BacPipe: A Rapid, User-Friendly Whole-Genome Sequencing Pipeline for Clinical Diagnostic Bacteriology

Abstract MutantHuntWGS is a user-friendly pipeline for analyzing Saccharomyces cerevisiae whole-genome sequencing data. It uses available open-source programs to: (1) perform sequence alignments for paired and single-end reads, (2) call variants, and (3) predict variant effect and severity. MutantHuntWGS outputs a shortlist of variants while also enabling access to all intermediate files. To demonstrate its utility, we use MutantHuntWGS to assess multiple published datasets; in all cases, it detects the same causal variants reported in the literature. To encourage broad adoption and promote reproducibility, we distribute a containerized version of the MutantHuntWGS pipeline that allows users to install and analyze data with only two commands. The MutantHuntWGS software and documentation can be downloaded free of charge from https://github.com/mae92/MutantHuntWGS.

Download Full-text

Low grade mosaicism in hereditary haemorrhagic telangiectasia identified by bidirectional whole genome sequencing reads through the 100,000 Genomes Project clinical diagnostic pipeline

Journal of Medical Genetics ◽

10.1136/jmedgenet-2019-106794 ◽

2020 ◽

Vol 57 (12) ◽

pp. 859-862 ◽

Cited By ~ 1

Author(s):

Jessica M Clarke ◽

Mary Alikian ◽

Sihao Xiao ◽

Dalia Kasperaviciute ◽

Ellen Thomas ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Low Grade ◽

Hereditary Haemorrhagic Telangiectasia ◽

Whole Genome ◽

Clinical Diagnostic

Download Full-text

MutantHuntWGS: A Pipeline for Identifying Saccharomyces cerevisiae Mutations

10.1101/2020.05.16.099259 ◽

2020 ◽

Author(s):

Mitchell A. Ellison ◽

Jennifer L. Walker ◽

Patrick J. Ropp ◽

Jacob D. Durrant ◽

Karen M. Arndt

Keyword(s):

Saccharomyces Cerevisiae ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Whole Genome Sequencing Data ◽

Whole Genome ◽

Sequencing Data ◽

Sequence Alignments ◽

Causal Variants ◽

User Friendly ◽

Analyze Data

ABSTRACTMutantHuntWGS is a user-friendly pipeline for analyzing Saccharomyces cerevisiae whole-genome sequencing data. It uses available open-source programs to: (1) perform sequence alignments for paired and single-end reads, (2) call variants, and (3) predict variant effect and severity. MutantHuntWGS outputs a shortlist of variants while also enabling access to all intermediate files. To demonstrate its utility, we use MutantHuntWGS to assess multiple published datasets; in all cases, it detects the same causal variants reported in the literature. To encourage broad adoption and promote reproducibility, we distribute a containerized version of the MutantHuntWGS pipeline that allows users to install and analyze data with only two commands. The MutantHuntWGS software and documentation can be downloaded free of charge from https://github.com/mae92/MutantHuntWGS.

Download Full-text

Centralised or Localised Pathogen Whole Genome Sequencing: Lessons Learnt From Implementation in a Clinical Diagnostic Laboratory

Frontiers in Cellular and Infection Microbiology ◽

10.3389/fcimb.2021.636290 ◽

2021 ◽

Vol 11 ◽

Author(s):

Alicia G. Beukers ◽

Frances Jenkins ◽

Sebastiaan J. van Hal

Keyword(s):

Public Health ◽

Infection Control ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Control Strategies ◽

Real Life ◽

Whole Genome ◽

Clinical Diagnostic Laboratory ◽

Diagnostic Laboratory ◽

Clinical Diagnostic

Whole genome sequencing (WGS) has had widespread use in the management of microbial outbreaks in a public health setting. Current models encompass sending isolates to a central laboratory for WGS who then produce a report for various levels of government. This model, although beneficial, has multiple shortcomings especially for localised infection control interventions and patient care. One reason for the slow rollout of WGS in clinical diagnostic laboratories has been the requirement for professionally trained personal in both wet lab techniques and in the analysis and interpretation of data, otherwise known as bioinformatics. A further bottleneck has been establishment of regulations in order to certify clinical and technical validity and demonstrate WGS as a verified diagnostic test. Nevertheless, this technology is far superior providing information that would normally require several diagnostic tests to achieve. An obvious barrier to informed outbreak tracking is turnaround time and requires isolates to be sequenced in real-time to rapidly identify chains of transmission. One way this can be achieved is through onsite hospital sequencing with a cumulative analysis approach employed. Onsite, as opposed to centralised sequencing, has added benefits including the increased agility to combine with local infection control staff to iterate through the data, finding links that aide in understanding transmission chains and inform infection control strategies. Our laboratory has recently instituted a pathogen WGS service within a diagnostic laboratory, separate to a public health laboratory. We describe our experience, address the challenges faced and demonstrate the advantages of de-centralised sequencing through real-life scenarios.

