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Callaghan DB, Rogic S, Tan PPC, Calli K, Qiao Y, Baldwin R, Jacobson M, Belmadani M, Holmes N, Yu C, Li Y, Li Y, Kurtzke F, Kuzeljevic B, Yu AY, Hudson M, Mcaughton AJ, Xu Y, Dionne‐Laporte A, Girard S, Liang P, Separovic ER, Liu X, Rouleau G, Pavlidis P, Lewis MS. Whole genome sequencing and variant discovery in the ASPIRE autism spectrum disorder cohort. Clin Genet 2019; 96:199-206. [DOI: 10.1111/cge.13556] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 04/15/2019] [Accepted: 04/23/2019] [Indexed: 01/14/2023]
Affiliation(s)
- Daniel Benjamin Callaghan
- Michael Smith LaboratoriesUniversity of British Columbia Vancouver Canada
- Department of PsychiatryUniversity of British Columbia Vancouver Canada
| | - Sanja Rogic
- Michael Smith LaboratoriesUniversity of British Columbia Vancouver Canada
- Department of PsychiatryUniversity of British Columbia Vancouver Canada
| | - Powell Patrick Cheng Tan
- Michael Smith LaboratoriesUniversity of British Columbia Vancouver Canada
- Department of PsychiatryUniversity of British Columbia Vancouver Canada
| | - Kristina Calli
- Department of Medical GeneticsBC Children's Hospital Research Institute, University of British Columbia Vancouver Canada
| | - Ying Qiao
- Department of Medical GeneticsBC Children's Hospital Research Institute, University of British Columbia Vancouver Canada
| | - Robert Baldwin
- Department of Biological SciencesBrock University St. Catharines Canada
| | - Matthew Jacobson
- Michael Smith LaboratoriesUniversity of British Columbia Vancouver Canada
- Department of PsychiatryUniversity of British Columbia Vancouver Canada
| | - Manuel Belmadani
- Michael Smith LaboratoriesUniversity of British Columbia Vancouver Canada
- Department of PsychiatryUniversity of British Columbia Vancouver Canada
| | - Nathan Holmes
- Michael Smith LaboratoriesUniversity of British Columbia Vancouver Canada
- Department of PsychiatryUniversity of British Columbia Vancouver Canada
| | - Chang Yu
- Medical Division, BGI‐Shenzhen Shenzhen China
| | - Yanchen Li
- Medical Division, BGI‐Shenzhen Shenzhen China
| | - Yingrui Li
- Medical Division, BGI‐Shenzhen Shenzhen China
| | - Franz‐Edward Kurtzke
- Department of Medical GeneticsBC Children's Hospital Research Institute, University of British Columbia Vancouver Canada
| | - Boris Kuzeljevic
- Clinical Research Support UnitBC Children's Hospital Research Institute, University of British Columbia Vancouver Canada
| | - An Yi Yu
- Department of Medical GeneticsBC Children's Hospital Research Institute, University of British Columbia Vancouver Canada
| | - Melissa Hudson
- Queen's Genomics Lab at OngwanadaOngwanada Resource Center Kingston Canada
- Department of PsychiatryQueen's University Kingston Canada
| | - Amy J.M. Mcaughton
- Queen's Genomics Lab at OngwanadaOngwanada Resource Center Kingston Canada
- Department of PsychiatryQueen's University Kingston Canada
| | - Yuchen Xu
- Department of Biological SciencesBrock University St. Catharines Canada
| | - Alexandre Dionne‐Laporte
- Montreal Neurological Institute Quebec Canada
- Department of Neurology and NeurosurgeryMcGill University Quebec Canada
| | - Simon Girard
- Département des sciences fondamentales, Université du Québec à Chicoutimi Chicoutimi Canada
| | - Ping Liang
- Department of Biological SciencesBrock University St. Catharines Canada
| | - Evica Rajcan Separovic
- Department of Pathology and Laboratory MedicineUniversity of British Columbia Vancouver Canada
| | - Xudong Liu
- Queen's Genomics Lab at OngwanadaOngwanada Resource Center Kingston Canada
- Department of PsychiatryQueen's University Kingston Canada
| | - Guy Rouleau
- Montreal Neurological Institute Quebec Canada
- Department of Neurology and NeurosurgeryMcGill University Quebec Canada
| | - Paul Pavlidis
- Michael Smith LaboratoriesUniversity of British Columbia Vancouver Canada
- Department of PsychiatryUniversity of British Columbia Vancouver Canada
| | - M.E. Suzanne Lewis
- Department of Medical GeneticsBC Children's Hospital Research Institute, University of British Columbia Vancouver Canada
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Doig KD, Fellowes A, Bell AH, Seleznev A, Ma D, Ellul J, Li J, Doyle MA, Thompson ER, Kumar A, Lara L, Vedururu R, Reid G, Conway T, Papenfuss AT, Fox SB. PathOS: a decision support system for reporting high throughput sequencing of cancers in clinical diagnostic laboratories. Genome Med 2017; 9:38. [PMID: 28438193 PMCID: PMC5404673 DOI: 10.1186/s13073-017-0427-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 04/07/2017] [Indexed: 01/08/2023] Open
Abstract
Background The 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. Results To 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. Conclusions The 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. Electronic supplementary material The online version of this article (doi:10.1186/s13073-017-0427-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kenneth D Doig
- Research Division, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia. .,Department of Pathology, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia. .,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia. .,Peter MacCallum Cancer Centre, 305 Grattan Street, Parkville, VIC, 3000, Australia.
| | - Andrew Fellowes
- Department of Pathology, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia
| | - Anthony H Bell
- Department of Pathology, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia
| | - Andrei Seleznev
- Department of Pathology, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia
| | - David Ma
- Department of Pathology, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia
| | - Jason Ellul
- Research Division, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia
| | - Jason Li
- Research Division, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia
| | - Maria A Doyle
- Research Division, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia
| | - Ella R Thompson
- Department of Pathology, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Amit Kumar
- Research Division, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia.,Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Children's Cancer Institute, University of New South Wales, Sydney, NSW, Australia
| | - Luis Lara
- Research Division, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Ravikiran Vedururu
- Department of Pathology, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia
| | - Gareth Reid
- Department of Pathology, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia
| | - Thomas Conway
- Research Division, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia
| | - Anthony T Papenfuss
- Research Division, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia.,Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Stephen B Fox
- Department of Pathology, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia.,Department of Pathology, University of Melbourne, Melbourne, VIC, Australia
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