Capturing it all

Kimmel Cancer Center to study genomics using febit’s sequence capture and microRNA solutions

Lloyd Dunlap
HEIDELBERG, Germany—From among a half-dozen competitors inthe rapidly expanding target-enrichment market, the Cancer Genomic MicroarrayFacility at the Kimmel Cancer Center of the Thomas Jefferson University inPhiladelphia has selected febit's Geniom RT Analyzer to advance its biomedicalresearch on targeted next-generation sequencing (NGS), genome-wide singlenucleotide polymorphism (SNP) and microRNA (miRNA) analysis.

The Kimmel Cancer Center focuses on the discovery of cancer riskfactors, prevention strategies and cancer diagnostics as well as targetedcancer treatment to improve survival and quality of life for patients.

The Kimmel Center will use the advanced microfluidics of thepatented Geniom Biochip, which according to febit, offers the highest degree ofautomation, flexibility and efficiency available. 

"Geniom is a flexible and high-throughput technology formiRNA analysis and targeted re-sequencing, and with our recent acquisition ofan NGS system, I believe that the febit HybSelect application will be apowerful complement to our repertoire," says Prof. Paolo M. Fortina, directorof the Laboratory of Cancer Genomics at the Kimmel Cancer Center. "Mylaboratory focuses on the development and validation of technologies fordiagnostics with emphasis on SNP detection, mRNA and miRNA profiling in avariety of cancers and other medical conditions. The automation and flexibilityof febit's technology allows us to investigate a variety of different diseasesin short periods of time."

Fortina notes that his lab talked to several systemproviders and selected febit for both its technology and willingness to beflexible in coming to an agreement to develop an assay. The new system has beenunpacked, installed and tested and training began the first week of January.

"We are obviously in the early stage but are workingactively in oncology—breast cancer, for example," he says. "We envision that inthe next year we'll have a project on the whole transcriptome and anothertargeting other specific cancers such as colon cancer. We think febit hasdeveloped highly interesting technology that has great potential."

Peer Staehler, CSO of febit biomed gmbh, notes that theinstrument sold to Kimmel does two assays—HybSelect and miRNA profiling, bothof which use microfluidic chips. And both share a common goal, he states, whichis exploration of the genome at the cutting edge in an automated system.

"HybSelect enables large-scale studies on biologicalvariations that lead to cancer," Staehler says.

In the past, studying variations in DNA across a largenumber of individuals was difficult. HybSelect resequences part of thegenome—50 to 60 gigabases in one run—to do 100 or 1,000 samples, not just one,to facilitate the study of biological variation between healthy indviduals andcancer patients or between different patients.

HybSelect is also used for miRNA profiling to determine thepresence and activity of the approximate 1,000 miRNAs that are involved inregulating cancer cells. The functional understanding of these genes will leadto biomarkers that may have clinical, research and diagnostic application.

"miRNA biomarkets are very information rich," Staehler notes. "Thedifference is almost like going from analog to digital. We are pleased that theKimmel Cancer Center will use the Geniom RT Analyzer to evaluate mutations andmiRNAs in a variety of diseases. The Geniom technology enables large cohortstudies with statistical relevance provided by Geniom's high degree ofautomation." 

Lloyd Dunlap

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