Download Full-text

Whole-Genome Sequencing Data for Serotyping Escherichia coli—It's Time for a Change!

Journal of Clinical Microbiology ◽

10.1128/jcm.01448-15 ◽

2015 ◽

Vol 53 (8) ◽

pp. 2402-2403 ◽

Cited By ~ 9

Author(s):

Claire Jenkins

Keyword(s):

Escherichia Coli ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Whole Genome Sequencing Data ◽

Whole Genome ◽

Sequencing Data ◽

Content Type ◽

Link Type ◽

Article Type ◽

User Friendly

The accessibility of whole-genome sequencing (WGS) presents the opportunity for national reference laboratories to provide a state-of-the-art public health surveillance service. The replacement of traditional serology-based typing ofEscherichia coliby WGS is supported by user-friendly, freely available data analysis Web tools. Anarticle in this issueof theJournal of Clinical Microbiology(K. G. Joensen, A. M. M. Tetzschner, A. Iguchi, F. M. Aarestrup, and F. Scheutz, J Clin Microbiol, 53:2410–2426, 2015,http://dx.doi.org/10.1128/JCM.00008-15) describes SerotypeFinder, an essential guide to serotypingE. coliin the 21st century.

Download Full-text

GenomeGraphR: A user-friendly open-source web application for foodborne pathogen whole genome sequencing data integration, analysis, and visualization

PLoS ONE ◽

10.1371/journal.pone.0213039 ◽

2019 ◽

Vol 14 (2) ◽

pp. e0213039 ◽

Cited By ~ 12

Author(s):

Moez Sanaa ◽

Régis Pouillot ◽

Francisco Garcés Vega ◽

Errol Strain ◽

Jane M. Van Doren

Keyword(s):

Data Integration ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Web Application ◽

Foodborne Pathogen ◽

Whole Genome Sequencing Data ◽

Whole Genome ◽

Sequencing Data ◽

User Friendly ◽

Integration Analysis

Download Full-text

Clinical diagnostic whole genome sequencing in a paediatric population: experience from our WGS genetics clinic

BMC Proceedings ◽

10.1186/1753-6561-6-s6-o11 ◽

2012 ◽

Vol 6 (S6) ◽

Cited By ~ 2

Author(s):

Elizabeth Worthey ◽

David Bick ◽

David Dimmock ◽

Mary Shimoyama ◽

Regan Veith ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Paediatric Population ◽

Whole Genome ◽

Clinical Diagnostic

Download Full-text

Whole genome sequencing in oncology: using scenario drafting to explore future developments

BMC Cancer ◽

10.1186/s12885-021-08214-8 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Michiel van de Ven ◽

Martijn J. H. G. Simons ◽

Hendrik Koffijberg ◽

Manuela A. Joore ◽

Maarten J. IJzerman ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Clinical Utility ◽

Turnaround Time ◽

Barriers And Facilitators ◽

Strategic Decision ◽

Molecular Diagnostic ◽

Whole Genome ◽

Future Developments ◽

Clinical Diagnostic

Abstract Background In oncology, Whole Genome Sequencing (WGS) is not yet widely implemented due to uncertainties such as the required infrastructure and expertise, costs and reimbursements, and unknown pan-cancer clinical utility. Therefore, this study aimed to investigate possible future developments facilitating or impeding the use of WGS as a molecular diagnostic in oncology through scenario drafting. Methods A four-step process was adopted for scenario drafting. First, the literature was searched for barriers and facilitators related to the implementation of WGS. Second, they were prioritized by international experts, and third, combined into coherent scenarios. Fourth, the scenarios were implemented in an online survey and their likelihood of taking place within 5 years was elicited from another group of experts. Based on the minimum, maximum, and most likely (mode) parameters, individual Program Evaluation and Review Technique (PERT) probability density functions were determined. Subsequently, individual opinions were aggregated by performing unweighted linear pooling, from which summary statistics were extracted and reported. Results Sixty-two unique barriers and facilitators were extracted from 70 articles. Price, clinical utility, and turnaround time of WGS were ranked as the most important aspects. Nine scenarios were developed and scored on likelihood by 18 experts. The scenario about introducing WGS as a clinical diagnostic with a lower price, shorter turnaround time, and improved degree of actionability, scored the highest likelihood (median: 68.3%). Scenarios with low likelihoods and strong consensus were about better treatment responses to more actionable targets (26.1%), and the effect of centralizing WGS (24.1%). Conclusions Based on current expert opinions, the implementation of WGS as a clinical diagnostic in oncology is heavily dependent on the price, clinical utility (both in terms of identifying actionable targets as in adding sufficient value in subsequent treatment), and turnaround time. These aspects and the optimal way of service provision are the main drivers for the implementation of WGS and should be focused on in further research. More knowledge regarding these factors is needed to inform strategic decision making regarding the implementation of WGS, which warrants support from all relevant stakeholders.

Download Full-text