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As Genotyping Costs Fall, Affy Calls for Study Change

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It’s no secret that Affymetrix’s unofficial flagship product is its Genome-Wide Human SNP Array 6.0, called the 6.0 for short, which helped buoy the firm’s second-quarter revenues by 10 percent year over year after only being on the market for part of the quarter.

But while Affy has been touting the 1.8 million marker array — which contains both SNP and copy number variation content — as the best chip in the market, it has also been strongly advocating that scientists using the arrays in whole-genome association studies take advantage of their relatively low cost to replicate their finding using the same array, rather than validating their SNPs of interest via custom genotyping methods.

Affy first slashed its genotyping prices in the summer of 2006 to regain a foothold in the market while facing intense competition from Illumina, which is the only other company with the resources to challenge Affy in the whole-genome genotyping array space.

Specifically, the company lowered the price of its 500K Mapping Array Set to $250 per chip, which was followed by the launch of its 1 million marker SNP 5.0 Array in January, and now the SNP 6.0, which sells for around $400. According to Affymetrix President Kevin King, the price factor could change the way researchers approach association studies and could ultimately benefit Affy’s top-selling product.

“It provides a cost-effective price point for larger studies, and it is allowing users to do replication studies instead of targeted genotyping,” King told investors during the UBS Global Healthcare Services Conference in New York this fall.

“In the past, because of whole-genome association cost, customers typically divided their experiments into two pieces,” he said. “What has changed with 6.0 with our higher content and compelling economics is that now customers can cost-effectively interrogate the entire population at both the whole-genome level as well as at the replication level with 6.0.”

— Justin Petrone

Short reads

Personal genetics firm Navigenics will begin offering consumer genotyping services based on the Affymetrix GeneChip platform in late 2007 or early 2008.

BioMicro Systems, which markets the MAUI hybridization product line, has closed a round of Series B financing, bringing the total it has raised since inception to $10 million.

UK-based molecular biology supplier GRI inked a distribution agreement with Applied Microarrays, through which it will market AMI’s CodeLink Gene Expression Bioarray System for human, mouse, and rat whole genomes in the UK and France. Applied Microarrays acquired CodeLink for an undisclosed sum from GE Healthcare in May.

Xceed Molecular, formerly known as Metrigenix, planned to launch this month a low-throughput and relatively affordable microarray platform called Ziplex. Xceed says the platform will be a good fit for clinicians who have not been interested in existing array-based tests.

Illumina will handle genotyping services for a joint study for the Type I Diabetes Genetics Consortium that aims to identify genes that influence the risk of developing the disease. Illumina expects to process more than 6,500 samples for the study, which is being conducted by the Center for Public Health Genomics at the University of Virginia on behalf of the National Institute of Diabetes and Digestive and Kidney Diseases.

Patents

US Patent 7,276,336. Methods of fabricating an addressable array of biopolymer probes. Inventors: Peter Webb, Michael Caren, Kyle Schleifer, and Jay Bass. Assignee: Agilent Technologies. Issued: October 2, 2007.

The patent claims a method of fabricating an addressable array of biopolymer probes on a substrate according to a target array pattern using a deposition apparatus, and a deposition apparatus that can execute the method and computer program products for the apparatus. The deposition apparatus, when operated according to a target drive pattern based on nominal operating parameters of the apparatus, provides the probes on the substrate in the target array pattern. The method includes examining at least one operating parameter for an error from a nominal value.

US Patent 7,280,922. System, method, and computer software for genotyping analysis and identification of allelic imbalance. Inventors: Rui Mei and Teresa Webster. Assignee: Affymetrix. Issued: October 9, 2007.

The patent covers a method and tools to determine the “genotype of a sample using a plurality of probes.” The call may also be “based upon the relative allele signals.”

Data point

$580

Cost of Illumina’s Human 1M chip for whole-genome association studies, launched in June 2007.

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