1
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Kulchak Rahm A, Walton NA, Feldman LK, Jenkins C, Jenkins T, Person TN, Peterson J, Reynolds JC, Robinson PN, Woltz MA, Williams MS, Segal MM. User testing of a diagnostic decision support system with machine-assisted chart review to facilitate clinical genomic diagnosis. BMJ Health Care Inform 2021; 28:bmjhci-2021-100331. [PMID: 33962988 PMCID: PMC8108675 DOI: 10.1136/bmjhci-2021-100331] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 04/01/2021] [Accepted: 04/20/2021] [Indexed: 11/21/2022] Open
Abstract
Objectives There is a need in clinical genomics for systems that assist in clinical diagnosis, analysis of genomic information and periodic reanalysis of results, and can use information from the electronic health record to do so. Such systems should be built using the concepts of human-centred design, fit within clinical workflows and provide solutions to priority problems. Methods We adapted a commercially available diagnostic decision support system (DDSS) to use extracted findings from a patient record and combine them with genomic variant information in the DDSS interface. Three representative patient cases were created in a simulated clinical environment for user testing. A semistructured interview guide was created to illuminate factors relevant to human factors in CDS design and organisational implementation. Results Six individuals completed the user testing process. Tester responses were positive and noted good fit with real-world clinical genetics workflow. Technical issues related to interface, interaction and design were minor and fixable. Testers suggested solving issues related to terminology and usability through training and infobuttons. Time savings was estimated at 30%–50% and additional uses such as in-house clinical variant analysis were suggested for increase fit with workflow and to further address priority problems. Conclusion This study provides preliminary evidence for usability, workflow fit, acceptability and implementation potential of a modified DDSS that includes machine-assisted chart review. Continued development and testing using principles from human-centred design and implementation science are necessary to improve technical functionality and acceptability for multiple stakeholders and organisational implementation potential to improve the genomic diagnosis process.
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Affiliation(s)
- Alanna Kulchak Rahm
- Genomic Medicine Institute, Geisinger Health System, Danville, Pennsylvania, USA
| | - Nephi A Walton
- Intermountain Precision Genomics, Intermountain Healthcare, St. George, Utah, USA
| | | | | | | | - Thomas N Person
- Genomic Medicine Institute, Geisinger Health System, Danville, Pennsylvania, USA
| | | | - Jonathon C Reynolds
- Genomic Medicine Institute, Geisinger Health System, Danville, Pennsylvania, USA
| | - Peter N Robinson
- Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA.,University of Connecticut, Farmington, Connecticut, USA
| | - Makenzie A Woltz
- Genomic Medicine Institute, Geisinger Health System, Danville, Pennsylvania, USA
| | - Marc S Williams
- Genomic Medicine Institute, Geisinger Health System, Danville, Pennsylvania, USA
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2
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Holtgrewe M, Stolpe O, Nieminen M, Mundlos S, Knaus A, Kornak U, Seelow D, Segebrecht L, Spielmann M, Fischer-Zirnsak B, Boschann F, Scholl U, Ehmke N, Beule D. VarFish: comprehensive DNA variant analysis for diagnostics and research. Nucleic Acids Res 2020; 48:W162-W169. [PMID: 32338743 PMCID: PMC7319464 DOI: 10.1093/nar/gkaa241] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 03/27/2020] [Accepted: 04/16/2020] [Indexed: 12/18/2022] Open
Abstract
VarFish is a user-friendly web application for the quality control, filtering, prioritization, analysis, and user-based annotation of DNA variant data with a focus on rare disease genetics. It is capable of processing variant call files with single or multiple samples. The variants are automatically annotated with population frequencies, molecular impact, and presence in databases such as ClinVar. Further, it provides support for pathogenicity scores including CADD, MutationTaster, and phenotypic similarity scores. Users can filter variants based on these annotations and presumed inheritance pattern and sort the results by these scores. Variants passing the filter are listed with their annotations and many useful link-outs to genome browsers, other gene/variant data portals, and external tools for variant assessment. VarFish allows users to create their own annotations including support for variant assessment following ACMG-AMP guidelines. In close collaboration with medical practitioners, VarFish was designed for variant analysis and prioritization in diagnostic and research settings as described in the software's extensive manual. The user interface has been optimized for supporting these protocols. Users can install VarFish on their own in-house servers where it provides additional lab notebook features for collaborative analysis and allows re-analysis of cases, e.g. after update of genotype or phenotype databases.
