JBrowse 2: a modular genome browser with views of synteny and structural variation

We present JBrowse 2, a general-purpose genome annotation browser offering enhanced visualization of complex structural variation and evolutionary relationships. It retains core features of JBrowse while adding new views for synteny, dotplots, breakpoints, gene fusions, and whole-genome overviews. It allows users to share sessions, open multiple genomes, and navigate between views. It can be embedded in a web page, used as a standalone application, or run from Jupyter notebooks or R sessions. These improvements are enabled by a ground-up redesign using modern web technology. We describe application functionality, use cases, performance benchmarks, and implementation notes for web administrators and developers.

JBrowse Jupyter: a Python interface to JBrowse 2

MOTIVATION

JBrowse Jupyter is a package that aims to close the gap between Python programming and genomic visualization. Web-based genome browsers are routinely used for publishing and inspecting genome annotations. Historically they have been deployed at the end of bioinformatics pipelines, typically decoupled from the analysis itself. However, emerging technologies such as Jupyter notebooks enable a more rapid iterative cycle of development, analysis and visualization.

RESULTS

We have developed a package that provides a Python interface to JBrowse 2's suite of embeddable components, including the primary Linear Genome View. The package enables users to quickly set up, launch and customize JBrowse views from Jupyter notebooks. In addition, users can share their data via Google's Colab notebooks, providing reproducible interactive views.

AVAILABILITY AND IMPLEMENTATION

JBrowse Jupyter is released under the Apache License and is available for download on PyPI. Source code and demos are available on GitHub at https://github.com/GMOD/jbrowse-jupyter.

Abstract 6400: JBrowse 2: An extensible open-source platform for modern genome analysis

Introduction: Genome browsers are useful tools for research in human genetics, able to display and integrate biological information such as long and short read sequencing data, variant calls, and annotations. While traditional linear genome browsers have demonstrated broad utility for many applications, there is an increasing need for visualizing complex structural variants (SVs) beyond the linear view. To meet these challenges, we created JBrowse 2: an extensible open-source platform for visualizing and integrating genomic data.

Results: JBrowse 2 is a flexible platform that provides the foundation for the development of applications and web dashboards that combine novel views and representations extending beyond linear displays in genomic reference coordinates. For example, a flagship JBrowse 2 application is the SV Inspector, which lets users open a list of structural variants in a data table and see the results in a whole-genome circular view. Clicking on a given variant in the table or circular view opens up a linear view that displays the read evidence supporting the SV, even across complex breakpoints like translocations. Dotplot and synteny views are built-in, enabling “long read vs reference” dotplot visualizations, or alignments of de-novo assembled contigs to the genome. These views are integrated with each other, so that (for example) a long read is just a few clicks away from the corresponding dotplot.

In addition to including these new views, the JBrowse 2 platform is designed from the ground up to enable third-party plugins to add new views, data adapters, and track types, which has facilitated the creation of new plugins that address some very specific use cases. These include our MSA view plugin for viewing multiple sequence alignments, data adapters that download data from UCSC and CIVIC APIs, and the Quantseq plugin for viewing quantitative motif scores as a genome browser track.

JBrowse 2 is available as both a web app or a local desktop app. We also offer re-usable components on NPM, and users of R can programmatically create an instance of JBrowse 2 with the JBrowseR package on CRAN. JBrowse 2 can also generate high quality SVG snapshots from inside the app, and we also created a CLI tool called jb2export to perform automated or bulk exports of JBrowse 2 visualizations. We anticipate that JBrowse 2 will better serve genome scientists with its structural variant visualization capabilities, and will provide the flexibility to adapt to new visualization and analysis challenges as they emerge in the coming years.

Citation Format: Scott Cain, Robin Haw, Caroline Bridge, Junjun Zhang, Robert Buels, Colin Diesh, Garrett Stevens, Teresa Martinez, Peter K. Xie, Elliot Hershberg, Shihab Dider, Lincoln Stein, Ian Holmes. JBrowse 2: An extensible open-source platform for modern genome analysis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6400.

