Ten years of pan-genome analyses Vernikos, George; Medini, Duccio; Riley, David R ...
Current opinion in microbiology,
02/2015, Volume:
23
Journal Article
Peer reviewed
Highlights • Next generation sequencing technologies have enabled large-scale genome analyses. • Pan-genome analyses provide a framework for predicting and modeling genomic diversity. • Analyses can ...be conducted at different scales, from single species to super kingdom level. • Datasets and technical implementations govern pan-genome analysis-derived conclusions.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK
Next-generation sequencing technologies have decentralized sequence acquisition, increasing the demand for new bioinformatics tools that are easy to use, portable across multiple platforms, and ...scalable for high-throughput applications. Cloud computing platforms provide on-demand access to computing infrastructure over the Internet and can be used in combination with custom built virtual machines to distribute pre-packaged with pre-configured software.
We describe the Cloud Virtual Resource, CloVR, a new desktop application for push-button automated sequence analysis that can utilize cloud computing resources. CloVR is implemented as a single portable virtual machine (VM) that provides several automated analysis pipelines for microbial genomics, including 16S, whole genome and metagenome sequence analysis. The CloVR VM runs on a personal computer, utilizes local computer resources and requires minimal installation, addressing key challenges in deploying bioinformatics workflows. In addition CloVR supports use of remote cloud computing resources to improve performance for large-scale sequence processing. In a case study, we demonstrate the use of CloVR to automatically process next-generation sequencing data on multiple cloud computing platforms.
The CloVR VM and associated architecture lowers the barrier of entry for utilizing complex analysis protocols on both local single- and multi-core computers and cloud systems for high throughput data processing.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Whitefly-transmitted Tomato yellow leaf curl virus (Family Geminiviridae; Genus Begomovirus) severely restricts tomato production in the Southeastern United States. Whitefly and tomato yellow leaf ...curl virus management studies typically investigate control tactics individually, but successful management of this pest complex more often relies on a combination of tactics. This study examined the individual and combined effects of tomato yellow leaf curl virus-resistant cultivars, insecticides, and metallic reflective mulch on whiteflies, tomato yellow leaf curl virus disease incidence, and marketable tomato yields using split-split plot trials over 3 yr. Reflective mulch significantly reduced whitefly adults and nymphs and tomato yellow leaf curl virus symptom severity in all 3 yr of the study. Reflective mulch treatments also provided greater marketable tomato yield in 2 out of 3 yr. Imidacloprid and cyantraniliprole treatments reduced whitefly adults and nymphs' establishment and marginally increased yields, but there was no significant insecticide effect on tomato yellow leaf curl virus incidence/symptom severity compared with the non-treated check. Virus-resistant tomato cultivars did not influence whitefly populations, but provided consistent reduction in virus disease incidence. Interactions between host plant resistance and insecticide treatments ranged from strongly additive in the standard white plastic mulch treatment to only marginally additive in the reflective mulch treatments in terms of enhancing tomato yields. tomato yellow leaf curl virus-resistant tomato cultivars and reflective mulch provided the bulk of the protection against tomato yellow leaf curl virus disease incidence. However, it was the combination of all the best tactics (reflective mulch, cyantraniliprole, ‘Security’ hyb. tomato yellow leaf curl virus-resistant) that provided the maximum increase in marketable tomato yield (2.8-fold) over the least effective combination (white mulch, no whitefly insecticide, ‘FL47′ hyb. tomato yellow leaf curl virus-susceptible).
There are 10× more bacterial cells in our bodies from the microbiome than human cells. Viral DNA is known to integrate in the human genome, but the integration of bacterial DNA has not been ...described. Using publicly available sequence data from the human genome project, the 1000 Genomes Project, and The Cancer Genome Atlas (TCGA), we examined bacterial DNA integration into the human somatic genome. Here we present evidence that bacterial DNA integrates into the human somatic genome through an RNA intermediate, and that such integrations are detected more frequently in (a) tumors than normal samples, (b) RNA than DNA samples, and (c) the mitochondrial genome than the nuclear genome. Hundreds of thousands of paired reads support random integration of Acinetobacter-like DNA in the human mitochondrial genome in acute myeloid leukemia samples. Numerous read pairs across multiple stomach adenocarcinoma samples support specific integration of Pseudomonas-like DNA in the 5'-UTR and 3'-UTR of four proto-oncogenes that are up-regulated in their transcription, consistent with conversion to an oncogene. These data support our hypothesis that bacterial integrations occur in the human somatic genome and may play a role in carcinogenesis. We anticipate that the application of our approach to additional cancer genome projects will lead to the more frequent detection of bacterial DNA integrations in tumors that are in close proximity to the human microbiome.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Bacterial genome sequencing has become so easy and accessible that the genomes of multiple strains of more and more individual species have been and will be generated. These data sets provide for in ...depth analysis of intra-species diversity from various aspects. The pan-genome analysis, whereby the size of the gene repertoire accessible to any given species is characterized together with an estimate of the number of whole genome sequences required for proper analysis, is being increasingly applied. Different models exist for the analysis and their accuracy and applicability depend on the case at hand. Here we discuss current models and suggest a new model of broad applicability, including examples of its implementation.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK
•The evolution of the design-make-test-analyse (DMTA) cycle, mainly within AstraZeneca, but also generalizing in the context of drug discovery, is presented.•The challenges faced by scientists ...throughout the DMTA cycle and the use of predictive modelling to improve its efficiency in drug discovery are discussed.•We present the Predictive Insight Platform (PIP), a bespoke infrastructure and collection of services for molecular predictive modelling created at AstraZeneca.•The PIP is described from a technical standpoint, aiming to inform the reader and provide suggestions to improve similar systems.•We speculate on the role of predictive modelling in the future of drug R&D.
