Stability of gene contributions and identification of outliers in multivariate analysis of microarray data

BACKGROUND: Multivariate ordination methods are powerful tools for the exploration of complex data structures present in microarray data. These methods have several advantages compared to common gene-by-gene approaches. However, due to their exploratory nature, multivariate ordination methods do not allow direct statistical testing of the stability of genes. RESULTS: In this study, we developed a computationally efficient algorithm for: i) the assessment of the significance of gene contributions and ii) the identification of sample outliers in multivariate analysis of microarray data. The approach is based on the use of resampling methods including bootstrapping and jackknifing. A statistical package of R functions was developed. This package includes tools for both inferring the statistical significance of gene contributions and identifying outliers among samples. CONCLUSION: The methodology was successfully applied to three published data sets with varying levels of signal intensities. Its relevance was compared with alternative methods. Overall, it proved to be particularly effective for the evaluation of the stability of microarray data

Adequate surgical margins for dermatofibrosarcoma protuberans – A multi-centre analysis

Background: Dermatofibrosarcoma protuberans (DFSP) is a locally aggressive tumour. Adequate margins have a positive impact on recurrence rates. The aim of this study is to assess how adequate margins are achieved and secondly which additional treatment modalities might be necessary to achieve adequate margins. Material & methods: Patients with DFSP treated between 1991 and 2016 at three tertiary centres were included. Patient- and tumour characteristics were obtained from a prospectively held database and patient files. Results: A total of 279 patients with a median age of 39 (Interquartile range [IQ], 31–50) years and a median follow-up of 50 (IQ, 18–96) months were included. When DFSP was preoperatively confirmed by biopsy and resected with an oncological operation in a tertiary centre, in 86% was had clear pathological margins after one excision. Wider resection margins were significantly correlated with more reconstructions (p = 0.002). A substantial discrepancy between the primary surgical macroscopic and the pathological margins was found with a median difference of 22 (range, 10–46) mm (Fig. 1). There was no significant influence of the width of the pathological clear margins (if > 1 mm) and the recurrence rate (p = 0.710). Conclusion: The wider the resection margins, the more likely it is to obtain clear pathological margins, but the more likely patients will need any form of reconstruction after resection. The aim of the primary excision should be wide surgical resection, where the width of the margin should be balanced against the need for reconstructions and surgical morbidity

Hospital variation and the impact of postoperative complications on the use of perioperative chemo(radio)therapy in resectable gastric cancer. Results from the Dutch Upper GI Cancer Audit

Dutch national guidelines on the diagnosis and treatment of gastric cancer recommend the use of perioperative chemotherapy in patients with resectable gastric cancer. However, adjuvant chemotherapy is often not administered. The aim of this study was to evaluate hospital variation on the probability to receive adjuvant chemotherapy and to identify associated factors with special attention to postoperative complications. All patients who received neoadjuvant chemotherapy and underwent an elective surgical resection for stage IB-IVa (M0) gastric adenocarcinoma between 2011 and 2015 were identified from a national database (Dutch Upper GI Cancer Audit). A multivariable linear mixed model was used to evaluate case-mix adjusted hospital variation and to identify factors associated with adjuvant therapy. Of all surgically treated gastric cancer patients who received neoadjuvant chemotherapy (n = 882), 68% received adjuvant chemo(radio)therapy. After adjusting for case-mix and random variation, a large hospital variation in the administration rates for adjuvant was observed (OR range 0.31-7.1). In multivariable analysis, weight loss, a poor health status and failure of neoadjuvant chemotherapy completion were strongly associated with an increased likelihood of adjuvant therapy omission. Patients with severe postoperative complications had a threefold increased likelihood of adjuvant therapy omission (OR 3.07 95% CI 2.04-4.65). Despite national guidelines, considerable hospital variation was observed in the probability of receiving adjuvant chemo(radio)therapy. Postoperative complications were strongly associated with adjuvant chemo(radio)therapy omission, underlining the need to further reduce perioperative morbidity in gastric cancer surger

Early body weight loss during concurrent chemo-radiotherapy for non-small cell lung cancer