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Affiliation(s)
- Manuel Holtgrewe
- CUBI - Core Unit Bioinformatics, Berlin Institute of Health, Berlin 10117, Germany.,Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 10117, Germany
| | - Oliver Stolpe
- CUBI - Core Unit Bioinformatics, Berlin Institute of Health, Berlin 10117, Germany.,Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 10117, Germany
| | - Mikko Nieminen
- CUBI - Core Unit Bioinformatics, Berlin Institute of Health, Berlin 10117, Germany.,Max Delbrück Center for Molecular Medicine, Berlin 13125, Germany
| | - Stefan Mundlos
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 13353, Germany.,Development and Disease Group, Max Planck Institute for Medical Genetics, Berlin 14195, Germany
| | - Alexej Knaus
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Bonn 53127, Germany
| | - Uwe Kornak
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 13353, Germany.,Development and Disease Group, Max Planck Institute for Medical Genetics, Berlin 14195, Germany
| | - Dominik Seelow
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 13353, Germany.,Berlin Institute of Health (BIH), Anna-Louisa-Karsch-Str. 2, 10178 Berlin, Germany
| | - Lara Segebrecht
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 13353, Germany
| | - Malte Spielmann
- Development and Disease Group, Max Planck Institute for Medical Genetics, Berlin 14195, Germany.,Institut für Humangenetik Lübeck, Universität zu Lübeck, 23538 Lübeck, Germany
| | - Björn Fischer-Zirnsak
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 13353, Germany.,Development and Disease Group, Max Planck Institute for Medical Genetics, Berlin 14195, Germany
| | - Felix Boschann
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 13353, Germany
| | - Ute Scholl
- Berlin Institute of Health (BIH), Anna-Louisa-Karsch-Str. 2, 10178 Berlin, Germany.,Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Nephrology and Medical Intensive Care, BCRT - Berlin Institute of Health Center for Regenerative Therapies, 13353 Berlin, Germany
| | - Nadja Ehmke
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 13353, Germany
| | - Dieter Beule
- CUBI - Core Unit Bioinformatics, Berlin Institute of Health, Berlin 10117, Germany.,Max Delbrück Center for Molecular Medicine, Berlin 13125, Germany
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3
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Schwarz JM, Hombach D, Köhler S, Cooper DN, Schuelke M, Seelow D. RegulationSpotter: annotation and interpretation of extratranscriptic DNA variants. Nucleic Acids Res 2020; 47:W106-W113. [PMID: 31106382 PMCID: PMC6602480 DOI: 10.1093/nar/gkz327] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 04/17/2019] [Accepted: 05/09/2019] [Indexed: 02/07/2023] Open
Abstract
RegulationSpotter is a web-based tool for the user-friendly annotation and interpretation of DNA variants located outside of protein-coding transcripts (extratranscriptic variants). It is designed for clinicians and researchers who wish to assess the potential impact of the considerable number of non-coding variants found in Whole Genome Sequencing runs. It annotates individual variants with underlying regulatory features in an intuitive way by assessing over 100 genome-wide annotations. Additionally, it calculates a score, which reflects the regulatory potential of the variant region. Its dichotomous classifications, ‘functional’ or ‘non-functional’, and a human-readable presentation of the underlying evidence allow a biologically meaningful interpretation of the score. The output shows key aspects of every variant and allows rapid access to more detailed information about its possible role in gene regulation. RegulationSpotter can either analyse single variants or complete VCF files. Variants located within protein-coding transcripts are automatically assessed by MutationTaster as well as by RegulationSpotter to account for possible intragenic regulatory effects. RegulationSpotter offers the possibility of using phenotypic data to focus on known disease genes or genomic elements interacting with them. RegulationSpotter is freely available at https://www.regulationspotter.org.
