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Affymetrix, Gene Network Sciences, National Center for Genome Resources, Ohio State University, Genomatica


Affy Plans Software Upgrade for New Resequencing Chip

Affymetrix said last week that it is rolling out a new custom array that can sequence 30,000 bases in two days at greater than 99.99 percent accuracy.

While it’s simply a new application area for the company's proven GeneChip technology platform, the data demands will be different, said Greg Yap, senior director of marketing for DNA analysis at Affy.

Affy is releasing a new software module to accompany the resequencing arrays, Yap said, which will run on the company's existing platform but will call bases rather than measure gene expression levels. The software comes with a “small charge” for existing customers, Yap said.

The data, which comes off the chip in the company’s proprietary GeneChip format, but can be easily exported into Fasta or other sequence-friendly formats, is then ready to manipulate just like any other sequence, Yap said.


GNS Wins ATP Grant

Ithaca, NY-based Gene Network Sciences was awarded a three-year, $2 million Advanced Technology Program grant to expand its cellular simulation technology.

The funding will permit the company to collect new experimental data points of mRNA, protein, and phosphorylated protein levels from its wet lab.

Last month, GNS received a $100,000 Phase One Small Business Innovation Research Grant from the National Institutes of Health to expand its technology platform.


NCGR and Ohio State Land NSF Plant Genomics Grant

The National Center for Genome Resources in collaboration with the Ohio Agricultural Research and Development Center at Ohio State University have been awarded a four-year National Science Foundation grant for $1.9 million to identify virulence genes in Phytophthora infestans. Researchers at both institutions will study the plant pathogen’s host interactions with potato and tomato and non-host interactions with tobacco.

NCGR will use its share of the funding to build the Phytophthora Functional Genomic Database and analysis system, a resource that will be available to all researchers worldwide and will encompass a broad range of gene expression and functional data.

NCGR will compare full-length open reading frames generated by the Ohio State researchers with publicly available P. infestans data.


Genomatica Awarded DOE Grant for Metabolic Model

San Diego-based Genomatica received a Small Business Innovative Research grant from the Department of Energy to develop a metabolic model of the soil bacterium Pseudomonas fluorescens, which degrades hazardous waste such as petroleum and crude oil compounds and toxic metals.

The aim of the model, according to the company, is to improve the bacterium’s use for toxic waste degradation.

The company will combine published draft genomic data of the bacterium with biochemical and physiological data to develop the model.

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The Scan

Unique Germline Variants Found Among Black Prostate Cancer Patients

Through an exome sequencing study appearing in JCO Precision Oncology, researchers have found unique pathogenic or likely pathogenic variants within a cohort of Black prostate cancer patients.

Analysis of Endogenous Parvoviral Elements Found Within Animal Genomes

Researchers at PLOS Biology have examined the coevolution of endogenous parvoviral elements and animal genomes to gain insight into using the viruses as gene therapy vectors.

Saliva Testing Can Reveal Mosaic CNVs Important in Intellectual Disability

An Australian team has compared the yield of chromosomal microarray testing of both blood and saliva samples for syndromic intellectual disability in the European Journal of Human Genetics.

Octopus Brain Complexity Linked to MicroRNA Expansions

Investigators saw microRNA gene expansions coinciding with complex brains when they analyzed certain cephalopod transcriptomes, as they report in Science Advances.