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Affomix, City of Hope Collaborate to Create Proteomic Profiles of Cancer

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This story originally ran on Jan. 19.

Antibody firm Affomix will supply the City of Hope with monoclonal antibodies that will be used to create proteomic profiles that are characteristic of certain cancers, the company announced today.

Under the collaboration, Affomix will use its high-throughput, automated antibody-selection technology to provide City of Hope with recombinant antibodies that are designed to be readily tagged with oligonucleotide "zipcodes" that will make them compatible with next-generation sequencers, Affomix said in a statement.

Financial terms of the deal were not disclosed.

In its statement, the company said that the collaboration focuses on the establishing the clinical utility of "digital proteomics" with next-generation sequencers. In an e-mail John Boyce, Affomix's head of business development defined "digital proteomics" as "the discovery and quantitation of proteomic signatures indicative of a particular phenotype. Similar to digital gene expression, whereby one counts the transcripts within a sample and does not rely on ratiometric comparison between samples – this will allow for the elucidation of pathways within a sample. "

Affomix is creating antibodies against a large set of proteins that are fused to oligonucleotide "zipcodes," which will be complementary to capture sequences on next-generation sequencing readout methodologies.

"By pulling down the proteins, removing any unreacted probes from the reaction, and then sequencing and counting the zipcodes, we will be able to determine how many of the corresponding proteins are present and thus create a digital proteomic profile for the phenotype in question," Boyce continued. "We are combining high-throughput protein pull-down in conjunction with next generation sequencing as a readout."

Cancers that Affomix and City of Hope hope to create profiles for include renal and prostate cancers.

Affomix, based in Branford, Conn., was founded in 2008 and utilizes a yeast two-hybrid-based technology dubbed Y2H Express that excises non-specific antibodies from a library of antibodies generated in yeast cells.

Michael Sherman, president of Affomix, told ProteoMonitor in April that the company's technology improves the specificity of antibodies from 5 percent to 30 percent in yeast two-hybrid systems. The long-term goal of the company is to develop a so-called "affome," an antibody equivalent to the proteome and genome, in which a set of antibodies would be generated for all proteins in the human proteome [See PM 04/09/09].

Affomix plans to do this by first generating antibodies against at least two epitopes of every protein in the human proteome, and then using its technology to select antibodies against polymorphisms, mutations, and post-translational modifications.

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