Abstract LB503: Using JBrowse 2 plugins to visualize cancer genomic data

Genome browsers are essential tools for integrating, exploring, and visualizing data from large cancer genomics datasets. JBrowse 2 is a JavaScript genome browser with novel features for visualizing structural variants, syntenic alignments, and multiple types of genomic data. Although JBrowse 2 is available as a web-based or desktop application, the capabilities and features are not fixed and can be expanded through a comprehensive plugin system. To help address users' needs, we launched the new JBrowse 2 Plugin Store (https://jbrowse.org/jb2/plugin_store/). The overarching goals of the Plugin Store are to showcase the crucial features plugins add to JBrowse 2, to enable researchers to search for plugins they need, and for developers to highlight their plugins. The plugin system spans all aspects of the JBrowse 2 application and enables new track types (e.g. Manhattan plots, Hi-C data, ideograms), data adapters (e.g. API endpoint adapters for NCI Genomic Data Commons and the International Cancer Genome Consortium), and views (e.g. dot plots and multiple sequence alignments). Here, we present the capabilities of JBrowse 2 plugins and describe usage scenarios for cancer biologists and bioinformaticians, and software developers.

Citation Format: Robin Andrew Haw, Colin Diesh, Caroline Bridge, Rob Buels, Garrett Stevens, Peter Xie, Teresa Martinez, Elliot Hershberg, Junjun Zhang, Shihab Dider, Scott Cain, Lincoln Stein, Ian Holmes. Using JBrowse 2 plugins to visualize cancer genomic data [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr LB503.

One-Dimensional Chromatography of Plasma in Manchester

The Manchester experience of the amino acid screening programme is described. The Scriver test is simple and allows the detection of six amino acid disorders in one test. The cost is not great and the programme does not require large initial capital outlay. The number of cases detected exceeds expectation and cannot be explained.

Intravenous pamidronate treatment in children with moderate-to-severe osteogenesis imperfecta started under three years of age

OBJECTIVE

Evaluate clinical outcome of early cyclic intravenous pamidronate treatment in children with moderate-to-severe osteogenesis imperfecta (OI), commenced before three years of age.

METHODS

A retrospective review of 17 patients with moderate-to-severe OI. Development, anthropometry, fracture history, bone mineral density (BMD) and biochemistry were collected at baseline, 12 and 24 months.

RESULTS

Four had OI type I, eleven had type III, one OI-FKBP10 type and one OI type V. Mean age at start of pamidronate was 14 ± 11 months. Pamidronate ranged from 6 to 12 mg/kg/year. No adverse reaction apart from fever and vomiting was noted. Long bone fracture decreased from a mean of 10.4/year to 1.2/year after 12 months and 1.4/year after 24 months (p = 0.02). Lumbar spine age- and height-matched BMD Z-scores increased (p < 0.005). Sixteen with vertebral compression fractures at baseline all showed improved vertebral shape (p < 0.001). Concavity index, likewise, improved (p < 0.005). Motor milestones compared to historical data show earlier attainment in rolling over, crawling, pulling to stand and walking independently but not sitting.

CONCLUSION

Cyclic intravenous pamidronate, started under 3 years of age in children with moderate-to-severe OI, was well tolerated and associated with an increase in lumbar spine BMD, reduced fracture frequency, vertebral remodelling and attainment of motor milestones at an earlier age.

Genetic differentiation across the social transition in a socially polymorphic sweat bee, Halictus rubicundus

Eusociality is widely considered a major evolutionary transition. The socially polymorphic sweat bee Halictus rubicundus, solitary in cooler regions of its Holarctic range and eusocial in warmer parts, is an excellent model organism to address this transition, and specifically the question of whether sociality is associated with a strong barrier to gene flow between phenotypically divergent populations. Mitochondrial DNA (COI) from specimens collected across the British Isles, where both solitary and social phenotypes are represented, displayed limited variation, but placed all specimens in the same European lineage; haplotype network analysis failed to differentiate solitary and social lineages. Microsatellite genetic variability was high and enabled us to quantify genetic differentiation among populations and social phenotypes across Great Britain and Ireland. Results from conceptually different analyses consistently showed greater genetic differentiation between geographically distant populations, independently of their social phenotype, suggesting that the two social forms are not reproductively isolated. A landscape genetic approach revealed significant isolation by distance (Mantel test r = 0.622, P < 0.001). The Irish Sea acts as physical barrier to gene flow (partial Mantel test r = 0.453, P < 0.01), indicating that geography, rather than expression of solitary or social behaviour (partial Mantel test r = -0.238, P = 0.053), had a significant effect on the genetic structure of H. rubicundus across the British Isles. Although we cannot reject the hypothesis of a genetic underpinning to differences in solitary and eusocial phenotypes, our data clearly demonstrate a lack of reproductive isolation between the two social forms.

