[show abstract][hide abstract] ABSTRACT: The Illumina HumanMethylation450 BeadChip (HM450K) measures the DNA methylation of 485,512 CpGs in the human genome. The technology relies on hybridization of genomic fragments to probes on the chip. However, certain genomic factors may compromise the ability to measure methylation using the array such as single nucleotide polymorphisms (SNPs), small insertions and deletions (INDELs), repetitive DNA, and regions with reduced genomic complexity. Currently, there is no clear method or pipeline for determining which of the probes on the HM450K bead array should be retained for subsequent analysis in light of these issues.
We comprehensively assessed the effects of SNPs, INDELs, repeats and bisulfite induced reduced genomic complexity by comparing HM450K bead array results with whole genome bisulfite sequencing. We determined which CpG probes provided accurate or noisy signals. From this, we derived a set of high-quality probes that provide unadulterated measurements of DNA methylation.
Our method significantly reduces the risk of false discoveries when using the HM450K bead array, while maximising the power of the array to detect methylation status genome-wide. Additionally, we demonstrate the utility of our method through extraction of biologically relevant epigenetic changes in prostate cancer.
[show abstract][hide abstract] ABSTRACT: In order to individually tailor prostate cancer (PCa) treatment, clinicians need better tools to predict prognosis and treatment response. Given the relationship between angiogenesis and cancer progression, circulating endothelial cells (CECs) and their progenitors have logically been proposed as potential biomarkers. The utility of their baseline levels and kinetics has been investigated for years. However, owing to a lack of standardization and validation of CEC and circulating endothelial progenitors enumeration protocols, results have been inconsistent in prostate and other cancers. Similarly, platelets play a significant part in cancer progression, yet the role of platelet-related biomarkers in PCa is unclear. While there have been a number of theoretically interesting platelet-related markers proposed, limited research has been conducted in PCa patients. Currently, CECs and platelets do not have a clear role as biomarkers in routine PCa care. Given the theoretical merits of these cells, prospective trials are warranted.
Biomarkers in Medicine 12/2013; 7(6):879-891. · 3.22 Impact Factor
[show abstract][hide abstract] ABSTRACT: Noninvasive biomarkers are used routinely in the clinical management of several cancers but bladder cancer detection and surveillance remains dependent on invasive procedures such as cystoscopy. No validated biomarker currently exists in routine clinical practice other than cytology. Gene-based testing has shown great promise for biomarker profiling and this review addresses the current state of biomarker research in bladder cancer.
A comprehensive review of all published literature on urinary biomarkers from 1970 - 2012 was conducted in PubMed. Keywords used alone or in combination were bladder cancer, diagnosis, surveillance, urinary biomarker, molecular biomarkers, methylation, gene expression, single nucleotide polymorphism and microRNA. The cited references of the manuscripts included in the review were also screened.
We have reviewed various strategies currently used for gene-based biomarker profiling of bladder cancer. We have comprehensively summarized the performance of several biomarkers in the diagnosis and surveillance of bladder cancer. Finally we have identified biomarkers that have shown potential and now deserve the opportunity to be validated in the clinical setting.
Several gene-based urinary biomarkers have demonstrated promise in initial studies, which now need to be rigorously validated in the clinical setting for them to be translated into clinically useful tests in diagnosis, surveillance or risk-stratification of bladder cancer.