BACKGROUND AND PURPOSE: Radiation-esophagitis and weight loss are frequently observed toxicities in patients treated with concurrent chemo-radiotherapy (CT-RT) for non-small cell lung cancer (NSCLC) and might be related. The purpose was to investigate whether weight loss already starts early after initiation of CT-RT and precedes radiation-esophagitis. MATERIALS AND METHODS: In a retrospective cohort, weight and esophagitis grade ≥2 were assessed during the first weeks of (CT-)RT in patients treated with concurrent (n = 102) or sequential (n = 92) therapy. In a prospective validation study, data on body weight, esophagitis grade ≥2, nutritional intake and muscle strength were obtained before, during and following CT-RT. RESULTS: In the retrospective cohort, early weight loss was observed in concurrently treated patients (p = 0.002), independent of esophagitis ≥ grade 2. Early weight loss was also observed in the prospective cohort (p = 0.003) and was not accompanied by decreases in nutritional intake. In addition lower limb muscle strength rapidly declined (p = 0.042). In the later weeks of treatment, further body weight loss occurred (p < 0.001) despite increased nutritional supplementation and body weight was only partly recovered after 4 weeks post CT-RT (p = 0.003). CONCLUSIONS: Weight loss during concurrent CT-RT for NSCLC starts early and prior to onset of esophagitis, requiring timely and intense nutritional rehabilitation.status: publishe

Postapproval trials versus patient registries: comparability of advanced melanoma patients with brain metastases

Postapproval trials and patient registries have their pros and cons in the generation of postapproval data. No direct comparison between clinical outcomes of these data sources currently exists for advanced melanoma patients. We aimed to investigate whether a patient registry can complement or even replace postapproval trials. Postapproval single-arm clinical trial data from the Medicines Evaluation Board and real-world data from the Dutch Melanoma Treatment Registry were used. The study population consisted of advanced melanoma patients with brain metastases treated with targeted therapies (BRAF- or BRAF-MEK inhibitors) in the first line. A Cox hazard regression model and a propensity score matching (PSM) model were used to compare the two patient populations. Compared to patients treated in postapproval trials (n = 467), real-world patients (n = 602) had significantly higher age, higher ECOG performance status, more often ≥3 organ involvement and more symptomatic brain metastases. Lactate dehydrogenase levels were similar between both groups. The unadjusted median overall survival (mOS) in postapproval clinical trial patients was 8.7 (95% CI, 8.1-10.4) months compared to 7.2 (95% CI, 6.5-7.7) months (P < 0.01) in real-world patients. With the Cox hazard regression model, survival was adjusted for prognostic factors, which led to a statistically insignificant difference in mOS for trial and real-world patients of 8.7 (95% CI, 7.9-10.4) months compared to 7.3 (95% CI, 6.3-7.9) months, respectively. The PSM model resulted in 310 matched patients with similar survival (P = 0.9). Clinical outcomes of both data sources were similar. Registries could be a complementary data source to postapproval clinical trials to establish information on clinical outcomes in specific subpopulations

Quality indicators for hip fracture care, a systematic review

Quality indicators are used to measure quality of care and enable benchmarking. An overview of all existing hip fracture quality indicators is lacking. The primary aim was to identify quality indicators for hip fracture care reported in literature, hip fracture audits, and guidelines. The secondary aim was to compose a set of methodologically sound quality indicators for the evaluation of hip fracture care in clinical practice. A literature search according to the PRISMA guidelines and an internet search were performed to identify hip fracture quality indicators. The indicators were subdivided into process, structure, and outcome indicators. The methodological quality of the indicators was judged using the Appraisal of Indicators through Research and Evaluation (AIRE) instrument. For structure and process indicators, the construct validity was assessed. Sixteen publications, nine audits and five guidelines were included. In total, 97 unique quality indicators were found: 9 structure, 63 process, and 25 outcome indicators. Since detailed methodological information about the indicators was lacking, the AIRE instrument could not be applied. Seven indicators correlated with an outcome measure. A set of nine quality indicators was extracted from the literature, audits, and guidelines. Many quality indicators are described and used. Not all of them correlate with outcomes of care and have been assessed methodologically. As methodological evidence is lacking, we recommend the extracted set of nine indicators to be used as the starting point for further clinical research. Future research should focus on assessing the clinimetric properties of the existing quality indicators