Mediastinal chest drain clearance for cardiac surgery

BACKGROUND

Cardiac tamponade may occur following cardiac surgery as a result of blood or fluid collecting in the pericardial space compressing the heart and reducing cardiac output. Mediastinal chest drains (including pericardial drains) are inserted as standard post-operative practice following cardiac surgery to assist the clearance of blood from the pericardial space and to prevent cardiac tamponade. To prevent chest tubes from blocking and so causing tamponade nurses manipulate them to prevent or remove clots. Manipulation methods including milking, stripping, fanfolding and tapping may be applied to the tubes to keep them from blocking. Evidence is required as to the safest and most effective means of preventing chest tube blockage and preventing cardiac tamponade.

OBJECTIVES

To compare different methods of chest drain clearance (i.e. varying levels of suction or suction in combination with milking, stripping, fanfolding and tapping of chest drains) in preventing cardiac tamponade in patients following cardiac surgery.

SEARCH STRATEGY

Over both the initial review and the 2004 revision, we searched the Cochrane Heart Group trials register, the Cochrane Controlled Trials Register (CCTR) (Issue 4, 2003) The Cochrane Database of Systematic Reviews (CDSR), the Database of Abstracts of Reviews of Effectiveness (DARE), Issue 4, 2003, MEDLINE (1966 to Nov Week 2, 2003), EMBASE (1980 to 2003 Week 47), CINAHL (1982 to Nov 2003), the Clinical Trials site of the NIH, (USA) (24.11.03) and reference lists of articles.

SELECTION CRITERIA

Randomised, quasi-randomised or systematically allocated clinical trials of chest tube manipulation methods in adults and children with mediastinal chest drains following cardiac surgery were included.

DATA COLLECTION AND ANALYSIS

Two reviewers independently assessed trial quality and extracted data. Study authors were contacted for additional information where required. Adverse effects information was collected from the trials.

MAIN RESULTS

Three studies with a total of 471 participants were included. There was no data, however, which could be included in a meta-analysis. This was due to inadequate data provision by two of the studies. Where adequate data were provided there were no common interventions or outcomes to pool. On the basis of single studies there was no evidence of a difference between groups on incidence of chest tube blockage, heart rate, cardiac tamponade or incidence of surgical re-entry.

REVIEWERS' CONCLUSIONS

There are insufficient studies which compare differing methods of chest drain clearance to support or refute the relative efficacy of the various methods in preventing cardiac tamponade. Nor can the need to manipulate chest drains be supported or refuted by results from RCT's.

Procedural restraint in children's nursing: using clinical benchmarks

This paper will explore the use of child restraint during common clinical procedures such as venepuncture, cannulation and lumbar puncture. A lack of research, guidelines and protocols on restraining children led a group of student nurses to develop a clinical practice benchmark on procedural restraint for the North West Clinical Practice Benchmarking Group.

Mediastinal chest drain clearance for cardiac surgery

BACKGROUND

Cardiac tamponade may occur following cardiac surgery as a result of blood or fluid collecting in the pericardial space compressing the heart and reducing cardiac output. Mediastinal chest drains (including pericardial drains) are inserted as standard post-operative practice following cardiac surgery to assist the clearance of blood from the pericardial space and to prevent cardiac tamponade. Manipulation techniques including milking, stripping, fanfolding and tapping may be applied to the tubes to keep them from blocking. Evidence is required as to the safest and most effective means of preventing chest tube blockage and preventing cardiac tamponade.

OBJECTIVES

To compare different methods of chest drain clearance (i.e. varying levels of suction or suction in combination with milking, stripping, fanfolding and tapping of chest drains) in preventing cardiac tamponade in patients following cardiac surgery.

SEARCH STRATEGY

We searched the Cochrane Heart Group specialised register, the Cochrane Controlled Trials Register (CCTR) (Issue 1, 2001) The Cochrane Database of Systematic Reviews (CDSR), the Database of Abstracts of Reviews of Effectiveness (DARE), Issue 1, 2001, MEDLINE (1966 to May Week 1, 2001), EMBASE (1980 to 2001 Week 35), CINAHL (1982 to March 2001), the Clinical Trials site of the NIH, (USA) (10.09.01) and reference lists of articles.

