Validated clinical pharmacodynamic (PD) assays that reliably quantify drug effects on molecular targets in tissue specimens are critical tools for converting molecular oncology breakthroughs into targeted therapeutics, and subsequently for translating these new drugs into patients by confirming that they work as intended in early clinical trials (Phase 0, I and II). The vision and pioneering effort of DCTD to develop, clinically implement and transfer to the oncology research community highly reproducible and informative PD assays, combined with the strategic decisions of its dedicated SAIC-Frederick support program to use only assay technologies that have proven clinical applicability and to apply diagnostic assay expertise and developmental principles to PD assays, have already yielded validated assays for several molecular targets since the program's inception in mid-2005. One of these assays accelerated the clinical development of a molecular targeted agent from Phase 0 trials directly into combination Phase 1 studies with best available therapies in five CTEP-sponsored trials. The molecular data from the validated assay justified bypassing any single agent Phase I or II trials, where it was not expected to show any single agent activity in most genetic backgrounds. The DCTD expects that using additional validated PD assays to simultaneously interrogate multiple molecular targets both within and across important signaling pathways in a single biopsy specimen and/or surrogate tissue will point to rational combinations of molecular targeted agents. Because many molecular targeted therapies are used in combination regimens with best available chemotherapy, there is also anticipated value in being able to evaluate the effects of molecular targeted therapy on markers of chemotherapeutic sensitivity and resistance to guide the selection of which chemotherapeutic regimens are suitable for combination with the molecular therapy, and which should be avoided in combination because, for example, the molecular targeted therapy induces high expression of a known molecular determinant of drug resistance. The DCTD envisions using extending the proven principles of assay development, validation and clinical implementation to develop and validate clinical PD assays for known chemotherapeutic markers, and then to deploy these in the Phase 0 trial setting under the FDA's Exploratory IND Guidance in order to not only confirm the molecular therapeutics intended action on drug target but also to confirm that it is not altering determinants of chemotherapeutic sensitivity for the best available regimens with which it is planned to be combined in Phase I and II trials. In addition, the rapid development, analytical validation of assay performance, SOP-driven validation transfer from the development lab to the clinical lab pioneered a formal process that solves two of the most vexing and intransigent problems regarding laboratory studies of experimental drug action in cancer patient specimens at academic medical centers: first, because the drugs are experimental, the drug effect assays are highly specialized, and are only used during early clinical drug development, they have little intrinsic market value. So, investigators must obtain the key reagents of the assay from R&D suppliers that do not adhere to quality assurance measures required of manufacturers of diagnostic tests that are critical for achieving consistent lot-to-lot content and performance. The SAIC-Frederick clinical PD support program has solved this issue by establishing an internal quality assurance program for key reagents and centrally procuring them, qualifying them for use in the validated assay, and then making them available upon request via the DCTD Biomarker's website to the oncology research community. In addition, this website provides access to the validated assay SOP, the specimen handling SOP to achieve valid assay results, and training courses offered at the NCI-F for laboratory staff from extramural institutions that wish to conduct a validated assay on site. To qualify to conduct their own assays, institutions are required to send laboratory staff for assay operator certification classes at NCI-Frederick, which include laboratory-based training in specimen handling, conduct of the assay, and data analysis and reporting by SAIC-Frederick senior scientific staff and lectures on PD assay theory and practice by senior DCTD staff. Via the convergence of DCTD direction and portfolio management with SAIC-Frederick's application of technical expertise in diagnostic testing, a number of validated assays are already in the clinic or moving into the clinic at this time, including assays for PARP target function, PARP pathway expression, DNA damage by chemotherapeutic agents, DNA methylation, tumor cellularity, tumor stem cell identification and enumeration of and molecular changes in circulating tumor cells. These validated assays are achieved using a number of clinically useful technology platforms of the SAIC-Frederick PS program: immunoassay, quantitative RT-PCR, quantitative immunofluorescence of tumor sections and cytospins, and the Veridex Cell Search instrument a clinically validated platform for enumerating circulating tumor cells. The steps of PD assay development, clinical implementation including SOP-based specimen handling, analytical validation and transfer to a recipient clinical lab have been formalized into milestones and metrics by the SAIC-Frederick PD support program, and rigorously achieving each milestone in the process is key to the successful introduction of additional clinical PD assays into the early clinical trial setting. These steps are definable and have objective metrics that allow decisions at each stage of development and validation regarding feasibility and go/no-go decisions by management. They are amenable to formalized statements of work that could be used to outsource this process to qualified vendors in order to accelerate the rate of PD assay development and validation and expand the capacity without any compromise in the quality of the process or the resulting assays. The SAIC-Frederick PD program already has demonstrated a high level of competence managing outside vendors and specifying similarly complex, specialized technical services, such as customized antibody generation and the scaled production of purified biologics used as key assay reagents. DCTD envisions that the SAIC-F PD support program can direct such an expanded effort via directing the technical development and validation of additional assays under contracts to highly qualified vendors with the technical capabilities to follow the steps exactly. Maximum numbers of clinical PD assays could be developed by the SAIC-Frederick PD program by using a strategy of tiered technical support services, in which a small number of highly qualified vendors are selected for some particular assays, but also manage a larger number of second tier vendors to develop assays with which they have unique specializations and hold the second tier vendors to the same high level of quality assurance. This management strategy offers several advantages, not the least of which is that is minimizes the number of projects with which the SAIC-Frederick senior staff will need to interact so as not to lessen the assay development effort at NCI-Frederick, it lessens the number of transactions that SAIC-Frederick Research Contracts department will need to oversee, and the two-tier system significantly increases the number of vendors that can be contributing to the effort with a small number of contract technical managers/project officers. There are assays in development at SAIC-Frederick that could be immediately transferred to accelerate reduction to SOP-driven assays that can be validated within 6-12 months and returned to the NCI for clinical implementation in the Developmental Therapeutics Clinic. It is also envisioned that as more assays are made ready for clinical use, the emphasis of the DCTD on unmet medical need in uncommon cancers will result in a more centralized center where physicians can access these validated assays that may be very useful in personalizing each cancer patient's therapy based on molecular markers. Many of these PD assays will provide important information about molecular targeted therapy trials sponsored by DCTD/CTEP, including inhibitors of molecular targets controlling stem cell proliferation and survival, angiogenesis, cell cycle progression and novel cytoreductive mechanisms like mitotic spindle inhibitors. Other PD assays in early to mid-development in the SAIC-Frederick PD program that will benefit from accelerated development and validation include assays of direct drug action on the DNA methyltransferases that play major roles in controlling DNA methylation and abnormal gene silencing in cancers, and drug action on the enzyme topoisomerase I which is already a validated therapeutic target via the market approval of the camptothecins. Outsourcing the final steps of the defined, formal process that has yielded past assay successes along with active project management will free up the SAIC-Frederic staff to focus on the development of much needed assays in areas of multi-channel analysis of drug response in rare tumor stem cells, new assays to distinguish cells recovering from chemotherapy damage or committing to cell death via apoptosis or necrosis, and the high-value payoff of adapting as many validated PD assays as possible to the customized use of the Veridex platform instrumentation to isolate circulating tumor cells.