Integration of copy number and transcriptomics provides risk stratification in prostate cancer: A discovery and validation cohort study

BACKGROUND: Understanding the heterogeneous genotypes and phenotypes of prostate cancer is fundamental to improving the way we treat this disease. As yet, there are no validated descriptions of prostate cancer subgroups derived from integrated genomics linked with clinical outcome.

METHODS: In a study of 482 tumour, benign and germline samples from 259 men with primary prostate cancer, we used integrative analysis of copy number alterations (CNA) and array transcriptomics to identify genomic loci that affect expression levels of mRNA in an expression quantitative trait loci (eQTL) approach, to stratify patients into subgroups that we then associated with future clinical behaviour, and compared with either CNA or transcriptomics alone.

FINDINGS: We identified five separate patient subgroups with distinct genomic alterations and expression profiles based on 100 discriminating genes in our separate discovery and validation sets of 125 and 103 men. These subgroups were able to consistently predict biochemical relapse (p = 0.0017 and p = 0.016 respectively) and were further validated in a third cohort with long-term follow-up (p = 0.027). We show the relative contributions of gene expression and copy number data on phenotype, and demonstrate the improved power gained from integrative analyses. We confirm alterations in six genes previously associated with prostate cancer (MAP3K7, MELK, RCBTB2, ELAC2, TPD52, ZBTB4), and also identify 94 genes not previously linked to prostate cancer progression that would not have been detected using either transcript or copy number data alone. We confirm a number of previously published molecular changes associated with high risk disease, including MYC amplification, and NKX3-1, RB1 and PTEN deletions, as well as over-expression of PCA3 and AMACR, and loss of MSMB in tumour tissue. A subset of the 100 genes outperforms established clinical predictors of poor prognosis (PSA, Gleason score), as well as previously published gene signatures (p = 0.0001). We further show how our molecular profiles can be used for the early detection of aggressive cases in a clinical setting, and inform treatment decisions.

INTERPRETATION: For the first time in prostate cancer this study demonstrates the importance of integrated genomic analyses incorporating both benign and tumour tissue data in identifying molecular alterations leading to the generation of robust gene sets that are predictive of clinical outcome in independent patient cohorts.

Heller's myotomy and pneumatic dilatation in the treatment of achalasia: a population-based case–control study assessing long-term quality of life

Long-term health-related quality-of-life (HRQL) outcomes have not been widely reported in the
treatment of achalasia. The aims of this study were to examine long-term disease-specific and general HRQL in
achalasia patients using a population-based case–control method, and to assess HRQL between treatment interventions.
Manometrically diagnosed achalasia cases (n = 120) were identified and matched with controls (n = 115)
using a population-based approach. Participants completed general (SF-12) and disease-specific (Achalasia Severity
Questionnaire [ASQ]) HRQL questionnaires, as appropriate, in a structured interview. Mean composite scores
for SF-12 (Mental Component Summary score [MCS-12] and Physical Component Summary score [PCS-12]) and
ASQ were compared between cases and controls, or between intervention groups, using an independent t-test.
Adjusted mean differences in HRQL scores were evaluated using a linear regression model. Achalasia cases were
treated with a Heller’s myotomy (n = 43), pneumatic dilatation (n = 44), or both modalities (n = 33). The median
time from last treatment to HRQL assessment was 5.7 years (interquartile range 2.4–11.5). Comparing achalasia
patients with controls, PCS-12 was significantly worse (40.9 vs. 44.2, P = 0.01), but MCS-12 was similar. However,
both PCS-12 (39.9 vs. 44.2, P = 0.03) and MCS-12 (46.7 vs. 53.5, P = 0.004) were significantly impaired in those
requiring dual treatment compared with controls. Overall however, there was no difference in adjusted HRQL
between patients treated with Heller’s myotomy, pneumatic dilatation or both treatment modalities. In summary,
despite treatment achalasia patients have significantly worse long-term physical HRQL compared with population
controls. No HRQL differences were observed between the treatment modalities to suggest a benefit of one
treatment over another.

Integration of Indicator Alarm Signals for Ecosystem‐Based Fishery Management

We consider the problem of regulating the rate of harvesting a natural resource, taking account of the wider system represented by a set of ecological and economic indicators, given differing stakeholder priorities. This requires objective and transparent decision making to show how indicators impinge on the resulting regulation decision. We offer a new scheme for combining indicators, derived from assessing the suitability of lowering versus not lowering the harvest rate based on indicator values relative to their predefined reference levels. Using the practical example of fisheries management under an “ecosystem approach,” we demonstrate how different stakeholder views can be quantitatively represented by weighting sets applied to these comparisons. Using the scheme in an analysis of historical data from the Celtic Sea fisheries, we find great scope for negotiating agreement among disparate stakeholders.

People with intellectual disabilities: promoting quality end of life care

Background: Internationally concerns have been highlighted about the quality of palliative care that people with intellectual disability receive. It has also been evidenced that people with intellectual disabilities are seldom referred to hospice and palliative care services. 

Aims: This study aimed to explore the experience of health and social care professionals in providing palliative care to people with intellectual disabilities. 

