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BioArray Briefs: Feb 15, 2002


Ciphergen: Protein Chips used in Seminal Ovarian Cancer Detection Study


In a new Lancet study finding distinct protein biomarkers for ovarian cancer, researchers used Ciphergen Biosystems’ protein chips, the company said this week.

The study, which was conducted by National Cancer Institute and US Food and Drug Administration researchers and is published in the February 16th issue of the Lancet, was released eight days early as the Lancet editors deemed its results too groundbreaking to delay any further: Currently there is no reliable early detection method for ovarian cancer, one of the most deadly forms of cancer in women.

The researchers compared blood serum samples from 50 ovarian cancer patients to those of 50 women without ovarian cancer using Ciphergen protein chips. They found signature proteins that were present in the 50 disease samples, and then successfully used these patterns to correctly select out 50 ovarian cancer patients from a blinded sample of 116 serum samples with and without the disease. In addition to this 100 percent sensitivity, the test had a 98 percent specificity level, and a 94 percent positive predictive value. In other words, three samples were read as false positives.

Ciphergen’s chips use a process known as surface enhanced laser desorption ionization(SELDI), a process similar to mass spectrometry on their surface. The latest version of this system is designed to enable analysis of protein expression in crude clinical samples such as the serum samples in this ovarian cancer study, as well as laser capture microdissection, biopsies, tissue, and urine.

The company has sold over 225 systems, and said this equipment has been used in studies of prostate, colon, lung, liver, pancreatic, bladder, and stomach cancer; as well as leukemia, cardiovascular and neurodegenerative diseases; and toxicological studies.


Fluidigm Sells Flexi-Fluidic chips to GlaxoSmithKline


Fluidigm, the South San Francisco microfluidics company that designs flexible rubber chips, has sold its technology to GlaxoSmithKline.

Under the deal, Fluidigm will provide GlaxoSmithKline with microfluidic tools and design software for chip customization, as well as microfluidic chips. Glaxo is planning to use these chips in the pharmaceutical development process.

The advantage of these chips, according to Fluidigm, is that their rubber material and manufacturing process enables them to be designed and fabricated significantly more cheaply than other microfluidics chips, and within a matter of weeks, not months as with other microfluidic chips. This process, multi-layer soft lithography, involves molding the two layers of the chip separately on top of channel designs etched in silicon, then sandwiching them together. Additionally, the flexible chip material enables the chips to be designed with tiny pressure-sensitive valves, pumps, and mixers that can facilitate fluid control and mixing at the micro level without using capillary electrophoresis.

This deal comes after Fluidigm’s November series C fundraising round, in which it raised $34 million. To date, Fluidigm has raised over $50 million.


HHS Center to Provide Landing Pad for Genomics Companies in Federal Government


The US Department of Health and Human Services has launched the Council on Private Sector Initiatives to Improve Security, Safety and Quality of Health Care, a new liaison between businesses with new health care ideas — especially ones related to bioterrorism preparedness — and the federal government.

The council was designed to hear business ideas that will improve “public health preparedness and the delivery of health care services,” said HHS secretary Tommy Thompson in a statement.

The new forum will serve as a switching station for companies that want to develop “new ideas,” apply for grants or programs, or sell new products to the federal government.

It was launched in order to make this process easier and more streamlined: Rather than navigate the alphabet soup of federal health agencies, companies can approach the council directly, which will then refer requests to the appropriate department.

Member agencies include the US Centers for Disease Control and Prevention, the US Food and Drug Administration, the US National Institutes of Health, the Office of Public Health Preparedness, the Agency for Healthcare Research and Quality, and the Centers for Medicare and Medicaid Services, among others.

The council held its first meeting on January 23, and is currently reviewing requests from 18 companies. Contact information is available at

The Scan

Study Points to Tuberculosis Protection by Gaucher Disease Mutation

A mutation linked to Gaucher disease in the Ashkenazi Jewish population appears to boost Mycobacterium tuberculosis resistance in a zebrafish model of the lysosomal storage condition, a new PNAS study finds.

SpliceVault Portal Provides Look at RNA Splicing Changes Linked to Genetic Variants

The portal, described in Nature Genetics, houses variant-related messenger RNA splicing insights drawn from RNA sequencing data in nearly 335,700 samples — a set known as the 300K-RNA resource.

Automated Sequencing Pipeline Appears to Allow Rapid SARS-CoV-2 Lineage Detection in Nevada Study

Researchers in the Journal of Molecular Diagnostics describe and assess a Clear Labs Dx automated workflow, sequencing, and bioinformatic analysis method for quickly identifying SARS-CoV-2 lineages.

UK Team Presents Genetic, Epigenetic Sequencing Method

Using enzymatic DNA preparation steps, researchers in Nature Biotechnology develop a strategy for sequencing DNA, along with 5-methylcytosine and 5-hydroxymethylcytosine, on existing sequencers.