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Additional file 1: Box 1S. Postoperative pulmonary complication diagnostic criteria. Table 1S Methodological instructions for collection of clinical criteria within the Melbourne Group Score postoperative pulmonary complication diagnostic tool. Table 2S. List of International Classification of Diseases (ICD-10) clinical codes extracted. Figure 1S Proportion of participants with positive clinical criteria on each postoperative day.

Purpose Fresh-frozen (FF) tissue is the optimal source of DNA for whole-genome sequencing (WGS) of cancer patients. However, it is not always available, limiting the widespread application of WGS in clinical practice. We explored the viability of using formalin-fixed, paraffin-embedded (FFPE) tissues, available routinely for cancer patients, as a source of DNA for clinical WGS. Methods We conducted a prospective study using DNAs from matched FF, FFPE, and peripheral blood germ-line specimens collected from 52 cancer patients (156 samples) following routine diagnostic protocols. We compared somatic variants detected in FFPE and matching FF samples. Results We found the single-nucleotide variant agreement reached 71% across the genome and somatic copy-number alterations (CNAs) detection from FFPE samples was suboptimal (0.44 median correlation with FF) due to nonuniform coverage. CNA detection was improved significantly with lower reverse crosslinking temperature in FFPE DNA extraction (80 °C or 65 °C depending on the methods). Our final data showed somatic variant detection from FFPE for clinical decision making is possible. We detected 98% of clinically actionable variants (including 30/31 CNAs). Conclusions We present the first prospective WGS study of cancer patients using FFPE specimens collected in a routine clinical environment proving WGS can be applied in the clinic.

Purpose: Organ-confined muscle-invasive bladder cancer is treated with cystectomy or bladder preservation techniques, including radiation therapy. There are currently no biomarkers to inform management decisions and aid patient choice. Previously we showed high levels of MRE11 protein, assessed by immunohistochemistry (IHC), predicted outcome after radiation therapy, but not cystectomy. Therefore, we sought to develop the MRE11 IHC assay for clinical use and define its relationship to clinical outcome in samples from 2 major clinical trials.Methods and Materials: Samples from the BCON and BC2001 randomized controlled trials and a cystectomy cohort were stained using automated IHC methods and scored for MRE11 in 3 centers in the United Kingdom.Results: Despite step-wise creation of scoring cards and standard operating procedures for staining and interpretation, there was poor intercenter scoring agreement (kappa, 0.32; 95% confidence interval, 0.17-0.47). No significant associations between MRE11 scores and cause-specific survival were identified in BCON (n = 132) and BC2001 (n = 221) samples. Reoptimized staining improved agreement between scores from BCON tissue microarrays (n = 116), but MRE11 expression was not prognostic for cause-specific survival.Conclusions: Manual IHC scoring of MRE11 was not validated as a reproducible biomarker of radiation-based bladder preservation success. There is a need for automated quantitative methods or a reassessment of how DNA-damage response relates to clinical outcomes.

A 51-year-old woman presented with a 2-month history of double vision and numbness around her left ear. She subsequently became unsteady on her feet and developed further cranial nerve abnormalities, before complaining of headache, nausea and vomiting. Imaging revealed features suggestive of two intracranial lesions; one non-contrast-enhancing high-signal area in the cerebellum with associated calcification, and a second contrast-enhancing low-signal area in association with the fourth ventricle, and at surgery there were two apparent components to the tumor. The histopathological features were those of a low-grade, focally calcified tumor comprising atypical ganglion and glial cells with interspersed Rosenthal fibres. Mitotic figures were not seen, and there was no necrosis. An infiltrate of small reactive lymphocytes was interspersed among the neoplastic cells. Immunohistochemistry revealed expression of synaptophysin by many of the dysplastic ganglion cells, with some co-expressing neurofilament protein and occasionally glial fibrillary acidic protein (GFAP). Several of the dysplastic ganglion cells also expressed CD34. The glial cell population was highlighted by GFAP. Ki-67 (MIB-1) activity was not noted among the neoplastic populations--the few positive nuclei in these areas were those of interspersed reactive CD3-positive T lymphocytes. In addition, at the edge of one of the biopsies was a dense infiltrate of mitotically-active large atypical CD 20-positive B lymphocytes, among which the Ki-67 (MIB-1) labeling index reached 80%. The final diagnosis was diffuse large B cell lymphoma arising within a ganglioglioma of the cerebellum, and this is believed to be the first reported case.

Aims: The coordinated expression of the Notch ligands Delta-like 4 (Dll4) and Jagged (Jag)1 is believed to define appropriate endothelial sensitivity to vascular endothelial growth factor (VEGF). Preclinical data suggest that Dll4-Notch signalling may confer resistance to anti-VEGF therapy with bevacizumab, and Jag1 may antagonize Dll4-Notch. The aims of this study were to characterize the expression of Dll4 and Jag1 in primary glioblastomas. Methods and results: Immunohistochemistry was performed on 40 glioblastomas and normal brain using validated antibodies against Dll4 and Jag1. In-situ hybridization for Dll4 was performed on serial sections and compared with protein expression. Dll4 expression was localized to the cytoplasm and membrane of endothelial cells in all glioblastomas; it was weak or absent in normal brain. Jag1 expression was observed in the cytoplasm and membrane of glomeruloid and non-glomeruloid endothelial cells from 76% and 67% of glioblastomas, respectively. However, endothelial Jag1 expression was less intense and less prevalent than Dll4. There was no association between Dll4 and Jag1 expression. Conclusions: In summary, Dll4 and Jag1 are expressed in glioblastoma vasculature. These data may define subsets of glioblastoma that might be sensitive (Dll4 +/Jag1 +) or resistant (Dll4 +/Jag1 -) to bevacizumab. Our data also suggest that anti-Dll4 therapy should be evaluated experimentally in glioblastoma. © 2012 Blackwell Publishing Limited.