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.

The Early Effects of Rapid Androgen Deprivation on Human Prostate Cancer.

UNLABELLED: The androgen receptor (AR) is the dominant growth factor in prostate cancer (PCa). Therefore, understanding how ARs regulate the human transcriptome is of paramount importance. The early effects of castration on human PCa have not previously been studied 27 patients medically castrated with degarelix 7 d before radical prostatectomy. We used mass spectrometry, immunohistochemistry, and gene expression array (validated by reverse transcription-polymerase chain reaction) to compare resected tumour with matched, controlled, untreated PCa tissue. All patients had levels of serum androgen, with reduced levels of intraprostatic androgen at prostatectomy. We observed differential expression of known androgen-regulated genes (TMPRSS2, KLK3, CAMKK2, FKBP5). We identified 749 genes downregulated and 908 genes upregulated following castration. AR regulation of α-methylacyl-CoA racemase expression and three other genes (FAM129A, RAB27A, and KIAA0101) was confirmed. Upregulation of oestrogen receptor 1 (ESR1) expression was observed in malignant epithelia and was associated with differential expression of ESR1-regulated genes and correlated with proliferation (Ki-67 expression). PATIENT SUMMARY: This first-in-man study defines the rapid gene expression changes taking place in prostate cancer (PCa) following castration. Expression levels of the genes that the androgen receptor regulates are predictive of treatment outcome. Upregulation of oestrogen receptor 1 is a mechanism by which PCa cells may survive despite castration.

Analysis of the genetic phylogeny of multifocal prostate cancer identifies multiple independent clonal expansions in neoplastic and morphologically normal prostate tissue.

Genome-wide DNA sequencing was used to decrypt the phylogeny of multiple samples from distinct areas of cancer and morphologically normal tissue taken from the prostates of three men. Mutations were present at high levels in morphologically normal tissue distant from the cancer, reflecting clonal expansions, and the underlying mutational processes at work in morphologically normal tissue were also at work in cancer. Our observations demonstrate the existence of ongoing abnormal mutational processes, consistent with field effects, underlying carcinogenesis. This mechanism gives rise to extensive branching evolution and cancer clone mixing, as exemplified by the coexistence of multiple cancer lineages harboring distinct ERG fusions within a single cancer nodule. Subsets of mutations were shared either by morphologically normal and malignant tissues or between different ERG lineages, indicating earlier or separate clonal cell expansions. Our observations inform on the origin of multifocal disease and have implications for prostate cancer therapy in individual cases.

Symptom classification in irritable bowel syndrome as a guide to treatment.

OBJECTIVE: The treatment of irritable bowel syndrome (IBS) remains unsatisfactory. There are no objective markers for diagnosis, and classification (currently based on symptoms) provides little insight into potential causes or optimal therapy. The aim of this study was to determine whether a Swedish classification of IBS based on cluster analysis of patients' symptoms might provide a guide to successful treatment. MATERIAL AND METHODS: Patients in a research clinic for IBS were classified according to criteria published by Ragnarsson & Bodemar (R&B) and also assessed independently by a clinician. Patients fulfilling the R&B criteria for subgroups 1 and 2 received specific treatments, either bulk laxatives or dietary treatment to reduce colonic fermentation, respectively. Patients who did not fit into these categories were given "best treatment" targeted at their predominant symptoms, but not limited in any way. Results before and after follow-up were assessed using a validated symptom-scoring scale. RESULTS: Seventy-one successive patients were recruited, and the numbers falling into R&B subgroups 1 and 2 were 15 (21%), and 28 (39%), respectively, leaving 28 (39%) unclassified. Receiver operating characteristic plots showed that the criteria for separation into subgroups 1 and 2 correlated well with the clinician's assessment. After treatment, symptom scores for the whole group showed a significant improvement (p<0.0001), but results were significantly better in subgroups 1 and 2 than in those unclassified, even when allowance was made for a potential therapeutic placebo effect of 40%. CONCLUSION: The R&B classification provides a helpful guide to treatment in many cases of IBS.

Assessing agreement between multiple raters with missing rating information, applied to breast cancer tumour grading.

