Appraising the relevance of DNA copy number loss and gain in prostate cancer using whole genome DNA sequence data.

A variety of models have been proposed to explain regions of recurrent somatic copy number alteration (SCNA) in human cancer. Our study employs Whole Genome DNA Sequence (WGS) data from tumor samples (n = 103) to comprehensively assess the role of the Knudson two hit genetic model in SCNA generation in prostate cancer. 64 recurrent regions of loss and gain were detected, of which 28 were novel, including regions of loss with more than 15% frequency at Chr4p15.2-p15.1 (15.53%), Chr6q27 (16.50%) and Chr18q12.3 (17.48%). Comprehensive mutation screens of genes, lincRNA encoding sequences, control regions and conserved domains within SCNAs demonstrated that a two-hit genetic model was supported in only a minor proportion of recurrent SCNA losses examined (15/40). We found that recurrent breakpoints and regions of inversion often occur within Knudson model SCNAs, leading to the identification of ZNF292 as a target gene for the deletion at 6q14.3-q15 and NKX3.1 as a two-hit target at 8p21.3-p21.2. The importance of alterations of lincRNA sequences was illustrated by the identification of a novel mutational hotspot at the KCCAT42, FENDRR, CAT1886 and STCAT2 loci at the 16q23.1-q24.3 loss. Our data confirm that the burden of SCNAs is predictive of biochemical recurrence, define nine individual regions that are associated with relapse, and highlight the possible importance of ion channel and G-protein coupled-receptor (GPCR) pathways in cancer development. We concluded that a two-hit genetic model accounts for about one third of SCNA indicating that mechanisms, such haploinsufficiency and epigenetic inactivation, account for the remaining SCNA losses.

Whole blood mRNA in prostate cancer reveals a four-gene androgen regulated panel.

Due to increased sensitivity, the expression of circulating nucleotides is rapidly gaining popularity in cancer diagnosis. Whole blood mRNA has been used in studies on a number of cancers, most notably two separate studies that used whole blood mRNA to define non-overlapping signatures of prostate cancer that has become castration independent. Prostate cancer is known to rely on androgens for initial growth, and there is increasing evidence on the importance of the androgen axis in advanced disease. Using whole blood mRNA samples from patients with prostate cancer, we have identified the four-gene panel of FAM129A, MME, KRT7 and SOD2 in circulating mRNA that are differentially expressed in a discovery cohort of metastatic samples. Validation of these genes at the mRNA and protein level was undertaken in additional cohorts defined by risk of relapse following surgery and hormone status. All the four genes were downregulated at the mRNA level in the circulation and in primary tissue, but this was not always reflected in tissue protein expression. MME demonstrated significant differences in the hormone cohorts, whereas FAM129A is downregulated at the mRNA level but is raised at the protein level in tumours. Using published ChIP-seq data, we have demonstrated that this may be due to AR binding at the FAM129A and MME loci in multiple cell lines. These data suggest that whole blood mRNA of androgen-regulated genes has the potential to be used for diagnosis and monitoring of prostate cancer.

Method for sampling tissue for research which preserves pathological data in radical prostatectomy.

BACKGROUND: The diagnosis and treatment of prostate cancer is a challenging global healthcare issue requiring significant molecular research. Such research frequently utilizes fresh frozen human tissue which needs to be obtained in a manner acceptable to the pathologist which does not compromise tumor diagnosis or staging. METHODS: Radical prostatectomy specimens were handled in a standardized method before being sliced fresh. Leaving the margins intact, multiple cylindrical cores were removed using a large skin punch and the sites were marked on a prostate map. The cylindrical cores were placed onto individual, pre-numbered foil squares and snap frozen in liquid nitrogen. Prostate maps were aligned with formalin-fixed paraffin embedded hematoxylin and eosin stained sections of the sampled slice to select tumor regions. Frozen tumor tissue cylinders were processed taking one section for hematoxylin and eosin staining, 6 µm × 50 µm sections for molecular studies and a further section for hematoxylin and eosin staining. This was performed for the length of the cylinder. RESULTS: A total of 150 prostates have been removed and sliced using this technique. Pathological assessment remained uncompromised. Using the sequential hematoxylin and eosin stained frozen sections, cellularity could be monitored closely in tissues processed for research. The yield of RNA and DNA extracted was high (tumor mean 2.4 µg (RNA) and 12.7 ng per 300 µm tissue) and of high quality (mean tumor RIN 5.9). CONCLUSIONS: This novel, rapid sampling and processing method provides high quality tissue for research without compromising pathology.

Formatively evaluating the importance of different aspects of an electronic blood transfusion system from the end users' point of view: a questionnaire study.

Blood transfusion is a process in which potential errors may result in serious adverse events to patients. To help improve the safety and efficiency of the blood transfusion process an electronic clinical transfusion management system is being piloted by NHS Connecting for Health. Evaluation of the implementation is being carried out in parallel. One component of the evaluation project aims to assess the importance placed in the various potential benefits of this new system by patients and healthcare workers. A questionnaire was generated and completed by healthcare workers and patients. Results indicate respondents viewing all factors as at least "important". "System" factors were deemed most important. Overall, clinical workers expressed the lowest importance to new process factors. Ultimately these results will be measured against final satisfaction with the system to assess 'fit' between perceived importance and satisfaction to guide areas for attention and resource allocation.

The Oxford clinical intranet: providing clinicians with access to patient records and multiple knowledge bases with internet technology.

The Oxford Clinical Intranet provides clinicians in primary and secondary care across Oxfordshire with: Access to information about their patients held on multiple remote disparate computer systems, including admissions and episodes, Laboratory Medicine reports, Radiology reports and hospital discharge letters. The patient records are managed using CSW Case Notes. Access to support and advisory information, developed both within the organization and collected from other sites and projects, a wide range of internal handbooks, directories and guidelines and links to external resources, including evidence-based resources, the Cochrane Collaboration and the NHS National electronic Library of Health. Automated retrieval and presentation of the support information that is contextually appropriate to the task being carried out by the clinician and the information held about the patient. For example laboratory reports are linked to handbooks and other reference sources using eLABook, a web-interfaced database subsystem. Internet technology has been used throughout, thus providing a thin-client architecture with cross-platform ability. Appropriate data standards have been used across the communicating systems and the intranet is compliant with the UK eGovernment Interoperability Framework. The intranet was developed at low cost and is now in routine use. This approach appears to be transferable across systems and organisations.

An integrated knowledge management system for the clinical laboratories: an initial application of an architectural model.

eLABook is a web-distributed knowledge management system designed to support the needs of clinicians and laboratory staff in the selection and interpretation of investigations in laboratory medicine. Access can be by hyperlinks at any point through the request-report cycle, by browsing down a hierarchy, and by various search approaches. The information describes service issues, which are predominantly locally determined, and clinical implications, which may be local, national, governmental and international. The application has been implemented across the Oxford Clinical Intranet to support secondary care in the four hospital sites of the Oxford Radcliffe Hospitals and by general practitioners in Oxfordshire. The knowledge base is capable of rapid changes in response to input from both developers and users. It supports authoring, editing and a full audit trail of changes. The selected architecture allows very large scale hierarchical structures and is designed to accommodate future needs for an object-distributed processing deployment.