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CNV-ClinViewer: enhancing the clinical interpretation of large copy-number variants online
Abstract Motivation Pathogenic copy-number variants (CNVs) can cause a heterogeneous spectrum of rare and severe disorders. However, most CNVs are benign and are part of natural variation in human genomes. CNV pathogenicity classification, genotype–phenotype analyses, and therapeutic target identifi...
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| Published in: | Bioinformatics (Oxford, England) England), 2023-05, Vol.39 (5) |
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| creator | Macnee, Marie Pérez-Palma, Eduardo Brünger, Tobias Klöckner, Chiara Platzer, Konrad Stefanski, Arthur Montanucci, Ludovica Bayat, Allan Radtke, Maximilian Collins, Ryan L Talkowski, Michael Blankenberg, Daniel Møller, Rikke S Lemke, Johannes R Nothnagel, Michael May, Patrick Lal, Dennis |
| description | Abstract
Motivation
Pathogenic copy-number variants (CNVs) can cause a heterogeneous spectrum of rare and severe disorders. However, most CNVs are benign and are part of natural variation in human genomes. CNV pathogenicity classification, genotype–phenotype analyses, and therapeutic target identification are challenging and time-consuming tasks that require the integration and analysis of information from multiple scattered sources by experts.
Results
Here, we introduce the CNV-ClinViewer, an open-source web application for clinical evaluation and visual exploration of CNVs. The application enables real-time interactive exploration of large CNV datasets in a user-friendly designed interface and facilitates semi-automated clinical CNV interpretation following the ACMG guidelines by integrating the ClassifCNV tool. In combination with clinical judgment, the application enables clinicians and researchers to formulate novel hypotheses and guide their decision-making process. Subsequently, the CNV-ClinViewer enhances for clinical investigators’ patient care and for basic scientists’ translational genomic research.
Availability and implementation
The web application is freely available at https://cnv-ClinViewer.broadinstitute.org and the open-source code can be found at https://github.com/LalResearchGroup/CNV-clinviewer. |
| doi_str_mv | 10.1093/bioinformatics/btad290 |
| format | article |
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Motivation
Pathogenic copy-number variants (CNVs) can cause a heterogeneous spectrum of rare and severe disorders. However, most CNVs are benign and are part of natural variation in human genomes. CNV pathogenicity classification, genotype–phenotype analyses, and therapeutic target identification are challenging and time-consuming tasks that require the integration and analysis of information from multiple scattered sources by experts.
Results
Here, we introduce the CNV-ClinViewer, an open-source web application for clinical evaluation and visual exploration of CNVs. The application enables real-time interactive exploration of large CNV datasets in a user-friendly designed interface and facilitates semi-automated clinical CNV interpretation following the ACMG guidelines by integrating the ClassifCNV tool. In combination with clinical judgment, the application enables clinicians and researchers to formulate novel hypotheses and guide their decision-making process. Subsequently, the CNV-ClinViewer enhances for clinical investigators’ patient care and for basic scientists’ translational genomic research.
Availability and implementation
The web application is freely available at https://cnv-ClinViewer.broadinstitute.org and the open-source code can be found at https://github.com/LalResearchGroup/CNV-clinviewer.</description><identifier>ISSN: 1367-4811</identifier><identifier>ISSN: 1367-4803</identifier><identifier>EISSN: 1367-4811</identifier><identifier>DOI: 10.1093/bioinformatics/btad290</identifier><identifier>PMID: 37104749</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>DNA Copy Number Variations ; Genome, Human ; Genomics ; Humans ; Original Paper ; Phenotype ; Software</subject><ispartof>Bioinformatics (Oxford, England), 2023-05, Vol.39 (5)</ispartof><rights>The Author(s) 2023. Published by Oxford University Press. 2023</rights><rights>The Author(s) 2023. Published by Oxford University Press.