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South Africa’s CPGR Looks to Array-Based Diagnostics

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The Center for Proteomic and Genomic Research, a new facility based in Cape Town, South Africa, has recently begun several studies with the goal of developing array-based theranostics and diagnostics for allergies and asthma, according to a CPGR official.

Reinhard Hiller, director of the CPGR, says the center opened its doors earlier this year. Among other projects, the center has been studying asthma using an allergen chip platform Hiller helped develop as an R&D director at Vienna-based VBC Genomics, where he worked before coming to Cape Town to lead the CPGR.

The center is funded through a ZAR 20 million (US $2.8 million) grant from Cape Biotech Trust and Plant Bio, biotech regional innovation centers that dispense government funds to help grow South Africa’s biotech resources. According to Hiller, the first projects are part of CPGR’s long-term objective to establish a high-throughput biology research facility that serves the needs of the life science and biotech communities in South Africa.

As a core facility, Hiller says that CPGR is mainly engaging in joint research initiatives with the scientific community who gain access to “cutting-edge technology and the respective expertise” through the CPGR.

“Based on a strong interest expressed by clinicians in South Africa, a key focus of research is on asthma,” he says. So far the CPGR has been involved in “simple disease marker monitoring, or allergen-specific antibody monitoring, in children suffering from Type-1 allergy-related asthma,” Hiller says. “What we are really looking for is antibody patterns and if there is something that is important to understand for treatment.”

Hiller is using the antibody arrays to study immunoglobulin E, an antibody frequently associated with hypersensitivity, and immunoglobulin G, an antibody resposible for adaptive immune response, in parallel in patients to discover protective IgG antibodies.

In a few months, the CPGR will also begin studying patients with occupational asthma — respiratory problems that are attributable to an individual’s work environment.
Justin Petrone

Short Reads

Under a non-exclusive agreement with Applied Biosystems, SuperArray Bioscience will market reagents and assay kits for PCR and real-time PCR that use ABI’s SYBR Green and probe-based methods, and will develop real-time PCR reagents and technologies.

Affymetrix launched its Genome-Wide Human SNP Array 6.0, a single microarray that measures more than 1.8 million markers for genetic variation. The SNP Array 6.0 contains more than 900,000 SNPs and more than 946,000 non-polymorphic probes for the detection of copy number variation.

Aushon BioSystems licensed Oxford Gene Technology’s Southern array patents, enabling it to manufacture and sell oligonucleotide microarrays worldwide and to perform services based on oligonucleotide arrays. 

German software-development company BioBase announced that two of its software platforms are compatible with Affymetrix’s microarrary platform. The ExPlain Analysis System, for transcription regulation and pathway analysis, and the Transfac database, which stores transcription factors, binding sites, and regulated gene data, are GeneChip-compatible, according to the company.
 
The South Korean government will use Affymetrix’s SNP microarray technology in a large human genome-wide association study to identify genetic causes of complex diseases prevalent in the country. This project is commissioned by Korea’s National Institute of Health and its Center for Disease Control and Prevention.

Patents

US Patent 7,224,474. Positioning method for biochip. Inventors: Tsung-Kai Chuang, Jiann-Hua Wang, Chun-Jung Li, Mei-Leng Choi, Shu-Fen Lin. Assignee: Kaiwood Technology. Issued: May 29, 2007.
The patent claims a positioning method for biochip spotting. The method includes steps of: a) providing reference points on a biochip substrate; b) taking an image of the position of each reference point; c) calculating a first spotting position and performing spotting according to position information of the image of the positions; d) taking and recording the image of the spotted position; and more.

US Patent 7,226,734. Multiplex decoding of array sensors with microspheres. Inventors: Mark Chee, John Stuelpnagel, Anthony Czarnik. Assignee: Illumina. Issued: June 5, 2007.
The patent describes a method of decoding an array so as to determine the location of a capture probe that has been randomly distributed on the array. The method includes steps to randomly distribute probes, hybridize and detect a signal, and more.

Data Point

$20 million

ShanghaiBio, one of the major biochip firms in China, said in a news report that the market for biochip R&D services is growing and that total revenues related to this business in China last year were approximately $20 million.

The Scan

Rare Genetic Disease Partnership

A public-private partnership plans to speed the development of gene therapies for rare genetic diseases, Stat News writes.

Approval Sought for Alzheimer's Drug

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DNA Barcoding Paper Retracted

Science reports that a 2014 DNA barcoding paper was retracted after a co-author brought up data validity concerns.

Nature Papers Present Genomic Analysis of Bronze Age Mummies, Approach to Study Host-Pathogen Interactions

In Nature this week: analysis finds Tarim mummies had local genetic origin, and more.