Design-Make-Test-Analyse (DMTA) is the discovery cycle through which molecules are designed, synthesised, and assayed to produce data that in turn are analysed to inform the next iteration. The process is repeated until viable drug candidates are identified, often requiring many cycles before reaching a sweet spot. The advent of artificial intelligence (AI) and cloud computing presents an opportunity to innovate drug discovery to reduce the number of cycles needed to yield a candidate. Here, we present the Predictive Insight Platform (PIP), a cloud-native modelling platform developed at AstraZeneca. The impact of PIP in each step of DMTA, as well as its architecture, integration, and usage, are discussed and used to provide insights into the future of drug discovery.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Abstract Background Well-written and transparent case reports (1) reveal early signals of potential benefits, harms, and information on the use of resources; (2) provide information for clinical ...research and clinical practice guidelines, and (3) inform medical education. High-quality case reports are more likely when authors follow reporting guidelines. During 2011–2012, a group of clinicians, researchers, and journal editors developed recommendations for the accurate reporting of information in case reports that resulted in the CARE (CAse REport) Statement and Checklist. They were presented at the 2013 International Congress on Peer Review and Biomedical Publication, have been endorsed by multiple medical journals, and translated into nine languages. Objectives This explanation and elaboration document has the objective to increase the use and dissemination of the CARE Checklist in writing and publishing case reports. Article Design and Setting Each item from the CARE Checklist is explained and accompanied by published examples. The explanations and examples in this document are designed to support the writing of high-quality case reports by authors and their critical appraisal by editors, peer reviewers, and readers. Results and Conclusion This article and the 2013 CARE Statement and Checklist, available from the CARE website www.care-statement.org and the EQUATOR Network www.equator-network.org , are resources for improving the completeness and transparency of case reports.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK, ZRSKP
Chronic traumatic encephalopathy is a progressive tauopathy that occurs as a consequence of repetitive mild traumatic brain injury. We analysed post-mortem brains obtained from a cohort of 85 ...subjects with histories of repetitive mild traumatic brain injury and found evidence of chronic traumatic encephalopathy in 68 subjects: all males, ranging in age from 17 to 98 years (mean 59.5 years), including 64 athletes, 21 military veterans (86% of whom were also athletes) and one individual who engaged in self-injurious head banging behaviour. Eighteen age- and gender-matched individuals without a history of repetitive mild traumatic brain injury served as control subjects. In chronic traumatic encephalopathy, the spectrum of hyperphosphorylated tau pathology ranged in severity from focal perivascular epicentres of neurofibrillary tangles in the frontal neocortex to severe tauopathy affecting widespread brain regions, including the medial temporal lobe, thereby allowing a progressive staging of pathology from stages I-IV. Multifocal axonal varicosities and axonal loss were found in deep cortex and subcortical white matter at all stages of chronic traumatic encephalopathy. TAR DNA-binding protein 43 immunoreactive inclusions and neurites were also found in 85% of cases, ranging from focal pathology in stages I-III to widespread inclusions and neurites in stage IV. Symptoms in stage I chronic traumatic encephalopathy included headache and loss of attention and concentration. Additional symptoms in stage II included depression, explosivity and short-term memory loss. In stage III, executive dysfunction and cognitive impairment were found, and in stage IV, dementia, word-finding difficulty and aggression were characteristic. Data on athletic exposure were available for 34 American football players; the stage of chronic traumatic encephalopathy correlated with increased duration of football play, survival after football and age at death. Chronic traumatic encephalopathy was the sole diagnosis in 43 cases (63%); eight were also diagnosed with motor neuron disease (12%), seven with Alzheimer's disease (11%), 11 with Lewy body disease (16%) and four with frontotemporal lobar degeneration (6%). There is an ordered and predictable progression of hyperphosphorylated tau abnormalities through the nervous system in chronic traumatic encephalopathy that occurs in conjunction with widespread axonal disruption and loss. The frequent association of chronic traumatic encephalopathy with other neurodegenerative disorders suggests that repetitive brain trauma and hyperphosphorylated tau protein deposition promote the accumulation of other abnormally aggregated proteins including TAR DNA-binding protein 43, amyloid beta protein and alpha-synuclein. (Contains 4 tables and 6 figures.)
Current criteria for the clinical diagnosis of pathologically confirmed corticobasal degeneration (CBD) no longer reflect the expanding understanding of this disease and its clinicopathologic ...correlations. An international consortium of behavioral neurology, neuropsychology, and movement disorders specialists developed new criteria based on consensus and a systematic literature review. Clinical diagnoses (early or late) were identified for 267 nonoverlapping pathologically confirmed CBD cases from published reports and brain banks. Combined with consensus, 4 CBD phenotypes emerged: corticobasal syndrome (CBS), frontal behavioral-spatial syndrome (FBS), nonfluent/agrammatic variant of primary progressive aphasia (naPPA), and progressive supranuclear palsy syndrome (PSPS). Clinical features of CBD cases were extracted from descriptions of 209 brain bank and published patients, providing a comprehensive description of CBD and correcting common misconceptions. Clinical CBD phenotypes and features were combined to create 2 sets of criteria: more specific clinical research criteria for probable CBD and broader criteria for possible CBD that are more inclusive but have a higher chance to detect other tau-based pathologies. Probable CBD criteria require insidious onset and gradual progression for at least 1 year, age at onset ≥ 50 years, no similar family history or known tau mutations, and a clinical phenotype of probable CBS or either FBS or naPPA with at least 1 CBS feature. The possible CBD category uses similar criteria but has no restrictions on age or family history, allows tau mutations, permits less rigorous phenotype fulfillment, and includes a PSPS phenotype. Future validation and refinement of the proposed criteria are needed.
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