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Beijing Genomics Institute, Affy, EBI, Xanthon, Aviva, Illumina, Genomic Solutions


Beijing Genomics Institute Presents Rice Chip

The Beijing Genomics Institute of the Chinese Academy of Sciences announced at the International Rice Congress in Beijing last week that it had developed a rice gene expression array, which it will make freely available to researchers.

The array, based on the indica rice genome published by the BGI earlier this year, contains about 54,000 genes, both a unigene set of cDNAs and physical clones of predicted genes, according to Bin Liu, head of research and collaboration at the BGI. It is provided on three glass slides.

The Institute of Electrical Engineering of the Chinese Academy of Sciences is involved in the production of the arrays, using an arrayer it developed and configured.

BGI will make the rice chip first available to the International Rice Research Institute as well as to Xingwang Deng’s group at Yale University. Moreover, several other centers — mainly academic and not-for-profit institutes — will also obtain access soon, according to Liu. Several institutes have expressed interest in working with the arrays at last week’s conference, he said.

An updated version of the array, based on “the complete map of the rice genome,” will probably be available by the end of this year.

Although researchers are currently not charged for the arrays, they may have to cover the manufacturing costs in the future if no funding source can be secured, according to Liu.


Affy and EBI Collaborate on Data Delivery

Affymetrix told BioArray News last week that it has been working with Alvis Brazma at the European Bioinformatics Institute to develop a pipeline to deliver array descriptions in MAGE-ML format. MAGE-ML data from Affymetrix will be available to the EBI by early October, and the EBI will likely incorporate it into ArrayExpress by the last quarter of 2002, according to Affymetrix. MAGE-ML data files for Affymetrix array information will also be available via NetAffx by the end of October.


Xanthon Loses Its Charge: Shuts Down and Lays off Remaining Employees

$24 million in venture financing was not enough for Xanthon, of Research Triangle Park, NC, to keep its batteries stoked. The company, which had been developing high-density electrochemical detection-based microarrays, closed its doors and laid off the 17 staffers left after an earlier round of layoffs, late this summer.

“They had trouble with their first product being delayed, and they just couldn’t work out the bugs and get it produced,” said Barry Teater, a spokesman for the North Carolina Biotechnology Center. ”And then they ran short of money, as everybody is these days. The combination of the two hitting at once really did them in.”

Xanthon’s technology relied on an electrochemical platform to help it detect nucleic acids without the need for sample preparation, amplification, or the use of fluorescent, chemiluminescent, or radioactive labels.

The company had collaborations with Duke University chemistry professor Michael Pirrung and University of North Carolina chemistry professor Holden Thorp to research higher-density arrays. Pirrung and Thorp have been developing electrochemical detection methods for arrays that could enable the arrays to include up to 10 million electrodes per square centimeter.

Last fall, after a roll out of the product was delayed, Xanthon responded by firing 10 of its 50 employees. Then in April, three months after CEO Jim Skinner called it quits, the company laid off additional staff that brought its headcount to 17.

Over the summer, the remaining staffers were laid off, with a couple of people left behind to close the company down.


Biochip Startup Aviva Lands $11.8 Million in Series B Venture Capital Financing

San Diego biochip startup Aviva Biosciences has closed on an $11.8 million Series B round of financing. The financing round brings the total amount the company has raised to $16.8 million.

China Development Industrial Bank of Taiwan, which has previously invested in Aviva, led the financing round. The company’s Asian roots go back to its founding, as its core technology is based on a patent for technology licensed from Tsinghua University in China.

Additional investors include Pac-Link Management of Taiwan, and spotting company Axon Instruments, with whom Aviva has signed a deal to develop a patch clamp chip to capture single cells for ion channel measurements and another chip for rare cell isolation.

The company just hired former Lynx chief executive Norrie Russell as its CEO.


Illumina Gets More SNP Business from GlaxoSmithKline

Illumina, which has counted GlaxoSmithKline as a customer since November of last year, just announced that the two had signed a new genotyping services agreement to develop a large set of validated SNP assays.

The company said it would also develop these assays into a “whole- genome linkage disequilibrium mapping product” that Glaxo can use for association studies of patient samples. The company hopes to identify disease loci in these studies.

This project is expected to take several months, and to involve a process of selecting a set of SNP markers for assay development, Illumina said.

“We’re very pleased to be working with GSK in such a seminal area of genomics research and we’re particularly excited by the opportunity to build one of the industry’s first high-quality linkage disequilibrium maps, Jay Flatley, Illumina’s president and CEO, said in a statement.


Genomic Solutions Says it Will Appeal Nasdaq Delisting

Genomic Solutions, which is in the process of being acquired by Harvard Bioscience, said it would appeal a September 12 notice from the Nasdaq notifying the company that it would be delisted because its stock had closed at under $1 a share for 90 days.

The company said it had requested a hearing before the Nasdaq Listing Qualifications Panel.


TM Bioscience Attracts $3M in Funding

Tm Bioscience of Toronto has obtained a commitment of CA $4.7 million ($3 million) in financing from MDS capital’s managed fund Canadian Medical Discoveries Fund.

The company said it expects the financing deal to close early in the fourth quarter.

“This minimally dilutive financing ensures that we are funded to complete the development, manufacturing, and commercialization of a suite of genetic tests for coagulation, P450, cystic fibrosis, melanoma and others,” said Greg Hines, President and CEO of Tm Bioscience, in a statement.

The Canadian Medical Discoveries fund has over $310 million under management.


Psychiatric Genomics Collaborates on Microarray Study with Budapest Institute

Psychiatric Genomics, which is using functional genomics to develop small-molecule drugs for mental disorders, has signed an agreement to collaborate with Hungary’s National Institute of Psychiatry and Neuro logy on microarray-based tissue analysis.

Peter Gaszner, the institute’s director and a professor of psychiatry, will work with scientists at Psychiatric Genomics to analyze brain tissue samples from the institute’s collection using microarrays to compare gene expression profiles. All research information will be shared among the parties.

The company intends to then screen targets it obtains from this collaboration.

The Scan

Single-Cell Sequencing Points to Embryo Mosaicism

Mosaicism may affect preimplantation genetic tests for aneuploidy, a single-cell sequencing-based analysis of almost three dozen embryos in PLOS Genetics finds.

Rett Syndrome Mouse Model Study Points to RNA Editing Possibilities

Investigators targeted MECP2 in mutant mouse models of Rett syndrome, showing in PNAS that they could restore its expression and dial down symptoms.

Investigators Find Shared, Distinct Genetic Contributors to Childhood Hodgkin Lymphoma

An association study in JAMA Network Open uncovers risk variants within and beyond the human leukocyte antigen locus.

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.