BACKGROUND: We consider the problem of assessing inter-rater agreement when there are missing data and a large number of raters. Previous studies have shown only 'moderate' agreement between pathologists in grading breast cancer tumour specimens. We analyse a large but incomplete data-set consisting of 24,177 grades, on a discrete 1-3 scale, provided by 732 pathologists for 52 samples. METHODOLOGY/PRINCIPAL FINDINGS: We review existing methods for analysing inter-rater agreement for multiple raters and demonstrate two further methods. Firstly, we examine a simple non-chance-corrected agreement score based on the observed proportion of agreements with the consensus for each sample, which makes no allowance for missing data. Secondly, treating grades as lying on a continuous scale representing tumour severity, we use a Bayesian latent trait method to model cumulative probabilities of assigning grade values as functions of the severity and clarity of the tumour and of rater-specific parameters representing boundaries between grades 1-2 and 2-3. We simulate from the fitted model to estimate, for each rater, the probability of agreement with the majority. Both methods suggest that there are differences between raters in terms of rating behaviour, most often caused by consistent over- or under-estimation of the grade boundaries, and also considerable variability in the distribution of grades assigned to many individual samples. The Bayesian model addresses the tendency of the agreement score to be biased upwards for raters who, by chance, see a relatively 'easy' set of samples. CONCLUSIONS/SIGNIFICANCE: Latent trait models can be adapted to provide novel information about the nature of inter-rater agreement when the number of raters is large and there are missing data. In this large study there is substantial variability between pathologists and uncertainty in the identity of the 'true' grade of many of the breast cancer tumours, a fact often ignored in clinical studies.

Hidden copy number variation in the HapMap population.

Recently, the extent of copy number variation (CNV) throughout the genome has been shown to be far greater than previously thought. Further, it has been demonstrated that specific copy number variable regions (CNVRs) are associated with particular diseases, suggesting that these genetic variations may have an important biological role. Hence, calling CNVRs and subsequently classifying samples as "losses" or "gains" is of great interest. A number of papers have been published containing classifications of CNVs, and here we show how the presence of pedigree information can be used for assessing the performance of those classification methods. In this article, by examining CNV classifications made in the HapMap samples, we show that estimates of the number of false-positive classifications per individual made by current approaches can be determined. Moreover, commonplace technologies for determining the locations of CNVRs aggregate information across the maternal and paternal chromosomes at the locus of interest. Here, we show that copy number variation on each chromosome can be inferred and, in particular, we discuss the existence of a class of CNVs that are inevitably misclassified and give an estimate of their prevalence. Although our focus is not on the development of calling algorithms per se, we describe and provide an example of how our model might be incorporated into the initial classification procedure to produce more robust results. Finally, we discuss how this methodology might be applied to future studies to obtain better estimates of the extent of CNV across the genome.

Serum albumin level as a predictor of outcome in traumatic brain injury: potential for treatment.

BACKGROUND: Serum albumin level is correlated with outcome in various clinical situations. Albumin has multiple physiologic properties that could be beneficial in brain injury. The Lund therapy for elevated intracranial pressure uses albumin as part of its protocol and demonstrates favorable outcome. We sought to find out if albumin is associated with outcome after traumatic brain injury to justify conducting a randomized trial. METHODS: A retrospective study of traumatic brain injury patients was conducted. Characteristics known to influence outcome were included in a multiple logistic regression model to analyze predictors of poor outcome at 6 months. RESULTS: Data were available for 138 patients. The majority of patients (65%) had a severe injury (Glasgow Coma Scale score <9). Seventy percent of patients had a favorable outcome. Albumin levels decrease considerably from normal values in the first few days after injury irrespective of outcome. Albumin remained <25 g/L for a longer period of time in patient with an unfavorable outcome (6 days vs. 3 days, p = 0.012). Multiple logistic regression analysis identified albumin levels, age, Glasgow Coma Scale score at admission, and Injury Severity Score as predictors of poor outcome. CONCLUSION: Serum albumin level seems to be an independent predictor of poor outcome. The model also identified classic predictors of poor outcome that tends to strengthen its adequacy. Because albumin level is the only modifiable factor influencing outcome, it seems justified to carry out a randomized trial of the use of albumin in the treatment of brain injury.

Suprarenal endograft fixation and medium-term renal function: systematic review and meta-analysis.

BACKGROUND: Suprarenal fixation is widely used in endovascular aneurysm repair. Numerous small, underpowered studies have concluded that it does not increase the risk of renal impairment compared with infrarenal fixation. A recent meta-analysis demonstrated that renal infarction is more common with suprarenal fixation, but the effect on renal function remains unclear. METHODS: Electronic abstract databases, article reference lists, and conference proceedings were searched for series reporting renal function data after suprarenal fixation. There was considerable study heterogeneity with respect to key factors such as pre-existing renal dysfunction and length of follow-up. Authors were contacted to obtain individual patient data for a pooled reanalysis using standardized criteria. RESULTS: Of 46 potentially relevant citations, only 11 were eligible for inclusion in the meta-analysis. Complete data sets were available for four studies (1065 patients), with a median follow-up of 33 months. Kaplan-Meier curves were constructed for postoperative renal impairment in the suprarenal fixation and infrarenal fixation groups and compared by the log-rank test. Median time free of renal impairment was 38.5 months in the infrarenal fixation group compared with 32.4 months in the suprarenal fixation group (P = .0038). However, to account for significant methodologic differences, further analysis was required using a Weibull regression model fitted in open Bayesian inference using Gibbs sampling (BUGS). The pooled hazard ratio for deterioration of renal function after suprarenal fixation was 0.6 (95% confidence interval, 0.3-10). CONCLUSION: Currently available data are insufficient to determine the precise effect of suprarenal fixation on medium-term renal function. Conventional Kaplan-Meier analysis of the pooled data set suggested that suprarenal fixation increased the risk of renal dysfunction; however, the effect disappeared when sophisticated statistical modelling was performed to account for study heterogeneity. A randomised controlled trial of suprarenal fixation may resolve this issue.

