they are collaborating on population-wide human genome studies.

During the first stage of this project, Complete Genomics will sequence five human genomes from samples provided by researchers at ISB.

Complete Genomics’ sequencing technology combines DNA nanotechnology, new ligation biochemistry, and ultra-high density arrays to do sequencing in solution with low reagent inputs.
The company said it plans to launch a sequencing services business in the second quarter of 2009 that will offer complete human genomes for $5,000.
Following a proof-of-concept stage, Complete Genomics and ISB will sequence a hundred human genomes in 2009 and 2,000 genomes in 2010. That represents ten percent of Complete Genomics’ expected overall 2009 and 2010 sequencing capacity.

“This $5,000 price point, combined with the scale of our sequencing center, will dramatically increase the availability and affordability of human genome sequencing,” said Clifford Reid, chairman, president and CEO of Complete Genomics, in a statement.

“For the first time, our customers can conduct systematic studies of the genetic basis of disease and drug response. Our sequencing services will be one of the core enablers of the impending revolution in personalized medicine.”

In total, the company plans to sequence a thousand human genomes on between 64 and 96 sequencers next year. In 2010, it intends to sequence 20,000 more human genomes on 192 sequencers.

Complete Genomics, which announced its official launch this week, has been operating in “stealth mode” since March 2006. The company and its partners plan to open additional sequencing centers in the US and abroad over the next five years. It estimates that ten such centers would be capable of sequencing a million human genomes.

ISB President Leroy Hood, a member of Complete Genomics’ scientific advisory board, expressed enthusiasm about the upcoming ISB-Complete Genomics collaboration.

“Using Complete Genomics human genome sequencing services to gather population-wide human genetic data will allow us to gain a more complete understanding of the genetic components and molecular processes of diseases in order to better manage, treat, and prevent human disease and better understand human health,” Hood said in a statement.


Johns Hopkins to Evaluate Rosetta Genomics' miRNA Lung Cancer Diagnostic
Rosetta Genomics said today that it is partnering with Johns Hopkins University School of Medicine on a clinical assessment study of its microRNA-based miRview Squamous diagnostic, which is designed to differentiate squamous from non-squamous non-small cell lung cancer.
The study will compare miRview squamous with available immunohistochemistry methods.
Rosetta said in a statement that the test is in the "final stages of development" and is expected to be commercially available by the end of 2008.
The company said that until recently differentiation between squamous and non-squamous non-small cell lung cancer “was not particularly relevant from a therapeutic or prognostic standpoint” because there were no therapies designed for a specific NSCLC sub-type.
However, Rosetta added, “a recently approved angiogenesis inhibitor for NSCLC has been shown to have severe side effects for squamous-cell lung cancer patients," which has led patients with squamous-cell histology "to be regarded by many as inappropriate candidates for therapy with this drug.”
In addition, the company said that “several other” targeted drugs for NSCLC currently under development “may require this type of accurate differentiation due to different side effect profiles or different levels of efficacy.”

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The Scan

Transcriptomic, Epigenetic Study Appears to Explain Anti-Viral Effects of TB Vaccine

Researchers report in Science Advances on an interferon signature and long-term shifts in monocyte cell DNA methylation in Bacille Calmette-Guérin-vaccinated infant samples.

DNA Storage Method Taps Into Gene Editing Technology

With a dual-plasmid system informed by gene editing, researchers re-wrote DNA sequences in E. coli to store Charles Dickens prose over hundreds of generations, as they recount in Science Advances.

Researchers Model Microbiome Dynamics in Effort to Understand Chronic Human Conditions

Investigators demonstrate in PLOS Computational Biology a computational method for following microbiome dynamics in the absence of longitudinally collected samples.

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.