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The emergence of next-generation sequencing (NGS) has revolutionized the way of reaching a genome sequence, with the promise of potentially providing a comprehensive characterization of DNA variations. Nevertheless, detecting somatic mutations is still a difficult problem, in particular when trying to identify low abundance mutations, such as subclonal mutations, tumour-derived alterations in body fluids or somatic mutations from histological normal tissue. The main challenge is to precisely distinguish between sequencing artefacts and true mutations, particularly when the latter are so rare they reach similar abundance levels as artefacts. Here, we present needlestack, a highly sensitive variant caller, which directly learns from the data the level of systematic sequencing errors to accurately call mutations. Needlestack is based on the idea that the sequencing error rate can be dynamically estimated from analysing multiple samples together. We show that the sequencing error rate varies across alterations, illustrating the need to precisely estimate it. We evaluate the performance of needlestack for various types of variations, and we show that needlestack is robust among positions and outperforms existing state-of-the-art method for low abundance mutations. Needlestack, along with its source code is freely available on the GitHub platform https//github.com/IARCbioinfo/needlestack. © World Health Organization and the authors, 2020. All rights reserved. The World Health Organization and the authors have granted the Publisher permission for the reproduction of this article.Many patients with inflammatory bowel disease experiment with marijuana for symptom control. Marijuana may help reduce abdominal pain but does not control inflammatory bowel disease related inflammation. Patients should discuss their marijuana use with their providers and continue appropriate medications if considering marijuana. © 2020 Crohn’s & Colitis Foundation. Published by Oxford University Press on behalf of Crohn's & Colitis Foundation.The COVID-19 pandemic was an unprecedented surprise, to say the least. Academia is rooted in group assemblies - from classroom to conferences - which were promptly cancelled and/or shifted to remote efforts. Here are some perspectives from Professors involved. Serine Protease inhibitor © 2020 Published by Elsevier Inc.Since the emergence of a novel coronavirus (SARS-CoV-2) in Wuhan, China, at the end of December 2019, its infection - COVID-19 - has been associated with severe morbidity and mortality and has left world governments, healthcare systems and providers caring for vulnerable populations, such as pregnant women, wrestling with the optimal management strategy. Unique physiologic and ethical considerations negate a one-size-fits-all approach to the care of critically ill pregnant women with COVID-19, and few resources exist to guide the multi-disciplinary team through decisions regarding optimal maternal-fetal surveillance, intensive care procedures, and delivery timing. We present a case of rapid clinical decompensation and development of severe Acute Respiratory Distress Syndrome (ARDS) in a woman at 31 weeks' gestation to highlight these unique considerations and present an algorithmic approach to the disease's diagnosis and management. © 2020 Elsevier Inc. All rights reserved.At our institution, 2 of the initial 7 pregnant patients with confirmed coronavirus disease 2019 severe infection (28.6%; 95% CI, 8.2%-64.1%) developed cardiac dysfunction with moderately reduced left ventricular ejection fractions of 40%-45% and hypokinesis. Viral myocarditis and cardiomyopathy have also been reported in nonpregnant coronavirus disease 2019 patients. A case series of nonpregnant patients with coronavirus disease 2019 found that 33% of those in intensive care developed cardiomyopathy. More data are needed to ascertain the incidence of cardiomyopathy from coronavirus disease 2019 in pregnancy, in all pregnant women with coronavirus disease 2019, and those with severe disease (eg, pneumonia). We suggest an echocardiogram in pregnant women with coronavirus disease 2019 pneumonia, in particular those necessitating oxygen, or those who are critically ill, and we recommend the use of handheld, point-of-care devices where possible to minimize contamination of staff and traditional large echocardiogram machines. © 2020 Elsevier Inc. All rights reserved.COVID-19 has been associated with cardiovascular complications including acute cardiac injury, heart failure and cardiogenic shock. The role of veno-arterial extracorporeal membrane oxygenation (VA-ECMO) in the event of COVID-19-associated cardiovascular collapse has not yet been established. We reviewed existing literature surrounding the role of VA-ECMO in the treatment of coronavirus-related cardiovascular collapse. COVID-19 is associated with higher incidence of cardiovascular complications compared to previous coronavirus outbreaks (SARS-CoV, MERS-CoV). We found only one case report from China where COVID-19-associated fulminant myocarditis and cardiogenic shock (CS) was successfully rescued using VA-ECMO as a bridge to recovery (BTR). We identified potential clinical scenarios (cardiac injury, myocardial infarction with and without obstructive coronary artery disease, viral myocarditis, and decompensated heart failure) leading to CS and risk factors for poor/uncertain benefit (age, sepsis, mixed/predominantly vasodilatory shock, prothrombotic state and/or coagulopathy, severe acute respiratory distress syndrome, multi-organ failure or high-risk prognostic scores) specific to using VA-ECMO as BTR in COVID-19 infection. Additional considerations and proposed recommendations specific to the COVID-19 pandemic were formulated with guidance from published data and expert consensus. A small subset of patients with cardiovascular complications from COVID-19 infection may progress to refractory CS. Accepting that resource scarcity may be the overwhelming concern for healthcare systems during this pandemic, VA-ECMO can be considered in highly selected cases of refractory CS and echocardiographic evidence of biventricular failure. The decision to initiate this therapy should take into consideration availability of resources, perceived benefit as well as risks of transmitting disease. © 2020 Published by Elsevier Inc. on behalf of the Canadian Cardiovascular Society.
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