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Clinical Data, ABI, Nanogen, Duke University, Illumina, Qiagen, Genome Diagnostics, FDA, NeoCodex, SureGene, Boston University, Howard University, Pressure Biosciences

Clinical Data to Begin Marketing Pain Dx as Service
Clinical Data said this week that its Cogenics Division will provide genomic testing services to the pain research community based on a panel of genetic markers developed by Algynomics.
The panel comprises more than 3,000 SNPs for drug and diagnostic development to “examine the genetic basis or underpinnings of human pain sensitivity, pain conditions, and responses to existing and new pharmacological agents used to treat pain, inflammation, and mood disorders,” Clinical Data said in a statement.
The panel will be initially offered as a microarray-based genotyping service and will be launched at the American Society of Human Genetics Annual Meeting in New Orleans this week.
“We envision this testing service to become a standard tool for clinical scientists and researchers to better understand the pathophysiology of pain conditions and the identification of useful clinical markers,” Luda Diatchenko, chief scientific officer of Algynomics, said in the statement.

ABI Releases TaqMan Assay Data to Public Database
Applied Biosystems has released into the public domain the validation data for its TaqMan drug metabolism genotyping assays, the company said this week.
The data, which was released through the Pharmacogenomics Knowledge Base, is aimed at helping researchers understand how genetic variation among individuals contributes to differences in reactions to drugs.
Researchers can use the data on validated genotyping assays available in PharmGKB to “expedite the design and execution of genetic studies correlating genotype to drug efficacy or toxicity,” Teri Klein, director of the PharmGKB project at Stanford University, said in a statement.
Applied Biosystems also said studies show that its TaqMan assays provide higher accuracy than other methodologies in identifying variations in genes that code for drug metabolism enzymes.

Nanogen to Cut 15 Percent of US Staff as It Seeks to Streamline Acquired Businesses
Nanogen last week said it plans to cuts its US headcount by 15 percent, or around 48 people, by the end of the year in an effort to improve its cash flow and profits.
The cuts will come from R&D, manufacturing, and sales and marketing, Nanogen said.
In a statement, Nanogen President and COO David Ludvigson said the company is taking the steps to consolidate several recent acquisitions, among them Epoch Biosciences, SynX, Spectral Diagnostics' cardiac assets, and an Amplimedical business.
“The integrations have occurred smoothly with consistent revenue performance,” Ludvigson said. “We are now moving into the second stage of integrating our acquisitions and have identified a number of areas where we can consolidate functions and eliminate redundant activities, which we expect will improve operational performance.”
The news comes a couple of days after Nanogen disclosed it has sold royalty rights to its MGB technology for five years. The company has already received a $20 million upfront payment from the buyer, Canadian healthcare investment shop Drug Royalty.
"Monetizing a portion of our royalty stream provides us with a non-dilutive means of raising capital,” Nanogen CEO Howard Birndorf said in a statement.
As part of the royalty deal, between July 2006 and December 2011 Nanogen will receive royalties up to a specified threshold, above which both companies will share royalties.
Nanogen will retain ownership of the technology and will receive all royalties after December 2011.
The MGB technology is used in 5' nuclease real-time PCR applications in biomedical research. Applied Biosystems has licensed the same technology for its TaqMan products.

Duke to Use Illumina's Infinium HumanHap550 BeadChip in Autism Study
Duke University’s Center for Human Genetics will use Illumina's Infinium HumanHap550 BeadChip in a large autism study, Illumina said last week.
The study will include over 1,800 individuals and their families.
Financial terms of the deal were not disclosed.

Qiagen to Market HLA Typing Technology from Genome Diagnostics
Qiagen secured commercial rights to sell reagents and software for Genome Diagnostics' sequencing-based typing technology, Genome Diagnostics said this week.
The Dutch company has developed a proprietary strategy for typing human leukocyte antigen genes. Qiagen will have global distribution rights to the technology as of January 2007.
Qiagen already has an exclusive sales and distribution agreement to distribute Olerup SSP's HLA sequence specific primer technology for HLA typing, Genome Diagnostics said. With this agreement, Qiagen can offer both products to researchers for a complete HLA typing solution.
Financial details were not disclosed.