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Affiliation(s)
- Jana Marie Schwarz
- Department of Neuropediatrics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Berlin, Germany.,Centrum für Therapieforschung, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Berlin, Germany.,NeuroCure Cluster of Excellence and NeuroCure Clinical Research Center, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Berlin, Germany
| | - Daniela Hombach
- Centrum für Therapieforschung, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Berlin, Germany.,NeuroCure Cluster of Excellence and NeuroCure Clinical Research Center, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Berlin, Germany
| | - Sebastian Köhler
- Centrum für Therapieforschung, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Berlin, Germany.,Berlin Institute of Health (BIH), Berlin, Germany.,Einstein Center for Digital Future, Berlin, Germany
| | - David N Cooper
- Institute of Medical Genetics, Cardiff University, Cardiff, UK
| | - Markus Schuelke
- Department of Neuropediatrics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Berlin, Germany.,NeuroCure Cluster of Excellence and NeuroCure Clinical Research Center, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Berlin, Germany
| | - Dominik Seelow
- Centrum für Therapieforschung, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Berlin, Germany.,Berlin Institute of Health (BIH), Berlin, Germany
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4
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Hombach D, Schuelke M, Knierim E, Ehmke N, Schwarz JM, Fischer-Zirnsak B, Seelow D. MutationDistiller: user-driven identification of pathogenic DNA variants. Nucleic Acids Res 2019; 47:W114-W120. [PMID: 31106342 PMCID: PMC6602447 DOI: 10.1093/nar/gkz330] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 04/12/2019] [Accepted: 05/10/2019] [Indexed: 01/10/2023] Open
Abstract
MutationDistiller is a freely available online tool for user-driven analyses of Whole Exome Sequencing data. It offers a user-friendly interface aimed at clinicians and researchers, who are not necessarily bioinformaticians. MutationDistiller combines MutationTaster's pathogenicity predictions with a phenotype-based approach. Phenotypic information is not limited to symptoms included in the Human Phenotype Ontology (HPO), but may also comprise clinical diagnoses and the suspected mode of inheritance. The search can be restricted to lists of candidate genes (e.g. virtual gene panels) and by tissue-specific gene expression. The inclusion of GeneOntology (GO) and metabolic pathways facilitates the discovery of hitherto unknown disease genes. In a novel approach, we trained MutationDistiller's HPO-based prioritization on authentic genotype-phenotype sets obtained from ClinVar and found it to match or outcompete current prioritization tools in terms of accuracy. In the output, the program provides a list of potential disease mutations ordered by the likelihood of the affected genes to cause the phenotype. MutationDistiller provides links to gene-related information from various resources. It has been extensively tested by clinicians and their suggestions have been valued in many iterative cycles of revisions. The tool, a comprehensive documentation and examples are freely available at https://www.mutationdistiller.org/.
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Affiliation(s)
- Daniela Hombach
- Berliner Institut für Gesundheitsforschung (BIH), Berlin, Germany Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität Berlin, and Berlin Institute of Health, Berlin, Germany
- Charité-Universitätsmedizin Berlin, Charité-BIH Centrum for Therapy and Research, Berlin, Germany
- NeuroCure Cluster of Excellence, Berlin, Germany
| | - Markus Schuelke
- NeuroCure Cluster of Excellence, Berlin, Germany
- Department of Neuropaediatrics, Berlin, Germany
| | - Ellen Knierim
- NeuroCure Cluster of Excellence, Berlin, Germany
- Department of Neuropaediatrics, Berlin, Germany
| | - Nadja Ehmke
- Institute of Medical Genetics and Human Genetics, Berlin, Germany
| | - Jana Marie Schwarz
- Charité-Universitätsmedizin Berlin, Charité-BIH Centrum for Therapy and Research, Berlin, Germany
- NeuroCure Cluster of Excellence, Berlin, Germany
- Department of Neuropaediatrics, Berlin, Germany
| | - Björn Fischer-Zirnsak
- Institute of Medical Genetics and Human Genetics, Berlin, Germany
- Max-Planck-Institute for Molecular Genetics, RG Development & Disease, Berlin, Germany
| | - Dominik Seelow
- Berliner Institut für Gesundheitsforschung (BIH), Berlin, Germany Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität Berlin, and Berlin Institute of Health, Berlin, Germany
- Charité-Universitätsmedizin Berlin, Charité-BIH Centrum for Therapy and Research, Berlin, Germany
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5
