Genomics In The Cloud Using Docker Gatk And Wdl In Terra Pdf

Genomics in the Cloud

Data in the genomics field is booming. In just a few years, organizations such as the National Institutes of Health (NIH) will host 50+ petabytesâ??or over 50 million gigabytesâ??of genomic data, and theyâ??re turning to cloud infrastructure to make that data available to the research community. How do you adapt analysis tools and protocols to access and analyze that volume of data in the cloud? With this practical book, researchers will learn how to work with genomics algorithms using open source tools including the Genome Analysis Toolkit (GATK), Docker, WDL, and Terra. Geraldine Van der Auwera, longtime custodian of the GATK user community, and Brian Oâ??Connor of the UC Santa Cruz Genomics Institute, guide you through the process. Youâ??ll learn by working with real data and genomics algorithms from the field. This book covers: Essential genomics and computing technology background Basic cloud computing operations Getting started with GATK, plus three major GATK Best Practices pipelines Automating analysis with scripted workflows using WDL and Cromwell Scaling up workflow execution in the cloud, including parallelization and cost optimization Interactive analysis in the cloud using Jupyter notebooks Secure collaboration and computational reproducibility using Terra

DNA-based Population Screening for Precision Public Health

Canine lymphoma pathogenesis, diagnosis, prognosis and treatment: current and future perspectives

Canine lymphoma is the most common hematopoietic neoplasm in dogs, arising from monoclonal expansion of B lymphocytes, T lymphocytes, or null cells (non-B and non-T, natural killer cells - NK). It might originate in any area of the body and its most striking feature is its heterogeneity, accounting for more than 30 different subtypes. Novel entities have recently been described and characterized in canine medicine, such as diffuse small B-cell lymphoma and small cell T cell intestinal lymphoma, to list a few. Despite extensive studies, recent progression in therapeutical approaches and improved outcomes, relapse or recurrence remain a common problem with conventional therapy for intermediate/high grade lymphomas, in contrast with indolent ones that are generally characterized by a fairer outcome. In light of the aforementioned considerations, differentiation among different subtypes is essential for predicting behavior and determining adequate treatment and this still largely relies on immunophenotyping through immunohistochemistry (IHC), flow cytometry, and polymerase chain reaction (PCR) for antigen receptor rearrangements (PARR). Paralleling these techniques, molecular biomarkers MicroRNAs (miRNAs) for accurate and rapid diagnosis are developing, together with blood-based liquid biopsies detecting circulating tumor DNA. We aim to showcase new insights into canine lymphoma pathogenesis, biology, early diagnosis, prognosis, clinical-pathological features and therapeutic approaches. To do this we strongly encourage contributions from veterinary oncologists, radiologists, pathologists, immunologists and geneticists to get a comprehensive approach to this entity. The aim of this Research Topic is to provide an overview on tools currently available in pathogenesis, diagnosis, prognosis and treatment and give insights of new advances in canine lymphoma with a comparative oncology perspective. Submissions that focus on the following are highly encouraged: - Novel canine lymphoma diagnostic tools (e.g. enabling early tumor detection); - The treatment of canine lymphoma with novel therapeutic approaches exploiting immune- or targeted therapy; - The molecular and biological pathways driving tumor development and multicentric dissemination of canine lymphoma; - Novel insights on the epidemiology and risk factors of canine lymphoma; - Comparative studies on the similarities and differences between canine and lymphoma in humans or other species; - Advances in canine lymphoma staging (including evaluation of prognostic factors); - Study of paraneoplastic syndromes associated with canine lymphoma. With regards to methodological approaches, we will welcome articles that include: - Cytology and immunocytochemistry; - Histopathology and immunohistochemistry; - Clonality testing (PARR); - Flow cytometry; - Molecular landscape and gene analysis; - Animal model characterization; - Biomarker discovery and validation; - Diagnostic imaging; - Surgical approaches. Vittoria Castiglioni is an employee for IDEXX Laboratories (Germany) and Sabina Soldati is an Associate in Pathology Experts GmbH.