[show abstract][hide abstract] ABSTRACT: Personalised oncology through mutational profiling of cancers requires the procurement of fresh frozen tumour samples for genomics applications. While primary cancers are often surgically excised and therefore yield such tissue, metastases in the setting of a known cancer diagnosis are not routinely sampled prior to systemic therapy. Our study aimed to determine the suitability of extracted nucleic acids for genomics applications using distant metastatic prostate cancer samples obtained via percutaneous or surgical biopsy. Patients with metastatic prostate cancer were recruited for image-guided biopsy of metastases. Patients undergoing surgical procedures for the complications of metastases were also recruited. Tissue samples were flash frozen and cryosectioned for histological examination. DNA and RNA were simultaneously extracted and genomic DNA hybridised onto SNP arrays for genome-wide copy number analysis. 37 samples of metastatic tissue from seven patients with prostate cancer were obtained. Five of these underwent image-guided biopsies whilst two had therapeutic surgical procedures performed. 22 biopsy samples were obtained across the image-guided biopsy patients with 80 % of samples being successfully processed for downstream analysis. Nucleic acid yield from these samples were satisfactory for genomics applications. Copy number analysis revealed a median estimated tumour purity of 53 % and all samples showed chromosomal abnormalities suggestive of malignancy. The procurement of osseous metastatic prostate cancer from live patients, including the use of image-guided biopsy, is safe and feasible. Sufficient tissue can be obtained in a manner such that extracted nucleic acids are suitable for genomics research.
Clinical and Experimental Metastasis 10/2013; · 3.46 Impact Factor
[show abstract][hide abstract] ABSTRACT: This study aimed to externally validate a previously described nomogram that predicts the need for renal exploration in the trauma setting.
The predicted probability of nephrectomy was manually calculated using prospectively collected data from consecutive patients with renal trauma who presented to our institution between May 2001 and January 2010. To assess nomogram performance, receiver operating characteristic curves against the observed exploration rate were generated, and areas under the curve were calculated. Calibration curves were generated to assess performance across the range of predicted probabilities. Logistic regression modeling was used to determine clinical factors predicting exploration in a contemporary setting, and a nomogram was derived and internally validated using bootstrapping.
The established nomogram was applied to the 320 patients who presented during the 9-year period. The global performance of the established nomogram was very high, with an area under the curve of 0.95. However, the model performance was poor for higher predicted probabilities, thus lacking predictive ability in the population where the model has the greatest potential utility. A clinical tool was generated to better predict trauma nephrectomy in our contemporary population, using platelet transfusion within the first 24 hours, blood urea nitrogen, hemoglobin, and heart rate on admission. The global accuracy for the new model was similar to the previous nomogram, but it was significantly better calibrated for patients with higher probabilities of nephrectomy, with good predictive accuracy even in patients with Grade 5 injuries.
Older nomogram fails to accurately predict renal exploration in high-grade injuries in the contemporary setting. A new nomogram that more accurately predicts the need for exploration is presented.
Therapeutic study, level IV; prognostic study, level III.
The journal of trauma and acute care surgery. 10/2013; 75(5):819-23.
[show abstract][hide abstract] ABSTRACT: Although the development of metastases correlates closely with depth of invasion in many tumor types, it is unclear if invasion into, but not through, the prostatic pseudocapsule has a negative impact on prognosis similar to extraprostatic extension (EPE). We aimed to define the impact of pseudocapsular invasion (PCI) on the risk of post-prostatectomy biochemical recurrence (BCR).
Patients with pT2-3a prostate cancer were identified from a prospectively recorded database. Patients with pT2 disease were categorized according to the presence or absence of PCI. The impact of PCI on BCR was determined by univariable and multivariable Cox regression analysis.
From a cohort of 1338, we identified 595 patients with organ-confined cancer positive for PCI. Compared to tumors without evidence of PCI, the presence of PCI was positively associated with tumors of higher Gleason grade (p<0.001) and tumor volume (1.2 vs. 1.9 cc, p<0.001). On univariable analysis, there was no difference in BCR-free survival between patients with or without PCI, although patients with EPE had a significantly lower BCR-free survival (p<0.001). This was confirmed on multivariable analysis, where EPE was a significant independent predictor of BCR (HR 1.53, p=0.018), whereas the presence of PCI had no effect (HR 0.81, p=0.33).
PCI is not a pathological feature associated with an adverse outcome post-prostatectomy. This indicates that depth of tumor invasion is not a continuum of risk, and access to the periprostatic adipose tissue is a more important determinant of disease behavior than the presence of an invasive phenotype.
