Aim is to develop a product that can be used to detect and visualize differences between normal and cancer tissues.

The National Human Genome Research Institute awarded Geospiza a phase 2 SBIR grant of $1.2 million to develop an application on its GeneSifter cloud computing platform that detects cancer-related DNA sequence variations. The firm will work with Weil Cornell Medical College, Mayo Clinic on a tool that can be used to identify and visualize variations found when comparing normal and cancer tissues.

“Through this funding we will be able to attack the biggest challenges researchers face when attempting to develop cancer tests,” explains Todd Smith, Geospiza’s CTO. “There are substantial DNA variations between normal and cancer tissue. Researchers wanting to develop a new cancer test need to figure out those differences and put them in a biological context. This process requires easy to use visual presentation of millions of data points to see those differences.”

The GeneSifter software provides integrated solutions for next-generation sequencing analysis and LIMS. The most recent release, which was announced this winter, features splice index analysis and base variant calling for next-generation sequencing as well as enhanced support for Affymetrix miRNA and Exon/Gene ST arrays.

“The new sequencing technologies are letting us probe cancer biology in ways we’ve never contemplated before,” comments David Smith, professor at the Mayo Clinic in Rochester, Minnesota. “It’s clear that the next generation of diagnostic tests can only be made by effectively combining whole transcriptome analysis with genome sequences on a per patient, per sample basis. The numbers of combinations are daunting. The application developed through this work will be well suited for translating research observations to actionable clinical tests.”

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