Geospiza has received a $1.2 million Phase II Small Business Innovative Research grant from the National Human Genome Research Institute to develop an application that lets users identify and visualize DNA sequence variations in comparative analyses of normal and cancer tissue samples using the firm’s GeneSifter platform, a statement said.
The company will develop the application in collaboration with investigators at Weill Cornell Medical College and the Mayo Clinic.
The partners hope to develop an application that will ultimately make it possible to use data from cancer research to develop new clinical tests for the disease.
The award follows on a Phase I SBIR grant awarded for the project in 2009 [BI 10/9/2009].
Part of the challenge, Todd Smith, Geospiza’s chief technology officer explained, is that researchers need to be able to view variations and “put them in a biological context.”
He said that the new application will provide a “visual presentation of millions of data points” that will make it easier to spot the differences between normal and cancerous samples.
According to the project's grant abstract, the partners will develop software "will have general use for any application where DNA sequencing is used to understand the genetic basis of human health, disease, and response to drug therapies."
Geospiza said in the abstract that it will develop methods "to combine assay results from many samples with de novo [next-generation sequencing] datasets for assays like RNA-seq and existing data such as those in [the Gene Expression Omnibus and the Sequence Read Archive], and information resources from dbSNP, cancer genome databases, and ENCODE."
In addition, the company said that it will "develop the necessary scalable computing infrastructure and novel [user interfaces] needed to organize and process the data and explore and annotate the results."