SELECTION CRITERIA

Randomised, quasi-randomised or systematically allocated clinical trials of chest tube manipulation techniques in adults and children with mediastinal chest drains following cardiac surgery were included.

DATA COLLECTION AND ANALYSIS

Two reviewers independently assessed trial quality and extracted data. Study authors were contacted for additional information where required. Adverse effects information was collected from the trials.

MAIN RESULTS

Three studies with a total of 471 participants were included. There was no data, however, which could be included in a meta-analysis. This was due to inadequate data provision by two of the studies and where adequate data were provided there were no common interventions or outcomes to pool. On the basis of single studies there was no difference between groups on incidence of chest tube blockage, heart rate, cardiac tamponade or incidence of surgical re-entry.

REVIEWER'S CONCLUSIONS

There are insufficient studies which compare differing methods of chest drain clearance to support or refute the relative efficacy of the various techniques in preventing cardiac tamponade. Nor can the need to manipulate chest drains be supported or refuted by results from RCT's.

Isolation of genomic DNA from blood using a novel filter-based DNA purification technology

A novel DNA purification technology is described that enables the purification of pure dsDNA from blood. When compared to existing DNA purification methods, the Whatman BioScience Purification System (WBPS) offers a fast and convenient way to recover high yields of DNA. WBPS is based on a unique filter system that entraps DNA within a matrix. This allows the process to be performed in a single unidirectional reaction vessel, reducing user interaction and multiple centrifugation steps.

Midwifery care for Australian Aboriginal women

Australian Aboriginal women have twice the number of still born babies as Australian non Aboriginal women and have babies who are five times more likely to die within the neonatal period. The perinatal mortality rate is three times higher and the infant mortality is more than five times the overall rate for babies of Australian Aboriginal women compared to Australian non Aboriginal women. These are the stark statistics compiled by the Midwives' Notification System in Western Australia (1998).

Strategies for the treatment of cystathionine beta-synthase deficiency: the experience of the Willink Biochemical Genetics Unit over the past 30 years

Strategies for the treatment of cystathionine beta-synthase (CBS) deficiency include (1) increasing residual enzyme activity by giving pyridoxine in those patients with vitamin responsive variants, (2) reducing the load on the affected pathway with a low methionine diet and supplementing the diet with cysteine; and (3) giving betaine in order to utilise alternative pathways to remove homocyst(e)ine. In our experience of over 30 years in the diagnosis and management of patients with CBS deficiency, a normal outcome can only be achieved in patients diagnosed and treated from infancy. Pyridoxine combined with folic acid prevents further deterioration in pyridoxine responsive patients. Dietary treatment of patients with non-pyridoxine responsive CBS deficiency becomes more difficult outside childhood but since late complications are not uncommon must be continued for life. Betaine can be effective in this group but compliance is often poor.

Adolescents and mental disorder: who consents to treatment?

Although English law recognises that developing adolescents may acquire the capacity to make decisions about medical treatment themselves it does not address the problem of mentally disturbed or disordered adolescents. This article examines the nature of adolescent refusal of treatment and suggests that a line be drawn between three categories of adolescent disturbance--the competent young person who refuses treatment that an adult too may refuse, the rebellious teenager whose refusal is triggered by simple teenage angst, and the mentally ill teenager whose refusal is triggered by mental illness. It suggests that adolescent autonomy needs to be more fully understood and the Mental Health Act more readily used in treating young people.

A deficit in care. The educational needs of thoracic patients

1. There is a need for increased educational input for thoracic surgical patients. 2. Information and health education are important aspects of holistic care. 3. Care plans should aim to help the patient regain and maintain a level of independence. 4. Discharge planning should ideally begin prior to admission for surgery.

The Manchester regional screening programme: a 10-year exercise in patient and family care

Up to the end of 1978 the Willink Biochemical Genetics Unit had screened 506821 babies for metabolic abnormalities over 10 years--98-99% of the children born in the region. Sixty-nine cases of phenylketonuria (PKU), 42 cases of histidinaemia, and six cases of homocystinuria were detected. As well as treating affected children, the staff of the unit have concentrated on providing full support for their families and maintaining good communications with parents, general practitioners, health visitors, and midwives. A clinic liaison sister has provided valuable support for health visitors and an important link between the unit and community services. A study of the costs of screening and treating cases of PKU for the year 1978 showed that this was cheaper, by pound 569000, than the costs of looking after patients with untreated PKU.