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c457t-3b76de881fbfecaf82aa74e354bb0f01fa07eb971f99f5160675d91068d8ffd93</citedby><cites>FETCH-LOGICAL-c457t-3b76de881fbfecaf82aa74e354bb0f01fa07eb971f99f5160675d91068d8ffd93</cites><orcidid>0000-0002-4217-5277 ; 0000-0003-0546-5141 ; 0000-0003-1268-9995 ; 0000-0001-6127-6308 ; 0000-0001-8698-3770 ; 0000-0002-4435-6610 ; 0000-0002-5173-9636 ; 0000-0002-6833-9049</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC10174702/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC10174702/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,885,1604,27924,27925,53791,53793</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/37104749$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Kendziorski, Christina</contributor><creatorcontrib>Macnee, Marie</creatorcontrib><creatorcontrib>Pérez-Palma, Eduardo</creatorcontrib><creatorcontrib>Brünger, Tobias</creatorcontrib><creatorcontrib>Klöckner, Chiara</creatorcontrib><creatorcontrib>Platzer, Konrad</creatorcontrib><creatorcontrib>Stefanski, Arthur</creatorcontrib><creatorcontrib>Montanucci, Ludovica</creatorcontrib><creatorcontrib>Bayat, Allan</creatorcontrib><creatorcontrib>Radtke, Maximilian</creatorcontrib><creatorcontrib>Collins, Ryan L</creatorcontrib><creatorcontrib>Talkowski, Michael</creatorcontrib><creatorcontrib>Blankenberg, Daniel</creatorcontrib><creatorcontrib>Møller, Rikke S</creatorcontrib><creatorcontrib>Lemke, Johannes R</creatorcontrib><creatorcontrib>Nothnagel, Michael</creatorcontrib><creatorcontrib>May, Patrick</creatorcontrib><creatorcontrib>Lal, Dennis</creatorcontrib><title>CNV-ClinViewer: enhancing the clinical interpretation of large copy-number variants online</title><title>Bioinformatics (Oxford, England)</title><addtitle>Bioinformatics</addtitle><description>Abstract
Motivation
Pathogenic copy-number variants (CNVs) can cause a heterogeneous spectrum of rare and severe disorders. However, most CNVs are benign and are part of natural variation in human genomes. CNV pathogenicity classification, genotype–phenotype analyses, and therapeutic target identification are challenging and time-consuming tasks that require the integration and analysis of information from multiple scattered sources by experts.
Results
Here, we introduce the CNV-ClinViewer, an open-source web application for clinical evaluation and visual exploration of CNVs. The application enables real-time interactive exploration of large CNV datasets in a user-friendly designed interface and facilitates semi-automated clinical CNV interpretation following the ACMG guidelines by integrating the ClassifCNV tool. In combination with clinical judgment, the application enables clinicians and researchers to formulate novel hypotheses and guide their decision-making process. Subsequently, the CNV-ClinViewer enhances for clinical investigators’ patient care and for basic scientists’ translational genomic research.
Availability and implementation
The web application is freely available at https://cnv-ClinViewer.broadinstitute.org and the open-source code can be found at https://github.com/LalResearchGroup/CNV-clinviewer.</description><subject>DNA Copy Number Variations</subject><subject>Genome, Human</subject><subject>Genomics</subject><subject>Humans</subject><subject>Original Paper</subject><subject>Phenotype</subject><subject>Software</subject><issn>1367-4811</issn><issn>1367-4803</issn><issn>1367-4811</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2023</creationdate><recordtype>article</recordtype><sourceid>TOX</sourceid><recordid>eNqNkU9P3DAQxa2qqMC2XwHlyCXdcf457qWqVrQgoXIBDr1YtjPedZXYwXa22m9P0C6IvfU0I83vvTfSI-SCwlcKvFwq660zPgwyWR2XKsmu4PCBnNGyYXnVUvrx3X5KzmP8CwA11M0ncloyChWr-Bn5s_r9mK966x4t_sPwLUO3kU5bt87SBjM9X6yWfWZdwjAGTHOed5k3WS_Degb8uMvdNCgM2VYGK12KmXezDD-TEyP7iF8Oc0Eefl7dr67z27tfN6sft7muapbyUrGmw7alRhnU0rSFlKzCsq6UAgPUSGCoOKOGc1PTBhpWd5xC03atMR0vF-T73nec1ICdRpeC7MUY7CDDTnhpxfHF2Y1Y-62gQFnFoJgdLg8OwT9NGJMYbNTY99Khn6IoWmC8gIKVM9rsUR18jAHNWw4F8dKMOG5GHJqZhRfvv3yTvVYxA3QP-Gn8X9Nnj1Sknw</recordid><startdate>20230504</startdate><enddate>20230504</enddate><creator>Macnee, Marie</creator><creator>Pérez-Palma, Eduardo</creator><creator>Brünger, Tobias</creator><creator>Klöckner, Chiara</creator><creator>Platzer, Konrad</creator><creator>Stefanski, Arthur</creator><creator>Montanucci, Ludovica</creator><creator>Bayat, Allan</creator><creator>Radtke, Maximilian</creator><creator>Collins, Ryan L</creator><creator>Talkowski, Michael</creator><creator>Blankenberg, Daniel</creator><creator>Møller, Rikke S</creator><creator>Lemke, Johannes