The Journal of urology 06/2013; · 4.02 Impact Factor
[show abstract][hide abstract] ABSTRACT: OBJECTIVE: To detail the 9-year experience of renal trauma at a modern Level 1 trauma centre and report on patterns of injury, management and complications. PATIENTS AND METHODS: We analysed 338 patients with renal injuries who presented to our institution over a 9-year period. Data on demographics, clinical presentation, management and complications were recorded. RESULTS: Males comprised 74.9% of patients with renal injuries and the highest incidence was amongst those aged 20-24 years. Blunt injuries comprised 96.2% (n = 325) of all the renal injuries, with road trauma being the predominant mechanism accounting for 72.5% of injuries. The distribution of injury grade was; 21.6% grade 1 (n = 73), 24.3% grade 2 (n = 82), 24.9% grade 3 (n = 84), 16.6% grade 4 (n = 56), and 12.7% grade 5 (n = 43). Conservative management was successful in all grade 1 and 2 renal injuries, and 94.9%, 90.7% and 35.1% of grade 3, 4 and 5 injuries respectively. All but one of the 13 patients with penetrating injuries were successfully managed conservatively. CONCLUSIONS: Road trauma is the greatest cause of renal injury. Most haemodynamically stable patients are successfully managed conservatively.
[show abstract][hide abstract] ABSTRACT: WHAT'S KNOWN ON THE SUBJECT? AND WHAT DOES THE STUDY ADD?: The presence of a positive pathological margin is an independent risk factor for clinically significant disease recurrence only in intermediate-risk disease when the a priori risk of micrometastatic disease is accounted for. The study examines patients with Gleason 7 prostate cancer to assess the relative importance of various margin-related variables (focality, linear length, tumour grade at margin, presence of diathermy artifact and plane of tumour) with regard to biochemical recurrence. We found that the presence or absence of a positive pathological margin outperforms any other margin-associated variable in predicting significant disease recurrence. OBJECTIVE: To determine the influence of pathological margin variables on the risk of clinically significant biochemical recurrence in Gleason 7 prostate cancer. MATERIALS AND METHODS: Patients with Gleason 7 prostate cancer with complete clinical and pathological data and detailed follow-up were identified from a prospectively recorded prostatectomy database. Slides from all patients with positive pathological margins were reviewed by a single expert uropathologist and the following information recorded: multifocality, linear length, predominant Gleason grade at the margin, diathermy artifact and margin plane. Cox regression models were generated to determine the impact of positive pathological margins on the risk of biochemical recurrence (using various definitions thereof). RESULTS: Of 1048 patients with Gleason 7 prostate cancer, 238 (23%) patients had positive margins. With a median follow-up of 11 months, biochemical recurrence occurred in 9.7% of patients with negative surgical margins and 28.4% of patients with positive margins. Positive margins were significantly associated with higher serum prostate-specific antigen (PSA) level, tumour grade, stage and volume. In patients with positive pathological margins, controlling for other factors, no margin-derived variable (focality, linear length, tumour grade at margin, diathermy artifact or plane of tumour) was a consistent predictor of biochemical recurrence, although the presence of Gleason score 4 or tertiary Gleason score 5 tumour at the margin edge was an independent predictor of recurrence with PSA doubling times ≤ 6 and ≤9 months. Similarly, in the cohort as a whole, the pathological margin status was a more important predictor of recurrence than any other margin-derived variable. CONCLUSIONS: In Gleason 7 prostate cancer, positive pathological margin status was the only consistent margin-derived variable determining biochemical failure. The presence of high-grade disease at the margin may also have an impact on the development of clinically significant biochemical recurrence.
[show abstract][hide abstract] ABSTRACT: Data errors are a well-documented part of clinical datasets as is their potential to confound downstream analysis. In this study, we explore the reliability of manually transcribed data across different pathology fields in a prostate cancer database and also measure error rates attributable to the source data.
Specialist urology service at a single centre in metropolitan Victoria in Australia.
Between 2004 and 2011, 1471 patients underwent radical prostatectomy at our institution. In a large proportion of these cases, clinicopathological variables were recorded by manual data-entry. In 2011, we obtained electronic versions of the same printed pathology reports for our cohort. The data were electronically imported in parallel to any existing manual entry record enabling direct comparison between them.