Methods An exploratory, qualitative design was used. A purposive sample of thirty health and social care professionals, working in intellectual disability and palliative care services, who had provided end-of-life care to adults with intellectual disabilities, were recruited to the study following informed consent. They were asked to reflect on a case scenario of a person with intellectual disability to whom they had provided end of life care. A semi-structured interview technique, with open questions and prompts, was used to explore their experiences and insights. The narrative from the case scenarios were content analysed using a recognised framework. 

Results: Three themes emerged from the data within the case scenarios: Identifying end of life care needs, meeting support needs and empowerment in partnership. Examples of good practice and issues in practice were apparent. 

Conclusion/ Discussion: This study contributes to the developing international evidence base to enhance end of life care for people with intellectual disabilities and provides further insights into this area of practice. Funder: HSC Research and Development Doctoral Fellowship Scheme

After the Liverpool Care Pathway clear guidance and support on end-of-life care is needed

Commentary on: Ramasamy Venkatasalu M, Whiting D, Cairnduff K. Life after the Liverpool Care Pathway (LCP): a qualitative study of critical care practitioners delivering end-of-life care. J Adv Nurs 2015;71:2108–18.

Integration of design of experiment, surface response methodology and multi-layer validation to predict the effect of blanching on colour of tomato juice

Response surface methodology was used to develop models to predict the effect of tomato cultivar, juice pH, blanching temperature and time on colour change of tomato juice after blanching. The juice from three tomato cultivars with adjusted pH levels ranging from 3.9 to 4.6 were blanched at temperatures from 60-100 °C for 1-5 min using the central composite design (CCD). The colour change was assessed by calculating the redness (a/b) and total colour change (∆E) after measuring the Hunter L, a and b values. Developed models for both redness and ∆E were significant (p<0.0001) with satisfactory coefficient of determination (R2 = 0.99 and 0.97) and low coefficient of variation (CV% = 1.89 and 7.23), respectively. Multilevel validation that was implemented revealed that the variation between the predicted and experimental values obtained for redness and ∆E were within the acceptable error range of 7.3 and 22.4%, respectively

Cataract surgical outcomes, visual function and quality of life in four rural districts in Vietnam.

BACKGROUND: To evaluate cataract surgical outcomes in four rural districts of Ha Tinh Province, Vietnam. DESIGN: Cross-sectional study. PARTICIPANTS: Post-cataract surgery patients sampled randomly from facilities in four rural districts of Ha Tinh Province >3 months after surgery. MAIN OUTCOME MEASURES: Postoperative visual acuity (VA), visual function and quality of life. RESULTS: Among 412 patients, the mean age was 74.5 ± 9.4 years, 67% (276) were female, and 377 (91.5%) received intraocular lenses (IOL). Nearly two-thirds of patients had no postoperative visits after discharge. Postoperatively, more than 40% of eyes had presenting VA <6/18, while 20% remained <6/60. The mean self-reported visual function and quality of life for all patients were 68.7 ± 23.8 and 73.8 ± 21.6, respectively. Most patients (89.5%) were satisfied with surgery and the majority (94.4%) would recommend surgery to others. One-third of patients paid ≥$US50 for surgery. In multiple regression modelling, older age (P < 0.01), intraoperative complications (P < 0.01) and failure to receive an IOL (P < 0.01) were associated with postoperative VA <6/60. CONCLUSION: Satisfaction with surgery was high, and many patients were willing to pay for their operations. Poor visual outcomes were common; however, and better surgical training is needed to reduce complications and their impact on visual outcomes. More intensive postoperative follow-up may also be beneficial. © 2011 The Authors. Clinical and Experimental Ophthalmology © 2011 Royal Australian and New Zealand College of Ophthalmologists.

Dedicated severe asthma services improve health-care use and quality of life

Background: Systematic assessment of severe asthma can be used to confirm the diagnosis, identify comorbidities, and address adherence to therapy. However, the prospective usefulness of this approach is yet to be established. The objective of this study was to determine whether the systematic assessment of severe asthma is associated with improved quality of life (QoL) and health-care use and, using prospective data collection, to compare relevant outcomes in patients referred with severe asthma to specialist centers across the United Kingdom. Methods: Data from the National Registry for dedicated UK Difficult Asthma Services were used to compare patient demographics, disease characteristics, and health-care use between initial assessment and a median follow-up of 286 days. Results: The study population consisted of 346 patients with severe asthma. At follow-up, there were significant reductions in health-care use in terms of primary care or ED visits (66.4% vs 87.8%, P < .0001) and hospital admissions (38% vs 48%, P = .0004). Although no difference was noted in terms of those requiring maintenance oral corticosteroids, there was a reduction in steroid dose (10 mg [8-20 mg] vs 15 mg [10-20 mg], P = .003), and fewer subjects required short-burst steroids (77.4% vs 90.8%, P = .01). Significant improvements were seen in QoL and control using the Asthma Quality of Life Questionnaire and the Asthma Control Questionnaire. Conclusions: To our knowledge, this is the first time that a prospective study has shown that a systematic assessment at a dedicated severe asthma center is associated with improved QoL and asthma control and a reduction in health-care use and oral steroid burden.