High grade glioma: imaging combined with pathological grade defines management and predicts prognosis.

INTRODUCTION: There is ambiguity in pathological grading of high grade gliomas within the WHO 2000 classification, especially those with predominant oligodendroglial differentiation. PATIENTS AND METHODS: All adult high grade gliomas treated radically, 1996-2005, were assessed. Cases in which pathology was grade III but radiology suggested glioblastoma (GBM) were classified as 'grade III/IV'; their pathology was reviewed. RESULTS: Data from 245 patients (52 grade III, 18 grade III/IV, 175 GBM) were analysed using a Cox Proportional Hazards model. On pathology review, features suggestive of more aggressive behaviour were found in all 18 grade III/IV tumours. Oligodendroglial components with both necrosis and microvascular proliferation were present in 7. MIB-1 counts for the last 8 were all above 14%, mean 27%. Median survivals were: grade III 34 months, grade III/IV 10 months, GBM 11 months. Survival was not significantly different between grade III/IV and GBM. Patients with grade III/IV tumours had significantly worse outcome than grade III, with a hazard of death 3.7 times higher. CONCLUSIONS: The results highlight the current inconsistency in pathological grading of high grade tumours, especially those with oligodendroglial elements. Patients with histological grade III tumours but radiological appearances suggestive of GBM should be managed as glioblastoma.

Breaking the waves: improved detection of copy number variation from microarray-based comparative genomic hybridization.

BACKGROUND: Large-scale high throughput studies using microarray technology have established that copy number variation (CNV) throughout the genome is more frequent than previously thought. Such variation is known to play an important role in the presence and development of phenotypes such as HIV-1 infection and Alzheimer's disease. However, methods for analyzing the complex data produced and identifying regions of CNV are still being refined. RESULTS: We describe the presence of a genome-wide technical artifact, spatial autocorrelation or 'wave', which occurs in a large dataset used to determine the location of CNV across the genome. By removing this artifact we are able to obtain both a more biologically meaningful clustering of the data and an increase in the number of CNVs identified by current calling methods without a major increase in the number of false positives detected. Moreover, removing this artifact is critical for the development of a novel model-based CNV calling algorithm - CNVmix - that uses cross-sample information to identify regions of the genome where CNVs occur. For regions of CNV that are identified by both CNVmix and current methods, we demonstrate that CNVmix is better able to categorize samples into groups that represent copy number gains or losses. CONCLUSION: Removing artifactual 'waves' (which appear to be a general feature of array comparative genomic hybridization (aCGH) datasets) and using cross-sample information when identifying CNVs enables more biological information to be extracted from aCGH experiments designed to investigate copy number variation in normal individuals.

Hemodynamic steroid responsiveness is predictive of neurological outcome after traumatic brain injury.

INTRODUCTION: To determine the impact of physiologic doses of hydrocortisone on neurologic outcome after traumatic brain injury (TBI). METHODS: We conducted a retrospective study in a neurocritical care unit at a university teaching hospital. We included 29 patients with moderate and severe TBI requiring vasoactive drugs to maintain adequate arterial blood pressure who received corticosteroid. Infected patients were excluded. Blood cortisol levels were measured before and 30 and 60 minutes after the administration of a high-dose corticotropin stimulation test (HDST). Patients received hydrocortisone replacement therapy (200-300 mg/day) and vasoactive drugs requirements were noted. Intracranial pressure was managed according to a predefined protocol. RESULTS: A total of 14 out of 29 (48%) of patients were classified as responders to hydrocortisone (stopping vasoactive drugs within 3 days of starting hydrocortisone). The Glasgow Outcome Score (GOS) was used to assess neurologic outcome at 6 months. A favorable outcome (GOS 4 and 5) was observed in 11 out of 14 (79%) of responders and five out of 15 (33%) of nonresponders (p = 0.03). Of the responders, 12 out of 14 (85%) had a baseline cortisol below 414 nmol/L, and five out of 14 (36%) had primary adrenal insufficiency (AI) (primary AI: low baseline cortisol, and poor response to the HDST). Age, severity of injury, and response to hydrocortisone were predictive of outcome in multiple logistic regression analysis. CONCLUSIONS: Adrenal insufficiency is frequent after TBI, and hydrocortisone replacement therapy seems to be associated with a favorable neurologic outcome.