Error rates of manually entered data compared with electronically imported data across clinicopathological fields.
421 patients had at least 10 comparable pathology fields between the electronic import and manual records and were selected for study. 320 patients had concordant data between manually entered and electronically populated fields in a median of 12 pathology fields (range 10-13), indicating an outright accuracy in manually entered pathology data in 76% of patients. Across all fields, the error rate was 2.8%, while individual field error ranges from 0.5% to 6.4%. Fields in text formats were significantly more error-prone than those with direct measurements or involving numerical figures (p<0.001). 971 cases were available for review of error within the source data, with figures of 0.1-0.9%.
While the overall rate of error was low in manually entered data, individual pathology fields were variably prone to error. High-quality pathology data can be obtained for both prospective and retrospective parts of our data repository and the electronic checking of source pathology data for error is feasible.
[show abstract][hide abstract] ABSTRACT: • To examine the impact of seminal vesicle invasion (SVI) in patients with locally advanced (pT3) prostate cancer on clinical outcome. • To explore the clinical association of SVI with metastatic disease. • To distinguish between the possibilities that either seminal vesicles possess their own biological significance and represent a privileged staging site for systemic tumour cell dissemination, or that their invasion is a surrogate marker for an aggressive large-volume poorly differentiated cancer.
• Patients with extraprostatic extension (EPE) and/or SVI were identified from a prospectively recorded and maintained prostate cancer database. • Patients were categorised according to the presence of SVI as determined by routine pathological assessment. Tumour volumes were measured routinely by computed planimetry at the time of histological assessment. • The impact of SVI on biochemical recurrence with a definition of a prostate-specific antigen (PSA) level of ≥0.2 ng/mL, as well as a clinically significant recurrence defined as failure with a PSA doubling time of <6 months, was determined by univariable and multivariable Cox regression analysis.
• Of 249 patients with pT3 disease, 46 (18%) had SVI, 40 (87%) by direct extension and six (13%) metastatic. • Tumours with SVI had significantly greater tumour burden as determined by total tumour volume (7.2 vs 3.7 mL, P < 0.001), index tumour volume (6.8 vs. 3.4 mL, P < 0.001) and percentage tumour volume (21.8 vs 12.4 %, P= 0.001). • After controlling for tumour volume and Gleason score, the presence of SVI did not significantly predict for the development of a significant PSA recurrence.
• Our results suggest that SVI is a surrogate marker of larger and more aggressive tumours with higher Gleason scores rather than a privileged site of tumour cell dissemination.
BJU International 12/2012; 110 Suppl 4:58-63. · 3.05 Impact Factor
[show abstract][hide abstract] ABSTRACT: What's known on the subject? and What does the study add? Nurse-led flexible cystoscopy (NLFC) has developed over the past decade in the UK with reports suggesting that adequately trained nurses can undertake FC competently. However, this is a relatively new concept in Australia and the feasibility and efficacy of this initiative in Australia has not yet been reported. We describe the various aspects that need to be addressed to implement a NLFC service in Australia. We have shown that NLFC is a safe and feasible option when established with strong departmental support, training, supervision and adherence to established guidelines. NLFC clinics can provide an efficient service and excellent continuity of care for patients with bladder cancer.
• To present our initial experience implementing a nurse-led flexible cystoscopy (NLFC) service in a Victorian tertiary hospital and our initial results from that service, as NLFC has developed over the past decade with reports suggesting that adequately trained nurses can undertake FC competently.
• We describe the implementation of a NLFC service including approval, funding, nurses' training, and protocols. • Outcomes of all patients having a NLFC or subsequent interventions were recorded prospectively and analysed retrospectively. • To gauge patients' response to NLFC, an anonymous feedback questionnaire was administered to 60 consecutive participating patients in the recovery unit. • The effect of NLFC on waiting times was determined from surgical scheduling records.
