New Affymetrix Software Helps Identify Cancer Driver Events

Affymetrix will highlight its new Concurrent Molecular Analysis Profiling (CoMAP™) capability at the 2015 annual meeting of the American Association for Cancer Research. The program enables cancer researchers to gain rapid insight into the functional impact of DNA copy-number alterations by combining whole-genome copy-number data with gene expression profiles to easily and cost-effectively visualize and identify cancer driver events.

Recent whole-genome DNA analysis of cancer samples has demonstrated that copy-number alterations affect more of the genome than any other DNA abnormality. Many of these alterations are “drivers” of cancer, while others are merely “passenger” events. Deciphering which DNA alterations are “driver” versus “passenger” events has been a challenge. The new Affymetrix CoMAP capability enables the concurrent correlation of genome-wide gene expression changes with copy-number alterations, helping to rapidly identify and prioritize the number of potential driver events, which in turn can lead to the identification of functional biomarkers. This is particularly valuable to researchers studying “C class” tumors, which are characterized by functional copy-number changes, as opposed to somatic mutations (“M class”).

The new CoMAP capability is now included in Affymetrix’ Chromosome Analysis Suite (ChAS) 3.0 Software, enabling researchers to easily and quickly analyze and visualize the functional impact of copy-number changes on gene expression in cancer samples, including degraded FFPE tissue. This capability instantaneously combines and correlates whole-genome copy-number data with mRNA and miRNA data generated from Affymetrix’ tools such as OncoScan® FFPE Assay Kit, GeneChip® Human Transcriptome Array 2.0, and GeneChip® miRNA 4.0 Array.

The Affymetrix approach with CoMAP enables researchers to go from samples to insights in just three days. Correlation maps may be generated for all RefSeq genes or a customized gene list.

“Despite the billions of dollars spent every year on research, cancer remains one of the leading causes of death worldwide,” said Andy Last, Ph.D., Chief Operating Officer of Affymetrix. “We are committed to enabling science with practical and cost-effective tools so that researchers can rapidly translate their discovery into improved cancer diagnosis and therapy.”