Detection of rare mutations, copy number alterations, and methylation in the same template DNA molecules.

The analysis of cell-free DNA (cfDNA) from plasma offers great promise for the earlier detection of cancer. At present, changes in DNA sequence, methylation, or copy number are the most sensitive ways to detect the presence of cancer. To further increase the sensitivity of such assays with limited amounts of sample, it would be useful to be able to evaluate the same template molecules for all these changes. Here, we report an approach, called MethylSaferSeqS, that achieves this goal, and can be applied to any standard library preparation method suitable for massively parallel sequencing. The innovative step was to copy both strands of each DNA-barcoded molecule with a primer that allows the subsequent separation of the original strands (retaining their 5-methylcytosine residues) from the copied strands (in which the 5-methylcytosine residues are replaced with unmodified cytosine residues). The epigenetic and genetic alterations present in the DNA molecules can then be obtained from the original and copied strands, respectively. We applied this approach to plasma from 265 individuals, including 198 with cancers of the pancreas, ovary, lung, and colon, and found the expected patterns of mutations, copy number alterations, and methylation. Furthermore, we could determine which original template DNA molecules were methylated and/or mutated. MethylSaferSeqS should be useful for addressing a variety of questions relating genetics and epigenetics.

Failure modes and effects analysis to assess COVID-19 protocols in the management of obstetric emergencies.

The Royal Free Hospital is one of four High Consequence Infectious Disease centres in England and as of the end of May 2020, seven women were confirmed COVID-19 peri-delivery. We developed a standard operating procedure (SOP) for suspected and confirmed COVID-19 women undergoing operative delivery. This was revised in response to our ongoing clinical experience and changes in guidance from medical and public health organisations. Following 10 weeks of clinical practice, we formally tested the SOP using point-of-care simulation to enable optimisation for a potential second surge. Our high-fidelity simulation of a COVID-19-positive parturient requiring an emergency caesarean was facilitated by the simulation team in our obstetric unit. It was designed to test the performance and safety of our SOP as well as staff performance. We used the Failure Modes and Effect Analysis tool (a systematic, prospective method of process mapping) to identify how a complex task might fail and assess the relative impact of different failures. The decision-to-delivery was 17 minutes, which we considered to be successful. However, a number of operational deficiencies were identified. The main failures related to lack of situational awareness, ill-fitting personal protective equipment and difficulties communicating between theatre and the neonatal teams located outside, posing serious potential risks to safe neonatal care. Subsequently, we have modified our SOP to include a communication check, implemented communication training for the neonatal team and organised further simulation training for theatre staff unfamiliar with COVID-19 considerations.

Predicting morbidity in liver resection surgery: external validation of the revised frailty index and development of a novel predictive model.

BACKGROUND: Perioperative complications of liver resection surgery are common but individual patient-level prediction is difficult. Most risk models are unvalidated and may not be clinically useful. We aimed to validate a risk prediction model for complications of liver resection, the Revised Frailty Index (rFI), at a high volume centre. We also aimed to derive a predictive model for complications in our cohort. METHODS: Records were reviewed for 300 patients undergoing liver resection. The rFI's discrimination of 90-day major complications was assessed by receiver operating curve analysis. Logistic regression analysis was then used to fit rFI covariates to our dataset. A further analysis produced a model with optimal discrimination of 90-day major complications. RESULTS: The rFI was a poor discriminator of 90-day major complications (AUROC 0.562) among patients at our centre. The rFI optimised fit model demonstrated improved discrimination of 90-day major complications (AUROC 0.685). We developed a novel model with improved fit and similar discrimination (AUROC 0.710). CONCLUSION: We were unable to validate the rFI as a predictor of complications. We developed a novel model with discrimination at least equal to other published risk models. However, there is an unmet need for well-validated, clinically useful risk tools in this area.

Diagnosing barriers to safety and efficiency in robotic surgery.

Recent studies exploring the effects of surgical robots on teamwork are revealing challenges not reflected in clinical studies. This study is a sub analysis of observational data collected from 89 procedures utilising the da Vinci systems. Previous analyses had demonstrated interactions between flow disruptions and contextual factors. This study sought a more granular analysis to provide better insight for improvement. Raters sub-classified disruptions, based upon the original notes, grouped according to four operative phases (pre-robot; docking; surgeon on console; undocking; and finish). The need for repeated utterances; additional supplies retrieval; fogging or matter on the endoscope and procedure-specific training were particularly disruptive. Variations across phases reflect differing demands across the operative course. Combined qualitative and quantitative observational methodologies can identify otherwise undocumented sources of process variation and potential failure. Future observational frameworks should attempt to merge human reliability analysis, a priori modelling, and post hoc analyses of observational data. Practioner Summary: Robotic surgery introduces new challenges into the operating room. Direct observation was used to classify and identify flow disruptions in order to diagnose problems in need of improvement. This technique complements other error prediction and system diagnostic methods which may not account for the complexity and transparency of health care.

Patient education and its effect on self-management in cirrhosis: a pilot study.

BACKGROUND AND AIMS: Patients with cirrhosis can contribute significantly to maintaining compensation through simple lifestyle measures. It is, however, unknown whether they possess sufficient knowledge to make informed decisions with regard to their health, with few resources invested in patient education. We aimed to determine the level of knowledge that patients with cirrhosis possess and whether an information leaflet can make a positive impact on this. METHODS: We prospectively recruited clinically stable patients with cirrhosis to take part in a preintervention/postintervention study. Thirty-nine patients were recruited either to take part in a telephone-based questionnaire followed by repeating the questionnaire 2 months after receipt of a leaflet or to receive the leaflet directly and complete the questionnaire 2 months later. RESULTS: The questionnaire demonstrated that baseline knowledge in the study group was poor, with a mean score of 3.4 out of a possible 9 points. There was a statistically significant improvement in the score to 7.5 in those who used the leaflet (Wilcoxon's signed-ranked test, P=0.0006). The mean score achieved by those who received the leaflet directly was 6.8, which is comparable to the scores of patients in the first cohort who read the leaflet and is significantly higher than the scores of the same participants before reading the leaflet (Wilcoxon's rank-sum test, P=0.001). CONCLUSION: Our results suggest that patients with cirrhosis lack the knowledge to effectively manage their disease. The introduction of a leaflet resulted in a statistically significant improvement in understanding. Longitudinal studies are required to assess whether such interventions can result in improved clinical outcomes.