Connected by ChIPs

Beckman Coulter Genomics partners with Genpathway to unravel complex DNA-protein interactions

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DANVERS, Mass.—Beckman Coulter Genomics Inc. and Genpathway Inc. will work together to offer customers whole-genome chromatin immunoprecipitation sequencing (ChIP-Seq) services, the companies announced last month.

The strategic partnership will provide researchers investigating gene regulation and genetic pathways a single source for services supporting genome-wide studies of transcription factor binding, gene transcription and epigenetic events.

"We wanted to partner with a larger organization with a broader reach into world markets," says Genpathway CEO Patrick Mallon.

Chromatin immunoprecipitation has become an increasingly valuable method for studying protein/DNA interactions that include standard transcription factors, co-regulating proteins, chromatin-associated enzymes and histone markers. The method has also been extended to the study of DNA methylation and even transcription itself. With the advent of whole-genome analysis using ChIP-on-Chip or ChIP-Seq, insights into genome-wide gene regulation, gene expression, mechanisms of chromatin modification and pathway analysis are emerging. However, while extremely useful, this method can also prove challenging.

"ChIP-Seq is more and more in demand," says Elizabeth Nickerson, global business line leader of DNA sequencing at Beckman Coulter Genomics. "It's a sophisticated process, so it made sense to partner with leading-edge innovators to respond to the dynamic research needs of scientists worldwide, which is fundamental to our goals as an essential genomic services provider. The alliance strategically leverages both companies' core competencies and expertise to supplement our DNA sequencing services with the highest quality, most reliable ChIP-Seq capabilities available."

ChIP-Seq combines the sophistication of chromatin immunoprecipitation with the power of ultra high-throughput, next-generation DNA sequencing to enable the study of complex interactions between proteins and nucleic acids. Mapping protein-DNA complexes in vivo on a genome-wide scale with ChIP-Seq builds a picture of the intricate network of interactions that regulate genes and genetic pathways in a sample. Comparing ChIP-Seq results from different conditions—diseased versus normal cells, for example—can reveal distinguishing patterns of genetic regulation that may be biologically significant.

The two companies will work in tandem, with Genpathway providing the ChIP-Seq sequencing portion. Beckman Coulter will then use Ilumina gene sequencing analysis before handing the process back to Genpathway for ChIP-Seq-specific data analysis.
DNA experiments aren't all black and white, notes Nickerson. Up- and down-regulation of genetic control can introduce gray areas, nuances of control, she states.
As Mallon observes, ChIP-Seq enables researchers to assess regulatory events—"the heads and nodes of actual pathways," as he puts it. The process elucidates the mechanism of action in DNA-protein interactions to demonstrate what is happening in the genetic pathway.

"Pharma researchers want to focus on the mechanism of action of disease processes in order to move toward personalized medicine, to identify new targets and patient populations that will be receptive to different treatments." Mallon says. "We are pleased that Beckman Coulter Genomics has selected Genpathway as its partner to accommodate the unprecedented requirement for ChIP-based technologies to advance studies of biological processes and disease states. This dynamic new alliance is a natural fit, coupling Beckman Coulter Genomics' sequencing and marketing capabilities with Genpathway's ChIP experience to offer the global research community an expert source of ChIP sequencing data and analysis."

The start-to-finish ChIP-Seq services will include experimental design and consultation, antibody qualification, performance of ChIP assays with post-ChIP QC, next-generation sequencing and comprehensive data analysis.

Beckman Coulter Genomics, a wholly owned subsidiary of Beckman Coulter, was created by combining Beckman Coulter's Agencourt Bioscience with the newly acquired Cogenics.

Genpathway is an early-stage pharmacogenomics company that provides specialized drug and biomarker discovery and development services that aid in predicting drug responses, enabling personalized treatments.

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