• In all, 272 patients had 720 NLFC done over a 2-year period. In all, 150 (21%) FCs had a suspected bladder cancer recurrence and were referred for a rigid cystoscopy. Of those, 83 (58%) revealed a recurrence comprising of 14 (17%) high-grade lesions, 45 (54%) low-grade lesions and 24 (29%) were diathermied without a biopsy. In all, 41 (27%) had benign pathology on biopsy and 21 (14%) had normal rigid cystoscopy. • There were two significant adverse events. • There was a 65% reduction in the waiting list for surveillance FC after introduction of the service. • Of 60 patients who completed the feedback questionnaire, 95% reported that they were given enough information by the nurses, 92% had all their questions answered satisfactorily and 97% had enough confidence and trust in the nurse. In all, 90% had a positive perception of the service overall and 93% were happy to have a FC performed by a nurse rather than a doctor.
• Results from our NLFC audit compare favourably with other published reports. NLFC is a safe and feasible option when established alongside strong departmental support, comprehensive nurses' training according to established guidelines, service supervision by a designated consultant and regular audits. • NLFC clinics can provide an efficient service and excellent continuity of care for patients with non-muscle-invasive bladder cancer.
BJU International 12/2012; 110 Suppl 4:46-50. · 3.05 Impact Factor
[show abstract][hide abstract] ABSTRACT: Study Type - Therapy (systematic review) Level of Evidence 1a What's known on the subject? and What does the study add? At present, little is known about the role of stereotactic ablative body radiotherapy in the treatment of primary renal cell carcinoma. The published evidence to date totals 126 patients worldwide. The majority of evidence is retrospective in nature. The present study adds context to the current literature by providing an overall summary of the evidence. OBJECTIVE: • To critically assess the use of stereotactic ablative body radiotherapy (SABR) for the treatment of primary renal cell carcinoma with particular focus on local control and toxicity outcomes. METHODS: • A systematic search on PubMed was performed in January 2012 independently by two radiation oncologists using structured search terms. • Secondary manual searches were performed on citations in relevant publications and abstracts in major radiotherapy journals. • Outcomes, techniques, biological doses and scientific rigour of the studies were analysed. RESULTS: • In total 10 publications (seven retrospective and three prospective) were identified. A wide range of techniques, doses and dose fractionation schedules were found. • A total of 126 patients were treated with between one and six fractions of SABR. Median or mean follow-up ranged from 9 to 57.5 months. A weighted local control was reported of 93.91% (range 84%-100%). • The weighted rate of severe grade 3 or higher adverse events was 3.8% (range 0%-19%). The weighted rate of grade 1-2 minor adverse events was 21.4% (range 0%-93%). The most commonly employed fractionation schedule was 40 Gy delivered over five fractions. CONCLUSIONS: • Current literature suggests that SABR for primary renal cell carcinoma can be delivered with promising rates of local control and acceptable toxicity. • However, there was insufficient evidence to recommend a consensus view for dose fractionation or technique. • This indicates the need for further prospective studies assessing the role of this technique in medically inoperable patients.
[show abstract][hide abstract] ABSTRACT: Background:Angiogenesis is one of the hallmarks of cancer driving tumour growth and ultimately metastasis. Circulating endothelial cells (CECs) and circulating endothelial progenitor (CEPs) cells have been reported as candidate surrogate markers for tumour vascularisation. Our aim was to investigate the potential use of these circulating cells levels as predictors of prostate cancer treatment failure and metastasis.Methods:We examined the levels of CD31(+)CD45(-) cells (CECs) and CD31(+)CD45(-)CD117(+) (CEPs) in s.c. and orthotopic models of human prostate cancers and correlated measurements with tumour size, volume and microvessel density (MVD). We then performed a prospective cohort study in 164 men with localised prostate cancer undergoing prostatectomy. The CD31(+)CD45(-), CD31(+)CD45(-)CD146(+) (CECs) and CD31(+)CD45(intermediate)CD133(+) (CEPs) populations were quantified and subsequently enriched for further characterisation.Results:In preclinical models, levels of CD31(+)CD45(-) cells, but not CEPs, were significantly elevated in tumour-bearing mice and correlated with tumour size, volume and MVD. In our human prospective cohort study, the levels of CD31(+)CD45(-) cells were significantly higher in men who experienced treatment failure within the first year, and on logistic regression analysis were an independent predictor of treatment failure, whereas neither levels of CECs or CEPs had any prognostic utility. Characterisation of the isolated CD31(+)CD45(-) cell population revealed an essentially homogenous population of large, immature platelets representing <0.1% of circulating platelets.Conclusion:Elevated levels of a distinct subpopulation of circulating platelets were an independent predictor for early biochemical recurrence in prostate cancer patients within the first year from prostatectomy.
