ArticleGenome medicine2017
PathOS: a decision support system for reporting high throughput sequencing of cancers in clinical diagnostic laboratories.
Article in Genome medicine, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- HIV is associated with an increased risk of age-related clonal hematopoiesis among older adults.Nature medicine · 2021Trial
- Using artificial intelligence (AI) to model clinical variant reporting for next generation sequencing (NGS) oncology assays.BioData mining · 2025Article
- Circulating Tumour DNA Is a Biomarker of Response in Angioimmunoblastic T-Cell Lymphoma.International journal of molecular sciences · 2025Article
- Whole genome sequencing improves tissue-of-origin diagnosis and treatment options for cancer of unknown primary.Nature communications · 2025Article
- Age-related clonal hematopoiesis and HIV infection are associated with geriatric outcomes: The ARCHIVE study.Cell reports. Medicine · 2024Observational
- Health 4.0 in the medical sector: a narrative review.Revista da Associacao Medica Brasileira (1992) · 2024Article
- Implementation and Clinical Adoption of Precision Oncology Workflows Across a Healthcare Network.The oncologist · 2022Article
- TRACEBACK: Testing of Historical Tubo-Ovarian Cancer Patients for Hereditary Risk Genes as a Cancer Prevention Strategy in Family Members.Journal of clinical oncology : official journal of the American Society of Clinical Oncology · 2022Article
- In vitro and in vivo drug screens of tumor cells identify novel therapies for high-risk child cancer.EMBO molecular medicine · 2022Article
- Findings from precision oncology in the clinic: rare, novel variants are a significant contributor to scaling molecular diagnostics.BMC medical genomics · 2022Article
- Knowledge bases and software support for variant interpretation in precision oncology.Briefings in bioinformatics · 2021Article
- Novel bioinformatics quality control metric for next-generation sequencing experiments in the clinical context.Nucleic acids research · 2019Article
- VIST - a Variant-Information Search Tool for precision oncology.BMC bioinformatics · 2019Article
- [Detection and interpretation of somatic variants in molecular pathology].Der Pathologe · 2019Article
- CNspector: a web-based tool for visualisation and clinical diagnosis of copy number variation from next generation sequencing.Scientific reports · 2019Article
- Dynamic molecular monitoring reveals that SWI-SNF mutations mediate resistance to ibrutinib plus venetoclax in mantle cell lymphoma.Nature medicine · 2019Article
- An integrated clinical and genomic information system for cancer precision medicine.BMC medical genomics · 2018Article
- Canary: an atomic pipeline for clinical amplicon assays.BMC bioinformatics · 2017Article
- Settling the score: variant prioritization and Mendelian disease.Nature reviews. Genetics · 2017Review
- Managing the genomic revolution in cancer diagnostics.Virchows Archiv : an international journal of pathology · 2017Review
Corrections and comments
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Authors and funding
16 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe increasing affordability of DNA sequencing has allowed it to be widely deployed in pathology laboratories. However, this has exposed many issues with the analysis and reporting of variants for clinical diagnostic use. Implementing a high-throughput sequencing (NGS) clinical reporting system requires a diverse combination of capabilities, statistical methods to identify variants, global variant databases, a validated bioinformatics pipeline, an auditable laboratory workflow, reproducible clinical assays and quality control monitoring throughout. These capabilities must be packaged in software that integrates the disparate components into a useable system.
resultsTo meet these needs, we developed a web-based application, PathOS, which takes variant data from a patient sample through to a clinical report. PathOS has been used operationally in the Peter MacCallum Cancer Centre for two years for the analysis, curation and reporting of genetic tests for cancer patients, as well as the curation of large-scale research studies. PathOS has also been deployed in cloud environments allowing multiple institutions to use separate, secure and customisable instances of the system. Increasingly, the bottleneck of variant curation is limiting the adoption of clinical sequencing for molecular diagnostics. PathOS is focused on providing clinical variant curators and pathology laboratories with a decision support system needed for personalised medicine. While the genesis of PathOS has been within cancer molecular diagnostics, the system is applicable to NGS clinical reporting generally.
conclusionsThe widespread availability of genomic sequencers has highlighted the limited availability of software to support clinical decision-making in molecular pathology. PathOS is a system that has been developed and refined in a hospital laboratory context to meet the needs of clinical diagnostics. The software is available as a set of Docker images and source code at https://github.com/PapenfussLab/PathOS .
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