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Lee JJY, van Karnebeek CDM, Wasserman WW. Development and user evaluation of a rare disease gene prioritization workflow based on cognitive ergonomics. J Am Med Inform Assoc 2019; 26:124-133. [PMID: 30535356 PMCID: PMC6339516 DOI: 10.1093/jamia/ocy153] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 10/26/2018] [Indexed: 02/06/2023] Open
Abstract
Objective The clinical diagnosis of genetic disorders is undergoing transformation, driven by whole exome sequencing and whole genome sequencing (WES/WGS). However, such nucleotide-level resolution technologies create an interpretive challenge. Prior literature suggests that clinicians may employ characteristic cognitive processes during WES/WGS investigations to identify disruptions in genes causal for the observed disease. Based on cognitive ergonomics, we designed and evaluated a gene prioritization workflow that supported these cognitive processes. Materials and Methods We designed a novel workflow in which clinicians recalled known genetic diseases with similarity to patient phenotypes to inform WES/WGS data interpretation. This prototype-based workflow was evaluated against the common computational approach based on physician-specified sets of individual patient phenotypes. The evaluation was conducted as a web-based user study, in which 18 clinicians analyzed 2 simulated patient scenarios using a randomly assigned workflow. Data analysis compared the 2 workflows with respect to accuracy and efficiency in diagnostic interpretation, efficacy in collecting detailed phenotypic information, and user satisfaction. Results Participants interpreted genetic diagnoses faster using prototype-based workflows. The 2 workflows did not differ in other evaluated aspects. Discussion The user study findings indicate that prototype-based approaches, which are designed to model experts’ cognitive processes, can expedite gene prioritization and provide utility in synergy with common phenotype-driven variant/gene prioritization approaches. However, further research of the extent of this effect across diverse genetic diseases is required. Conclusion The findings demonstrate potential for prototype-based phenotype description to accelerate computer-assisted variant/gene prioritization through complementation of skills and knowledge of clinical experts via human–computer interaction.
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Affiliation(s)
- Jessica J Y Lee
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Clara D M van Karnebeek
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Pediatrics and Clinical Genetics, Emma Children's Hospital, Amsterdam University Medical Centres, Amsterdam, The Netherlands
| | - Wyeth W Wasserman
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
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6
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Abstract
Next-generation sequencing (NGS) approaches are highly applicable to clinical studies. We review recent advances in sequencing technologies, as well as their benefits and tradeoffs, to provide an overview of clinical genomics from study design to computational analysis. Sequencing technologies enable genomic, transcriptomic, and epigenomic evaluations. Studies that use a combination of whole genome, exome, mRNA, and bisulfite sequencing are now feasible due to decreasing sequencing costs. Single-molecule sequencing increases read length, with the MinIONTM nanopore sequencer, which offers a uniquely portable option at a lower cost. Many of the published comparisons we review here address the challenges associated with different sequencing methods. Overall, NGS techniques, coupled with continually improving analysis algorithms, are useful for clinical studies in many realms, including cancer, chronic illness, and neurobiology. We, and others in the field, anticipate the clinical use of NGS approaches will continue to grow, especially as we shift into an era of precision medicine.
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Affiliation(s)
- Priyanka Vijay
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York. Tri-Institutional Training Program in Computational Biology and Medicine, Weill Cornell Medical College, New York, New York
| | - Alexa B.R. McIntyre
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York. Tri-Institutional Training Program in Computational Biology and Medicine, Weill Cornell Medical College, New York, New York
| | - Christopher E. Mason
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York. Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York. Feil Family Brain and Mind Research Institute, New York, New York
| | - Jeffrey P. Greenfield
- Department of Neurological Surgery, New York-Presbyterian Hospital, Weill Cornell Medical College, New York, New York
| | - Sheng Li
- Department of Neurological Surgery, New York-Presbyterian Hospital, Weill Cornell Medical College, New York, New York
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