Analysis workflow to assess de novo genetic variants from human whole-exome sequencing

Here, we present a protocol to analyz

Comprehensive Molecular Characterization of Pheochromocytoma and Paraganglioma

SummaryWe report a comprehensive molecular characterization of pheochromocytomas and paragangliomas (PCCs/PGLs), a rare tumor type. Multi-platform integration revealed that PCCs/PGLs are driven by diverse alterations affecting multiple genes and pathways. Pathogenic germline mutations occurred in eight PCC/PGL susceptibility genes. We identified CSDE1 as a somatically mutated driver gene, complementing four known drivers (HRAS, RET, EPAS1, and NF1). We also discovered fusion genes in PCCs/PGLs, involving MAML3, BRAF, NGFR, and NF1. Integrated analysis classified PCCs/PGLs into four molecularly defined groups: a kinase signaling subtype, a pseudohypoxia subtype, a Wnt-altered subtype, driven by MAML3 and CSDE1, and a cortical admixture subtype. Correlates of metastatic PCCs/PGLs included the MAML3 fusion gene. This integrated molecular characterization provides a comprehensive foundation for developing PCC/PGL precision medicine

Single-Cell Transcriptomic Atlas Reveals Molecular Drivers Of Human Inner Ear Development

Introduction: Improving the therapeutic landscape for hearing loss necessitates an improved understanding of inner ear biology. Historically, our molecular understanding of inner ear physiology has lagged behind our knowledge of mechanistic understanding of signal transduction due to the rare, diverse, and fragile cell types of the inner ear. However, recent advances in high-throughput sequencing have allowed us to decode the molecular underpinnings of physiologic changes in the murine inner ear. Herein, we single-cell RNA sequence fetal tissue and present a comprehensive atlas of the developing human inner ear. Harnessing newer approaches in computational analysis, we delineate diversity of cell types and highlight molecular changes underlying developmental phenomena. Materials and Methods: First, donated fetal inner tissue at various gestational timepoints — 15, 17, 18, 23, 24 weeks, and adult — underwent microdissection to separate cochlea and vestibule from surrounding structures. Tissue underwent preparation, including library preparation, for 10X sequencing. Part of the each tissue underwent fluorescence activated cell sorting to enrich for cells expressing EpCAM before preparation. Lastly, the tissue underwent microfluidics-based single-cell RNA sequencing with barcodes as unique molecular identifiers for each cell. After all data was sequenced, the expression matrices were merged using CellRanger. The combined expression matrix first underwent quality analysis and filtering to remove poor quality cells and doublets. Then, the data was inputted into CellFindPy, an unbiased hierarchical clustering approach utilizing biologically relevant parameters to cluster cells to a high resolution. The highly dimensional expression matrix underwent advanced dimension reduction algorithms, UMAP and PHATE, for visualization of the intercellular relationships. Cells were separated for subgroup analysis, in which trajectory analysis and differential gene expression was used. Results: We present an atlas with 140,007 transcriptomes of 26,429 genes remaining after quality analysis and filtering. CellFindPy clustering yielded 9 groups of cells at the highest level originating from 5 tissues. Analysis of epithelial cell subclusters reveals enrichment of rare epithelial cells across the sequenced timepoints, further evidenced by gene markers of cochlear and vestibular hair cell subtypes. Furthermore, rare cell types of stria vascularis are also found among 3 different tissues of origin. Velocity analysis reveals molecular hallmarks of vestibular hair cell maturation and differentiation of Schwann cells from neural crest progenitors. Conclusions: The present work is a proof-of-concept for creating a pan-tissue atlas of the developing human inner ear. However, single-cell sequencing is limited by dropout, batch variation, and challenges in analysis across multiple axes of change. Future work should focus on validating findings, evaluating intercellular interactions driving development, and analyzing dynamic change over time

Clinical trial publication trends within neurology

Timely dissemination of results from clinical studies is crucial for the advancement of knowledge and clinical decision making. A large body of research has shown that up to half of clinical trials do not publish their findings. In this study, we sought to determine whether clinical trial publication rates within neurology have increased over time. Focusing on neurology clinical trials completed between 2008 to 2014, we found that while the overall percentage of published trials has not changed (remaining at approximately 50%), time to publication has significantly decreased. Our findings suggest that clinical trials within neurology are being published in a more timely manner

Percutaneous Coronary Intervention Outcomes Based on Decision-Making Capacity.

Background Long-term outcomes of percutaneous coronary intervention (PCI) based on patients\u27 decision-making ability have not been studied. Our objective was to assess long-term outcomes after PCI in patients who provided individual versus surrogate consent. Methods and Results Data were collected retrospectively for patients who underwent PCI at Cleveland Clinic between January 1, 2015 and December 31, 2016. Inclusion criteria consisted of hospitalized patients aged ≥20 years who had PCI. Patients with outpatient PCI, or major surgery 30 days before or 90 days after PCI, were excluded. Patients who underwent PCI with surrogate consent versus individual consent were matched using the propensity analysis. Kaplan-Meier, log rank

Evidence-Based Guidelines for the Management of Large Hemispheric Infarction

Large hemispheric infarction (LHI), also known as malignant middle cerebral infarction, is a devastating disease associated with significant disability and mortality. Clinicians and family members are often faced with a paucity of high quality clinical data as they attempt to determine the most appropriate course of treatment for patients with LHI, and current stroke guidelines do not provide a detailed approach regarding the day-to-day management of these complicated patients. To address this need, the Neurocritical Care Society organized an international multidisciplinary consensus conference on the critical care management of LHI. Experts from neurocritical care, neurosurgery, neurology, interventional neuroradiology, and neuroanesthesiology from Europe and North America were recruited based on their publications and expertise. The panel devised a series of clinical questions related to LHI, and assessed the quality of data related to these questions using the Grading of Recommendation Assessment, Development and Evaluation guideline system. They then developed recommendations (denoted as strong or weak) based on the quality of the evidence, as well as the balance of benefits and harms of the studied interventions, the values and preferences of patients, and resource considerations

Evidence-based guidelines for the management of large hemispheric infarction : a statement for health care professionals from the Neurocritical Care Society and the German Society for Neuro-intensive Care and Emergency Medicine

Large hemispheric infarction (LHI), also known as malignant middle cerebral infarction, is a devastating disease associated with significant disability and mortality. Clinicians and family members are often faced with a paucity of high quality clinical data as they attempt to determine the most appropriate course of treatment for patients with LHI, and current stroke guidelines do not provide a detailed approach regarding the day-to-day management of these complicated patients. To address this need, the Neurocritical Care Society organized an international multidisciplinary consensus conference on the critical care management of LHI. Experts from neurocritical care, neurosurgery, neurology, interventional neuroradiology, and neuroanesthesiology from Europe and North America were recruited based on their publications and expertise. The panel devised a series of clinical questions related to LHI, and assessed the quality of data related to these questions using the Grading of Recommendation Assessment, Development and Evaluation guideline system. They then developed recommendations (denoted as strong or weak) based on the quality of the evidence, as well as the balance of benefits and harms of the studied interventions, the values and preferences of patients, and resource considerations