Final Activity Report Summary - PHARMACODIAGNOSTICS (Pharmacodiagnostics for prediction of breast cancer treatment) Breast cancer is the most prevalent cancer appearing in woman. Every year approximately 4 000 women are diagnosed in Denmark. Pharmacodiagnostics is an emerging discipline with a major potential for improving future clinical care. The principle behind pharmacodiagnostic is the linkage of treatment outcome and the underlying molecular alteration. In oncology pharmacodiagnostics occurred silently with development of anti-estrogenic treatments targeting oestrogen receptor (ER) positive breast cancers in late 1960s. Recently the development of Herceptin (targeting the HER2 oncoprotein in breast cancer) has demonstrated the close relationship between molecular alteration and clinical response. The main objectives of this reintegration grant was for Tove Kirkegaard to use the knowledge she obtained as a Marie Curie Research fellow in Dr Bartlett's research group in Glasgow regarding identification, testing and validating pharmacodiagnostics in clinical settings. The work has mainly been based on the following three parts: 1) To finish analysing gene copy number status of CCND1 and EMSY, located adjacent on chromosome 11. Both genes have been proposed to be involved in cancer development. We found using fluorescence in situ hybridisation (FISH) that patients with genetic changes (amplification) of CCND1 (n = 42) and EMSY (n = 9) had decreased survival (OS) as compared to patients whose tumours had normal CCND1 gene copy number. Patients with both CCND1 and EMSY gene amplification (n = 25) exhibited decreased OS as compared to patients whose tumours had normal CCND1 and EMSY gene copy number or patients having amplification of either CCND1 or EMSY. 2) HER2 gene amplification is essential for identifying breast cancer patients that might benefit from treatment with Herceptin. Genetic changes of other genes, MYC (alias c-MYC) and PTEN, have also been implicated in breast cancers and patients with HER2 and MYC co-amplification have shown to benefit from treatment with chemotherapy alone compared to patients treated with a combination of chemotherapy and Herceptin and we therefore hypothesised that PTEN and MYC gene copy number changes are predictive for clinical benefit of Herceptin and vinorelbine in advanced breast cancer. HER2 amplified tumours from 39 patients were collected. FISH analysis for MYC and PTEN was successful for 36 (92 %) and 39 (100 %) of the 39 patients. In contrast to our hypothesis, there was a trend that patients with PTEN deleted tumours were more likely to benefit from treatment as compared to patients with normal PTEN gene copy numbers. To further analyse the role of MYC and PTEN in resistance to Herceptin in a larger patient cohort should be analysed. 3) As with other treatments, a large number of cancer patients do not respond to chemotherapy and identification of markers to predict patient response and outcome to specific chemotherapeutics i.e. treatment with 5-fluorouracil (5-FU) containing chemotherapy are desired. The efficacy of 5-FU is mediated through a functioning pathway and the aim was to investigate gene copy numbers using FISH of three key candidate genes from this cycle, TYMS, TP and DHFR in three different kind of cancer; head and neck, colorectal and breast cancer. Genetic changes of all three analysed markers in the thymidylate synthase pathway were detected using FISH. Unfortunately, we did not see any association between copy number changes of the three genes either separately or combined and patient outcome. Further studies need to be performed to identify the role of the thymidylate synthase pathway in mediating resistance to 5-FU containing chemotherapy. In this project, we have validated gene copy numbers of specific markers in three different clinical settings using FISH and confirmed that the FISH technique is a very valuable and precise method to identify genetic changes in tumour tissue.