TY - JOUR
T1 - Development and validation of Houston Methodist Variant Viewer version 3
T2 - Updates to our application for interpretation of next-generation sequencing data
AU - Christensen, Paul A.
AU - Subedi, Sishir
AU - Pepper, Kristi
AU - Hendrickson, Heather L.
AU - Li, Zejuan
AU - Thomas, Jessica S.
AU - Wesley Long, S.
AU - Olsen, Randall J.
N1 - Publisher Copyright:
© The Author(s) 2020. Published by Oxford University Press on behalf of the American Medical Informatics Association.
PY - 2020/7/1
Y1 - 2020/7/1
N2 - Objectives: Informatics tools that support next-generation sequencing workflows are essential to deliver timely interpretation of somatic variants in cancer. Here, we describe significant updates to our laboratory developed bioinformatics pipelines and data management application termed Houston Methodist Variant Viewer (HMVV). Materials and Methods: We collected feature requests and workflow improvement suggestions from the end-users of HMVV version 1. Over 1.5 years, we iteratively implemented these features in five sequential updates to HMVV version 3. Results: We improved the performance and data throughput of the application while reducing the opportunity for manual data entry errors. We enabled end-user workflows for pipeline monitoring, variant interpretation and annotation, and integration with our laboratory information system. System maintenance was improved through enhanced defect reporting, heightened data security, and improved modularity in the code and system environments. Discussion and Conclusion: Validation of each HMVV update was performed according to expert guidelines. We enabled an 8⨯ reduction in the bioinformatics pipeline computation time for our longest running assay. Our molecular pathologists can interpret the assay results at least 2 days sooner than was previously possible. The application and pipeline code are publicly available at https://github.com/hmvv.
AB - Objectives: Informatics tools that support next-generation sequencing workflows are essential to deliver timely interpretation of somatic variants in cancer. Here, we describe significant updates to our laboratory developed bioinformatics pipelines and data management application termed Houston Methodist Variant Viewer (HMVV). Materials and Methods: We collected feature requests and workflow improvement suggestions from the end-users of HMVV version 1. Over 1.5 years, we iteratively implemented these features in five sequential updates to HMVV version 3. Results: We improved the performance and data throughput of the application while reducing the opportunity for manual data entry errors. We enabled end-user workflows for pipeline monitoring, variant interpretation and annotation, and integration with our laboratory information system. System maintenance was improved through enhanced defect reporting, heightened data security, and improved modularity in the code and system environments. Discussion and Conclusion: Validation of each HMVV update was performed according to expert guidelines. We enabled an 8⨯ reduction in the bioinformatics pipeline computation time for our longest running assay. Our molecular pathologists can interpret the assay results at least 2 days sooner than was previously possible. The application and pipeline code are publicly available at https://github.com/hmvv.
KW - Clinical laboratory information systems
KW - Computational biology
KW - High-throughput nucleotide sequencing
KW - Informatics
KW - Molecular
KW - Pathology
UR - http://www.scopus.com/inward/record.url?scp=85094221744&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85094221744&partnerID=8YFLogxK
U2 - 10.1093/jamiaopen/ooaa004
DO - 10.1093/jamiaopen/ooaa004
M3 - Article
AN - SCOPUS:85094221744
SN - 2574-2531
VL - 3
SP - 299
EP - 305
JO - JAMIA Open
JF - JAMIA Open
IS - 2
ER -