Sequencing and de novo assembly of 150 genomes from Denmark as a population reference

Hundreds of thousands of human genomes are now being sequenced to characterize genetic variation and use this information to augment association mapping studies of complex disorders and other phenotypic traits. Genetic variation is identified mainly by mapping short reads to the reference genome or by performing local assembly. However, these approaches are biased against discovery of structural variants and variation in the more complex parts of the genome. Hence, large-scale de novo assembly is needed. Here we show that it is possible to construct excellent de novo assemblies from high-coverage sequencing with mate-pair libraries extending up to 20 kilobases. We report de novo assemblies of 150 individuals (50 trios) from the GenomeDenmark project. The quality of these assemblies is similar to those obtained using the more expensive long-read technology. We use the assemblies to identify a rich set of structural variants including many novel insertions and demonstrate how this variant catalogue enables further deciphering of known association mapping signals. We leverage the assemblies to provide 100 completely resolved major histocompatibility complex haplotypes and to resolve major parts of the Y chromosome. Our study provides a regional reference genome that we expect will improve the power of future association mapping studies and hence pave the way for precision medicine initiatives, which now are being launched in many countries including Denmark

Proteomic analysis of the extracellular matrix of human atherosclerotic plaques shows marked changes between plaque types

Cardiovascular disease is the leading cause of death, with atherosclerosis the major underlying cause. While often asymptomatic for decades, atherosclerotic plaque destabilization and rupture can arise suddenly and cause acute arterial occlusion or peripheral embolization resulting in myocardial infarction, stroke and lower limb ischaemia. As extracellular matrix (ECM) remodelling is associated with plaque instability, we hypothesized that the ECM composition would differ between plaques. We analyzed atherosclerotic plaques obtained from 21 patients who underwent carotid surgery following recent symptomatic carotid artery stenosis. Plaques were solubilized using a new efficient, single-step approach. Solubilized proteins were digested to peptides, and analyzed by liquid chromatography-mass spectrometry using data-independent acquisition. Identification and quantification of 4498 plaque proteins was achieved, including 354 ECM proteins, with unprecedented coverage and high reproducibility. Multidimensional scaling analysis and hierarchical clustering indicate two distinct clusters, which correlate with macroscopic plaque morphology (soft/unstable versus hard/stable), ultrasound classification (echolucent versus echogenic) and the presence of hemorrhage/ulceration. We identified 714 proteins with differential abundances between these groups. Soft/unstable plaques were enriched in proteins involved in inflammation, ECM remodelling, and protein degradation (e.g. matrix metalloproteinases, cathepsins). In contrast, hard/stable plaques contained higher levels of ECM structural proteins (e.g. collagens, versican, nidogens, biglycan, lumican, proteoglycan 4, mineralization proteins). These data indicate that a single-step proteomics method can provide unique mechanistic insights into ECM remodelling and inflammatory mechanisms within plaques that correlate with clinical parameters, and help rationalize plaque destabilization. These data also provide an approach towards identifying biomarkers for individualized risk profiling of atherosclerosis

International implementation of a PROficiency based StePwise Endovascular Curricular Training (PROSPECT) in daily practice

Objective: A randomised controlled trial (RCT) showed superior real life endovascular performance of trainees after PROficiency based StePwise Endovascular Curricular Training (PROSPECT) compared with traditional training. This study aimed to determine whether PROSPECT can be implemented routinely in surgical training (registry) and to identify the associated effects, facilitators, and barriers to implementation. Methods: This was a multicentre prospective registry to evaluate real life PROSPECT implementation effects. Cognitive ability was tested with a Multiple Choice Question test (MCQ) (max. score 20 points), while technical skills were assessed with a Global Rating Scale (GRS) (max. score 55 points), Examiner's Checklist (max, score 85 points), and simulator metrics. A cross sectional anonymous survey for both trainees and faculty evaluated the programme's implementation. Results: The PROSPECT registry was implemented in five centres in four countries over a period of three years. Only 17 of 48 starting trainees completed PROSPECT, resulting in a dropout rate of 65%. Participants who completed the programme showed significant improvement in the GRS (median 26 vs. 44, p = .018) and Examiner's Checklist (median 53.5 vs. 80, p = .028) after the programme. The survey was completed by 13/17 faculty members (76%) and 38/57 trainees who participated either in the initial PROSPECT RCT or the registry (67%). PROSPECT was perceived to provide more endovascular training opportunities, but non-availability of logistical/technical support, lack of training time within the working schedule, and little trainee motivation hindered broad implementation. Conclusion: PROSPECT has a significant effect on performance, and trainees and faculty agree that PROSPECT is a valuable addition to surgical training. However, external and internal factors pose significant barriers to integration of this simulation based programme into daily practice leading to a high dropout rate. To integrate PROSPECT into contemporary surgical training, it should be a prerequisite to treating real patients and protected training time should be provided, combined with accessible support

