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BioArray Briefs: 2009.01.20


Coriell Using Affy's DMET in Gene/Drug Interaction Studies

The Coriell Personalized Medicine Collaborative will use Affymetrix's DMET Plus biomarker panel for a national study of markers for drug response, Affy said last week.

The CPMC, a branch of the Coriell Institute for Medical Research, is using the panel to expand studies it has already been conducting with Affy's Genome-Wide Human SNP Array 6.0 to identify genes that are associated with complex health conditions, such as diabetes, cancer, and heart and blood vessel diseases.

The DMET Plus panel includes an array, reagents, and software. Affy said it offers a cost-effective method for measuring variations in genes associated with drug metabolism and transport.

The CPMC's intent is to enroll 10,000 individuals by the end of the year, and ultimately 100,000, in an effort to understand why some subpopulations and individuals respond differently to a drug than anticipated.

Affy said that five organizations are now using the DMET Plus for pharmacogenomic studies and that 18 more organizations are scheduled to be trained on the platform.

Financial terms of the agreement were not released.

Sheep Genomics Consortium Develops SNP Chip with Illumina

The International Sheep Genomics Consortium and Illumina have completed part of a project aimed at developing a SNP microarray for characterizing variations in sheep genomes, and during 2009 ISGC plans to sequence the genomes of as many as six sheep, ISGC said last week.

IGSC is an international group of institutes and companies that are funded by AgResearch of New Zealand, Australia, the UK, and the US Department of Agriculture. IGSC is aimed at developing tools to explore the sheep genome.

Initial sequencing for the project was conducted in parallel at Otago University in Dunedin, New Zealand, and the Human Genome Sequencing Center at Baylor College of Medicine, while Illumina provided additional sequencing.

The genome assembly, SNP detection, and selection were conducted by AgResearch and Australia's Commonwealth Scientific and Industrial Research Organization. Illumina used this data to create the OvineSNP50 BeadChip for use in selecting traits for breeding.

The goal of this part of the project was to develop a chip that could collect data from over 60 breeds of sheep that could be used in pinpointing traits that may be important economically, ISGC said.

"Groups will use the chip for a variety of objectives ranging from whole-genome association studies to unraveling the process of domestication and impact of selection," ISGC Secretary James Kijas said in a statement.

"We took the opportunity to use new DNA sequencing technologies which allowed us to identify over 300,000 SNPs," AgResearch's John McEwan said.

The ISGC, which began in 2002, still plans to produce a reference sequence of the sheep genome and a preliminary study of copy number variation in sheep.

"We began this work by creating what we called a virtual sheep genome, which contained the best bet about where the sheep's vast amount of hereditary information could be found on its 26 chromosomes," ISGC researcher Brian Dalrymple said in a statement.

"We drew on the work that had already been done to sequence the human, cow, horse, and dog genomes to create our virtual sheep genome assembly," Dalrymple added.

As sequencing costs decrease over the coming year, Dalrymple continued, "We plan to complete the sequencing of six individual sheep genomes."

"During 2009, as sequencing costs continue to decline, we plan to complete the sequencing of six individual sheep genomes. This will be really important as the availability of reference genome sequences will open up a range of possibilities."

Cogenics Partners with SinoGenoMax in China

Beijing-based genomics research services company SinoGenoMax will offer Cogenics' genotyping services in China, Cogenics' parent company, Clinical Data, said this week.

"Our partnership with SinoGenoMax provides us with an established presence in China and an experienced international service partner who operates with similar platforms and high quality standards," Cogenics Global Manager Michael Lutz said in a statement.

"The extensive pharmaceutical and biotechnology infrastructure and large number of clinical trials conducted in China make this an increasingly important market for clinical genotyping services."

SinoGenoMax CEO Danny Ching said the partnership also "represents a significant opportunity for SinoGenoMax to widen its international spectrum."

Cogenics has facilities in North Carolina, Texas, the UK, France, and Germany.

Arrayit Licenses Microarrays, Reagents to Belmedtechnika

Arrayit has licensed its microarray platform and associated reagents to Belmedtechnika, an equipment provider in Belarus, Arrayit said last week.

Arrayit, a subsidiary of Integrated Media Holdings, said that Belmedtechnika will deploy its high-throughput genotyping platform to screen and test number patient samples "quickly, affordably, and accurately."

The licensing agreement permits Belmedtechnika to use Arrayit's multi-patient platform to examine many patients' DNA samples at one time. Belmedtechnika also gained the right to use Arrayit's contact printing technology for diagnostic applications.

Financial terms of the agreement were not released.

Accelr8 Faces Delisting from NYSE Alternext

Accelr8 said last week that it has received notice from the NYSE Alternext that it is not in compliance with certain listing standards concerning its amount of stockholder equity, and that it must submit and implement a plan to regain compliance within 18 months.

The company said it is not in compliance with a section of the NYSE Alternext's listing standards because it holds stockholder equity of less than $6 million and it has had losses from continuing operations and net losses in its five most recent fiscal years.

According to Accelr8, it will have until Feb. 6 to draft a plan to regain compliance, and it will have until July 6, 2010, to implement that plan. In the interim, the company will be subject to periodic review to determine its progress.

The company said it has informed NYSE Alternext that it intends to submit a plan in a timely fashion to resolve its listing deficiencies and regain compliance.

The Scan

Study Examines Insights Gained by Adjunct Trio RNA Sequencing in Complex Pediatric Disease Cases

Researchers in AJHG explore the diagnostic utility of adding parent-child RNA-seq to genome sequencing in dozens of families with complex, undiagnosed genetic disease.

Clinical Genomic Lab Survey Looks at Workforce Needs

Investigators use a survey approach in Genetics in Medicine Open to assess technologist applications, retention, and workforce gaps at molecular genetics and clinical cytogenetics labs in the US.

Study Considers Gene Regulatory Features Available by Sequence-Based Modeling

Investigators in Genome Biology set sequence-based models against observational and perturbation assay data, finding distal enhancer models lag behind promoter predictions.

Genetic Testing Approach Explores Origins of Blastocyst Aneuploidy

Investigators in AJHG distinguish between aneuploidy events related to meiotic missegregation in haploid cells and those involving post-zygotic mitotic errors and mosaicism.