FDA Approves Gen-Probe’s HIV-1 RNA Test
The US Food and Drug Administration this week approved Gen-Probe’s molecular diagnostic for detecting HIV-1 RNA, the agency said this week.
The test, APTIMA HIV-1 RNA qualitative assay, detects the RNA of the HIV-1 virus and is the first test approved for the detection of HIV-1 RNA to help diagnose HIV-1 infection.
The FDA said the test “has important implications for medical diagnostic use because it could be a potential alternative to the traditional Western blot test now used for confirmation of HIV-1 infection when screening tests for HIV-1 antibodies are positive. 
“In addition, the Western blot can, in some instances, be difficult to interpret and may not always provide a conclusive result. In such cases, the APTIMA test may be helpful in HIV-1 diagnosis,” the FDA said. “The APTIMA test can also be used in clinical laboratories and public health facilities to detect early HIV-1 infection, before the appearance of antibodies to HIV-1.”
"This product offers medical diagnostic laboratories the ability to perform a gene-based test for HIV-1 that, until now, was only available as part of a larger kit used to screen blood and plasma donors," Jay Epstein, director of the FDA’s Office of Blood Research and Review, Center for Biologics Evaluation and Research.  "This test also can detect infection with HIV-1 earlier than HIV antibody tests when used to detect primary HIV-1 infection."

NeoCodex Wins US, EU Patent for HFCC Technology
NeoCodex last week said it has won a patent in the US and the EU protecting its Hypothesis-Free Clinical Cloning technology for conducting whole genome-association studies. 
According to NeoCodex, HFCC enables researchers to “analyze millions of SNPs from many individuals to identify specific points of variation in human DNA that underlie particular diseases or determine effects of medicines.”
NeoCodex said that HFCC is designed to overcome problems such as epistatic occlusion, aberrant noise signaling, and false marker association, and can enable researchers to conduct WGA studies using a “multi-locus approach that capitalizes on a new noise-filtering strategy crafted to circumvent the common multiple-testing errors characteristic of traditional genetic association studies.”
By applying internal and genome-wide case-control validation checkpoints throughout the process, HFCC can simultaneously look for genetic markers associated with different clinical charts and identify shared phenotypes, “and thereby easily detect loci-specific deviations from neutrality,” NeoCodex said.

SureGene Nabs $500K SBIR Grant to Develop Mutation-Based Schizophrenia Drug
SureGene has received a $497,000 phase one Small Business Innovation Research grant to further develop and market a test aimed at early detection of schizophrenia.
The grant will also support research into the genetics of bipolar disorder and help develop a second-generation test that incorporates genetic biomarkers for schizophrenia susceptibility.
The schizophrenia test is based on genetic variations linked to the disorder and could be “useful for people with a family history of the disease,” researcher Mark Brennan said in a statement.
Brennan’s research led to the creation of SureGene, which is expected to bring the test to market within the next two years.

Affy 500K Arrays Selected for Whole-Genome Scan of African American Cohort
Boston University and Howard University researchers will use Affymetrix arrays to perform the first genome-wide scan of an African-American cohort for genes associated with obesity and other metabolic disorders, Affymetrix said this week.
The researchers will use Affy's GeneChip Human Mapping 500K Array Set to search for genes associated with obesity, hypertension, diabetes and metabolic syndrome.
The collected data will be included within the Affymetrix Control Program, which provides free public access to control cohort data for whole-genome association studies using the GeneChip technology.
The initial phase of the project will take less than a year, Affymetrix said.

Pressure Biosciences Wins $149K SBIR Grant to Develop Methods to Extract Biomarkers
Pressure Biosciences last week said it has received a $149,470 Phase I Small Business Innovation Research Grant from the National Institutes of Health. The grant is for six months.
The company will use it to fund experiments demonstrating the feasibility of its Pressure Cycling Technology for extracting clinically important protein biomarkers, sub-cellular molecular complexes, and organelles from cells and tissues, Pressure Biosciences said.

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The Scan

Breast Cancer Risk Related to Pathogenic BRCA1 Mutation May Be Modified by Repeats

Several variable number tandem repeats appear to impact breast cancer risk and age at diagnosis in almost 350 individuals carrying a risky Ashkenazi Jewish BRCA1 founder mutation.

Study Explores Animated Digital Message Approach to Communicate Genetic Test Results to Family Members

In the Journal of Genetic Counseling, the approach showed promise in participants presented with a hypothetical scenario related to a familial hereditary breast and ovarian cancer syndrome diagnosis.

Computational Tool Predicts Mammalian Messenger RNA Degradation Rates

A tool called Saluki, trained with mouse and human messenger RNA data, appears to improve mRNA half-life predictions by taking RNA and genetic features into account, a Genome Biology paper reports.

UK Pilot Study Suggests Digital Pathway May Expand BRCA Testing in Breast Cancer

A randomized pilot study in the Journal of Medical Genetics points to similar outcomes for breast cancer patients receiving germline BRCA testing through fully digital or partially digital testing pathways.