Achieving consensus to define curricular content for simulation based education in vascular surgery : a Europe wide needs assessment initiative

Objective: To gather consensus among European educators about technical procedures that should be included in a future simulation based curriculum in vascular surgery. Methods: A three round modified Delphi survey was initiated among 189 key opinion leaders (KOL) from 34 countries across Europe who were identified according to their positions in the European Society for Vascular Surgery, the European Journal of Vascular and Endovascular Surgery, and Union Europeenne des Medecins Specialistes Section and Board of Vascular Surgery. The first round was a brainstorming phase to identify technical procedures that a newly qualified vascular surgeon should be able to perform. The answers were analysed qualitatively. The second round investigated how often the identified procedures are performed, the number of vascular surgeons that should be able to perform these procedures, whether the procedures pose a risk to the patients, and whether simulation based education (SBE) is feasible. In the third round, elimination and re-ranking of procedures were performed. Only procedures that gained more than 70% support were included. An international steering group consisting of open and endovascular surgeons and medical educators governed the process. Results: Response rates in the three rounds were 75% (142/189), 89% (126/142), and 85% (107/126), respectively. In the final prioritised list of 30 technical procedures for SBE, the top five procedures focus on basic open vascular skills, basic endovascular skills, vascular imaging interpretation, femoral endarterectomy, and open peripheral bypass. Twenty-six procedures were eliminated, including peripheral pressure measurement, wound management, open management of complications, major amputations, and highly advanced endovascular skills. Conclusion: The prioritised list of technical procedures from this ESVS supported project could be used to guide planning and development of future SBE programs to meet the needs of vascular surgeons across Europe

Continuous Glucose Monitoring Reveals Perioperative Hypoglycemia in Most Patients With Diabetes Undergoing Major Surgery:A Prospective Cohort Study

Objective:To investigate the frequency and duration of hypo- and hyperglycemia, assessed by continuous glucose monitoring (CGM) during and after major surgery, in departments with implemented diabetes care protocols. Summary Background Data:Inadequate glycemic control in the perioperative period is associated with serious adverse events, but monitoring currently relies on point blood glucose measurements, which may underreport glucose excursions.Methods: Adult patients without (A) or with diabetes [non-insulin-treated type 2 (B), insulin-treated type 2 (C) or type 1 (D)] undergoing major surgery were monitored using CGM (Dexcom G6), with an electrochemical sensor in the interstitial fluid, during surgery and for up to 10 days postoperatively. Patients and health care staff were blinded to CGM values, and glucose management adhered to the standard diabetes care protocol. Thirty-day postoperative serious adverse events were recorded. The primary outcome was duration of hypoglycemia (glucose < 70 mg/dL). Clinicaltrials.gov: NCT04473001. Results:Seventy patients were included, with a median observation time of 4.0 days. CGM was recorded in median 96% of the observation time. The median daily duration of hypoglycemia was 2.5 minutes without significant difference between the 4 groups (A-D). Hypoglycemic events lasting ≥15 minutes occurred in 43% of all patients and 70% of patients with type 1 diabetes. Patients with type 1 diabetes spent a median of 40% of the monitoring time in the normoglycemic range 70 to 180 mg/dL and 27% in the hyperglycemic range >250 mg/dL. Duration of preceding hypo- and hyperglycemia tended to be longer in patients with serious adverse events, compared with patients without events, but these were exploratory analyses.Conclusions:Significant duration of both hypo- and hyperglycemia was detected in high proportions of patients, particularly in patients with diabetes, despite protocolized perioperative diabetes management