British Journal of Cancer 10/2012; 107(9):1564-73. · 5.08 Impact Factor
[show abstract][hide abstract] ABSTRACT: Background:The controversies concerning possible overtreatment of prostate cancer, highlighted by debate over PSA screening, have highlighted active surveillance (AS) as an alternative management option for appropriate men. Regional differences in the underlying prevalence of PSA testing may alter the pre-test probability for high-risk disease, which can potentially interfere with the performance of selection criteria for AS. In a multicentre study from three different countries, we examine men who were initially suitable for AS according to the Toronto and Prostate Cancer Research International: Active Surveillance (PRIAS) criteria, that underwent radical prostatectomy (RP) in regards to:1.the proportion of pathological reclassification(Gleason score 7, pT3 disease),2.predictors of high-risk disease,3.create a predictive model to assist with selection of men suitable for AS.Methods:From three centres in the United Kingdom, Canada and Australia, data on men who underwent RP were retrospectively reviewed (n=2329). Multivariable logistic regression was performed to identify predictors of high-risk disease. A nomogram was generated by logistic regression analysis, and performance characterised by receiver operating characteristic curves.Results:For men suitable for AS according to the Toronto (n=800) and PRIAS (410) criteria, the rates for upgrading were 50.6, 42.7%, and upstaging 17.6, 12.4%, respectively. Significant predictors of high-risk disease were:•Toronto criteria: increasing age, cT2 disease, centre of diagnosis and number of positive cores.•PRIAS criteria: increasing PSA and cT2 disease.Cambridge had a high pT3a rate (26 vs 12%). To assist selection of men in the United Kingdom for AS, from the Cambridge data, we generated a nomogram predicting high-risk features in patients who meet the Toronto criteria (AUC of 0.72).Conclusion:The proportion of pathological reclassification in our cohort was higher than previously reported. Care must be used when applying the AS criteria generated from one population to another. With more stringent selection criteria, there is less reclassification but also fewer men who may benefit from AS.
British Journal of Cancer 10/2012; 107(9):1467-73. · 5.08 Impact Factor
[show abstract][hide abstract] ABSTRACT: Purpose: A lifetime psychiatric history has been reported to be associated with poorer seizure outcome following temporal lobectomy for drug-resistant focal epilepsy, but it remains unclear whether this is confounded by the nature of the epileptogenic pathology. Here we examined this association in a pathologically homogeneous group of patients with mesial temporal sclerosis (MTS). Methods: The study population included 72 consecutive patients who underwent a temporal lobectomy for drug resistant temporal lobe epilepsy (TLE) and had histopathologically proven MTS. All patients were assessed preoperatively by a neuropsychiatrist. Chi-square analysis was undertaken to look for demographic, clinical, psychiatric, or neurologic factors associated with seizure outcome at 1 year. The relationship between having a psychiatric disorder and seizure outcome was examined by generating Kaplan-Meier curves and comparing between groups the log rank test as well as generating Cox regression models to estimate hazard ratios. Key Findings: There were no significant associations between postsurgery seizure outcome and a current or lifetime history of any psychiatric disorder. Significance: A history of psychiatric disorder, in particular depression and psychosis, is not associated with a poorer surgical outcome in patients with MTS. These findings have implications for the clinical management of patients under consideration for temporal lobectomy.