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NCI Proteomics Push Continues with $120M Program

By Matt Jones

NEW YORK (GenomeWeb News) – The National Cancer Institute wants to push forward protein-focused cancer research technologies by investing between $75 million and $120 million in centers that will conduct biomarker discovery, verification, and new cancer proteomics studies.

The Proteome Characterization Centers (PCC) grants program is the second phase in NCI's Clinical Proteomic Technologies for Cancer (CPTC) initiative, which was started four years ago to develop technologies for identifying and quantifying proteins that could be useful as cancer biomarkers.

Phase one of the CPTC program established five multidisciplinary centers that showed they could be effective in addressing analytical variability problems in proteomics. Now, the second phase will build a network of centers that will target biomarkers and will aim to improve tools for protein detection, identification, and quantification.

The PCCs will use discovery units and verification units to implement the two-step process in the biomarker development pipeline, and the findings from these studies will be made public through a central data center.

"[We] want to develop a much greater understanding of cancer at the molecular level," Chris Kinsinger of NCI's Office of Cancer Clinical Proteomics Research told GenomeWeb Daily News this week.

To do that, Kinsinger said, "You have to have a greater understanding of how the genomic component of cancer is now translated into the functional world of proteomics.

"We feel like we have enjoyed some successes in terms of understanding the variability for the mass spec technology as it relates to proteins, and we've also produced a number of monoclonal antibodies" Kinsinger said of the CPTC program.

He added that the program has yielded "a more refined pipeline to use proteomics to discover biomarkers" that NCI ultimately hopes to "hand off to labs that can do clinical validation."

Henry Rodriguez, who is director of NCI's Clinical Proteomic Technologies for Cancer programs, told GWDN that the program, with the combination of the research centers and the publicly-open portal for feeding proteomics to the research community, is modeled on The Cancer Genome Atlas project.

"They start with a common sample," he said. "They farm it out to labs that do different types of characterization on that sample, and then they share all of that data through a pretty niftily designed web portal that provides a boon to the research community. Our intent is to have all of this data going public," Rodriguez explained.

NCI will fund between six and eight PCCs under the program. They will be charged with identifying and characterizing proteins from tumor and normal biospecimens, and any biomarkers will then be prioritized for verification and assay development.

For the verification process, the PCCs will develop analytically validated multiplex assays that will be conducted on a large number of biospecimens. Any proteins passing through this screening will be considered high-value targets for translation into other initiatives into clinical qualification studies.

The centers also will use the funding to pursue improvements in proposed technologies for protein detection, identification, and quantification, and they are expected to share information and leverage it from other centers in the network.

The CPTC also is reaching out to partners that are critical to getting cancer proteomics technologies translated out into the clinical realm, including working with the US Food and Drug Administration and the American Association of Clinical Chemistry.

"One of the things we recognized is that ultimately you want to get these assays into a clinical environment, and to get them there that would involve the clinical chemistry community," Kinsinger said.

Earlier this year, NCI-CPTC inked a memorandum of understanding with AACC that expands and formalizes collaborations between the two groups. The agreement covers principles including the exchange of information, research and data, the development and use of proteomics technologies for use in clinical applications, and mutual collaborations with industry, academia, government entities, and other non-profits.

"Our organization has spent quite a lot of time with NCI getting them to understand and recognize the value of clinical chemists and clinical laboratories when it comes to translating biomarkers," Chairman of the AACC Proteomics division, Saeed Jortani, told GWDN sister publication ProteoMonitor in March.

The CPTC network also met with FDA in a workshop to present technology it was developing, and it later submitted a 510(k) application in order to receive FDA input and comments.

"One of the things that we recognized then was that, ultimately, you want to get these assays in the clinical environment, [which] involves the clinical chemistry community," Kinsinger said.

Kinsinger said the program now has created a "beautiful triad," that will include the new PCC network and the CPTC centers, the FDA's regulatory arm that is looking at the analytical validation of the new methodologies, and the clinical laboratories that are represented in this program by AACC.

The idea of the team network structure, Kinsinger and Rodriguez agreed, is a critical part of this program.

"We think we're taking on some issues here that can't be solved by one lab alone, that you really need a team approach to address them," Rodriguez said. He said that a "flexible network" would be essential to address some of the overarching themes in the cancer proteomics field.

"If you have a team-based structure it allows different laboratories to quickly ascertain an issue as a network, and they can do a divide-and-conquer approach," said Kinsinger. "They could quickly adjust some of the technologies to see how to optimize them in a cross-network environment."

According to the RFA announcing the program, NCI expects to award between $15 million and $24 million to the CPTC-PCC centers in 2011.

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