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Affy’s New Algorithm Cuts 500K Price Tag


Affymetrix, armed with a new genotyping algorithm and facing increasing competition in the whole-genome genotyping market, says it will reduce the price of its Mapping Array 500K set by as much as 75 percent.

According to Affy, the new algorithm, co-developed with researchers at the University of California at Berkeley and the Broad Institute, has freed up half the space on the two 250K chips that comprise its 500K set and has enabled the company to “immediately” cut its price to $250. Depending on whether the customer is academic or non-academic, the price has been cut by between 70 percent and 75 percent.

The algorithm has also enabled the company to consolidate the two chips into a single 500K product, which is due to become available before the end of the year.

Gregory Marcus, senior product manager of DNA analysis at Affymetrix, says that the new algorithm is based on work done on the firm’s 100K Array by Terry Speed at UC Berkeley. The algorithm, called the Bayesian Robust Linear Model with Mahalanobis distance classifier, or BRLMM, was first published in Bioinformatics in January.

“Affymetrix was able to eliminate the mismatch probes that were not used by the BRLMM algorithm,” Marcus says. “This freed up half of the chip real estate, which enabled us to load more content on each array.”

Marcus says that the BRLMM algorithm is delivered in three forms: via software with a user interface, a command line tool, and an open source tool. He adds that the “call rate for heterozygote genotypes are now the same as the call rates for homozygote genotypes.”

“The previous algorithm tended to under-call heterozygotes, which could have introduced a bias in downstream analysis,” Marcus says.

— Justin Petrone


US Patent 7,080,766. Manufacture of singulated supports comprising arrays. Inventors: John McEntee and Alexander Williamson. Assignee: Agilent Technologies. Issued: July 25, 2006.

According to the abstract, this invention provides methods and an apparatus “for cutting a sheet of material into single supports where each of the single support has an array area to which is bound an array of chemical compounds.” The apparatus includes “an input conveyor, an output conveyor, a driver for moving the sheet from the input conveyor to the output conveyor and a breaking mechanism for breaking the sheet into single supports.”


US Patent 7,081,617. Gas-phase purification of biomolecules by ion mobility for patterning microarrays and protein crystal growth. Inventors: John McLean, David Russell, and J. Albert Schultz. Assignee: The Texas A&M University System. Issued: July 25, 2006.

This patent describes “a method and device for the gas-phase separation of ionic biomolecules including peptide, and protein or inorganic cluster ions or nanoparticles by ion mobility and for depositing them intact on a surface in a spatially addressable manner.” The surface can be modified for constructing microarrays of biologically relevant materials or for promoting highly ordered protein crystal growth.

Merck and Shanghai Biochip will collaborate in an oncology research program using SBC’s microarray-based gene expression profiling technology. Under the agreement, Merck will provide specimen samples, expertise, financial and technical support, and will train SBC personnel.

NimbleGen Systems has selected a number of limited access partners to work with its second-generation NimbleChip HD2 microarrays, which contain 2 million probes. Some of the early access partners include the Yale Center for Genomics and Proteomics, the UC Davis Genome Center, and the Laboratory for Gene Regulation at the Ludwig Institute for Cancer Research at UC San Diego.

CapitalBio will offer genotyping services using Affymetrix’s GeneChip human mapping 500K array set. The company is a certified Affymetrix Service Provider and has used Affy’s array technology as part of its existing services in China for more than a year.

Japan’s NGK Insulators has licensed from Oxford Gene Technology patents for oligonucleotide microarrays in order to manufacture its own arrays. The company will make the arrays using a technology called Geneshot, which uses piezoelectric ceramic microactuators.

Scientists at the Duke University Medical Center have built the first genomic test to predict which patients with early-stage lung cancer will need chemotherapy and which won’t. The array-based test will be part of a clinical trial next year.



Value of phase I grant from NIH to QBI Life Sciences to create drug absorption profiles for early stage drug candidates. The company will be developing a surface plasmon resonance imaging-based microarray assay with GWC Technologies.

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