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BioArray Briefs: Dec 9, 2008

Cincinnati Hospital Uses Affymetrix Technology to Develop Jaundice Test
Affymetrix this week said that researchers at the Cincinnati Children’s Hospital Medical Center have used the firm’s microarray technology to develop a molecular diagnostic test for patients with inheritable forms of jaundice.
According to the firm, the Cincinnati hospital has developed a test that is CLIA- and CAP-approved and is available worldwide. The Jaundice Chip is intended to more precisely identify patients at high risk for progressive liver disease. The chip detects the five most common genetic mutations in children with inherited causes of jaundice, which represent around half of all pediatric chronic liver disease cases, said Affy.
The firm noted that jaundice occurs in one out of every 2,200 live births in the US, and in patients with pathological jaundice the disease may progress to end-stage liver disease or cirrhosis.

UK Hospitals to Perform Validation Studies on Pathwork Tumor Test
Pathwork Diagnostics this week said that Guy’s and St. Thomas’ NHS Foundation Trust in London will be the first UK hospitals to conduct validation studies on its Tissue of Origin test.
The test uses a microarray to measure the RNA expression pattern of a tumor and compare it to a panel of 15 known tumor types, representing 60 morphologies overall, to help the determine the tumor’s origin. It is based on Pathwork’s PathChip gene-expression array, which runs on Affymetrix’s GCS3000Dx diagnostic platform.
This past summer, the US Food and Drug Administration cleared the test for marketing in the US. It was the second in vitro diagnostic multivariate index assay, or IVDMIA, device to be cleared by the FDA, following Agendia’s MammaPrint test, which the agency approved in February 2007 (see BAN 8/5/2008).
"In this study, pathologists and oncologists at Guy's and St Thomas' will not only be able to validate the test for use in their institution, but more importantly, soon be able to use information generated to help them determine the most effective, cancer-specific treatment regimen for hard-to-diagnose cases," said Pathwork President and CEO Deborah Neff in a statement.
Further terms of the collaboration were not disclosed.

Doctors' Network to Offer Navigenics' Genotype Test
Navigenics will provide its genomic testing service through a network of physicians in order to help their patients learn about their potential genetic risks for certain diseases, Navigenics said this week.
Under the agreement, Redwoods Shores, Calif.-based Navigenics will provide its services to doctors in the MDVIP network, which is spread across 25 states and Washington, DC. These physicians practice preventive, proactive, and personalized healthcare, the company said.
The Navigenics test will be used to identify markers that could indicate a patient’s risk levels for developing conditions such as type 2 diabetes, cancer, heart attack, and celiac disease. Navigenics launched the test, which is based on the Affymetrix GeneChip platform, last year (see BAN 11/13/2007).
Navigenics said it spent six months working with MDVIP studying how doctors and patients integrated preventive genomics in more than 40 clinical encounters.
MDVIP CEO Edward Goldman said in a statement that patients involved in the study “overwhelmingly found the experience positive, they felt empowered rather than anxious, and they indicated a desire to change their lifestyles and more productively work with their physicians.
The network of 280 doctors, which serves over 100,000 patients, will discuss the testing process with patients. Patients may also consult with a genetic counselor, and Navigenics will conduct the genome scanning and the personal risk analysis.

French Cancer Institute Expands Agilent Microarray Service, Training Agreement
Agilent Technologies said this week that France’s Institut de cancerologie Gustave Roussy Genomic Center has renewed and expanded an agreement making it a service provider and training center for Agilents microarray technologies.
The company said that IGR, which became an Agilent service provider for gene expression microarrays in 2005, has renewed that status to offer “a broad panel of microarray technologies, such as comparative genomic hybridization, one-color and dual-color gene expression, and microRNA profiling.
The new agreement gives IGR an expanded panel of services for CGH and miRNA applications, and the center also received authorization to perform training for technologies that meet Agilents certification standards.
Agilent gave IGR the new and extended service provider status after assessments of the center’s proficiency in analyzing Agilents 60-mer oligo microarrays and using the Agilent 2100 Bioanalyzer, as well as sample labeling, hybridization, array scanning, feature extraction, and data analysis.
"The partnership between IGR and Agilent is very comprehensive and efficient, ranging from Certified Service Provider, to European Training Center but also at the R&D level," Agilent Diagnostics Senior Director Michael McNulty said in a statement. "We will considerably reinforce our partnership, and are very impressed by the efficient integration of our CGH, gene expression and miRNA technologies in the innovative research programs and efforts aiming to improve knowledge that leads to more patient-specific treatments."

Biobase to Integrate imaGene’s Clones Into Databases
Biobase will integrate imaGene’s molecular resources, including full open reading frame clones, into its biological databases, the firms announced this week.
Under the agreement, Biobase has integrated direct links from imaGene’s research tools into the gene and protein report pages of its Transfac, Transpath, and Proteome databases. Biobases database customers will now have access to imaGenes clones, including those from the International ORFeome Collaboration, Genecopoeia, and Life Technologies.
Further terms of the agreement were not disclosed.

NIH Awards BUSM $2.9M to Study Lung Disease
The National Institutes of Health has awarded $2.9 million to the Boston University School of Medicine to study the causes of chronic obstructive pulmonary disease, a disease associated with smoking that is characterized by airflow limitation.
According to BUSM, the purpose of the study is to develop an understanding of the processes that contribute to COPD pathogenesis that will ultimately yield tools for stratifying and treating COPD patients based on the molecular processes that are responsible for their disease.
Principal Investigator Avrum Spira, an associate professor of medicine and pathology at BUSM, said in a statement that it is possible to detect signs of disease-specific processes occurring deep in the lung by examining, using microarray technology.
In this study, we will use this approach to help figure out the molecular processes that give rise to COPD in individual patients, Spira said. BUSM is one of is one of seven centers to receive a four-year grant from the NIH to use genomic technologies to study lung disease.

Bayer to Evaluate Protagen's UNIarray
Protagen last week said that Bayer HealthCare will evaluate the firm’s UNIarray technology for discovering biomarkers for patient stratification and predictive diagnosis of atrial fibrillation.
Protagen’s UNIarray is designed to help develop diagnostics based on indication-specific autoantibody patterns in blood samples. The firm said that such autoantibody patterns are present not only in several autoimmune diseases but also in cancer, neurodegenerative disorders, and some healthy individuals.
Bayer HealthCare is currently studying atrial fibrillation after heart surgery, a condition that cannot be predicted with current diagnostic tools, Protagen said.
The firms did not say how long the evaluation period would last, and they did not disclose any financial terms of the pact.

The Scan

Drug Response Variants May Be Distinct in Somatic, Germline Samples

Based on variants from across 21 drug response genes, researchers in The Pharmacogenomics Journal suspect that tumor-only DNA sequences may miss drug response clues found in the germline.

Breast Cancer Risk Gene Candidates Found by Multi-Ancestry Low-Frequency Variant Analysis

Researchers narrowed in on new and known risk gene candidates with variant profiles for almost 83,500 individuals with breast cancer and 59,199 unaffected controls in Genome Medicine.

Health-Related Quality of Life Gets Boost After Microbiome-Based Treatment for Recurrent C. Diff

A secondary analysis of Phase 3 clinical trial data in JAMA Network Open suggests an investigational oral microbiome-based drug may lead to enhanced quality of life measures.

Study Follows Consequences of Early Confirmatory Trials for Accelerated Approval Indications

Time to traditional approval or withdrawal was shorter when confirmatory trials started prior to accelerated approval, though overall regulatory outcomes remained similar, a JAMA study finds.