R</creator><creator>Nothnagel, Michael</creator><creator>May, Patrick</creator><creator>Lal, Dennis</creator><general>Oxford University Press</general><scope>TOX</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0002-4217-5277</orcidid><orcidid>https://orcid.org/0000-0003-0546-5141</orcidid><orcidid>https://orcid.org/0000-0003-1268-9995</orcidid><orcidid>https://orcid.org/0000-0001-6127-6308</orcidid><orcidid>https://orcid.org/0000-0001-8698-3770</orcidid><orcidid>https://orcid.org/0000-0002-4435-6610</orcidid><orcidid>https://orcid.org/0000-0002-5173-9636</orcidid><orcidid>https://orcid.org/0000-0002-6833-9049</orcidid></search><sort><creationdate>20230504</creationdate><title>CNV-ClinViewer: enhancing the clinical interpretation of large copy-number variants online</title><author>Macnee, Marie ; Pérez-Palma, Eduardo ; Brünger, Tobias ; Klöckner, Chiara ; Platzer, Konrad ; Stefanski, Arthur ; Montanucci, Ludovica ; Bayat, Allan ; Radtke, Maximilian ; Collins, Ryan L ; Talkowski, Michael ; Blankenberg, Daniel ; Møller, Rikke S ; Lemke, Johannes R ; Nothnagel, Michael ; May, Patrick ; Lal, Dennis</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c457t-3b76de881fbfecaf82aa74e354bb0f01fa07eb971f99f5160675d91068d8ffd93</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2023</creationdate><topic>DNA Copy Number Variations</topic><topic>Genome, Human</topic><topic>Genomics</topic><topic>Humans</topic><topic>Original Paper</topic><topic>Phenotype</topic><topic>Software</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Macnee, Marie</creatorcontrib><creatorcontrib>Pérez-Palma, Eduardo</creatorcontrib><creatorcontrib>Brünger, Tobias</creatorcontrib><creatorcontrib>Klöckner, Chiara</creatorcontrib><creatorcontrib>Platzer, Konrad</creatorcontrib><creatorcontrib>Stefanski, Arthur</creatorcontrib><creatorcontrib>Montanucci, Ludovica</creatorcontrib><creatorcontrib>Bayat, Allan</creatorcontrib><creatorcontrib>Radtke, Maximilian</creatorcontrib><creatorcontrib>Collins, Ryan L</creatorcontrib><creatorcontrib>Talkowski, Michael</creatorcontrib><creatorcontrib>Blankenberg, Daniel</creatorcontrib><creatorcontrib>Møller, Rikke S</creatorcontrib><creatorcontrib>Lemke, Johannes R</creatorcontrib><creatorcontrib>Nothnagel, Michael</creatorcontrib><creatorcontrib>May, Patrick</creatorcontrib><creatorcontrib>Lal, Dennis</creatorcontrib><collection>Oxford Academic Journals (Open Access)</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Bioinformatics (Oxford, England)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Macnee, Marie</au><au>Pérez-Palma, Eduardo</au><au>Brünger, Tobias</au><au>Klöckner, Chiara</au><au>Platzer, Konrad</au><au>Stefanski, Arthur</au><au>Montanucci, Ludovica</au><au>Bayat, Allan</au><au>Radtke, Maximilian</au><au>Collins, Ryan L</au><au>Talkowski, Michael</au><au>Blankenberg, Daniel</au><au>Møller, Rikke S</au><au>Lemke, Johannes R</au><au>Nothnagel, Michael</au><au>May, Patrick</au><au>Lal, Dennis</au><au>Kendziorski, Christina</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>CNV-ClinViewer: enhancing the clinical interpretation of large copy-number variants online</atitle><jtitle>Bioinformatics (Oxford, England)</jtitle><addtitle>Bioinformatics</addtitle><date>2023-05-04</date><risdate>2023</risdate><volume>39</volume><issue>5</issue><issn>1367-4811</issn><issn>1367-4803</issn><eissn>1367-4811</eissn><abstract>Abstract
Motivation
Pathogenic copy-number variants (CNVs) can cause a heterogeneous spectrum of rare and severe disorders. However, most CNVs are benign and are part of natural variation in human genomes. CNV pathogenicity classification, genotype–phenotype analyses, and therapeutic target identification are challenging and time-consuming tasks that require the integration and analysis of information from multiple scattered sources by experts.
Results
Here, we introduce the CNV-ClinViewer, an open-source web application for clinical evaluation and visual exploration of CNVs. The application enables real-time interactive exploration of large CNV datasets in a user-friendly designed interface and facilitates semi-automated clinical CNV interpretation following the ACMG guidelines by integrating the ClassifCNV tool. In combination with clinical judgment, the application enables clinicians and researchers to formulate novel hypotheses and guide their decision-making process. Subsequently, the CNV-ClinViewer enhances for clinical investigators’ patient care and for basic scientists’ translational genomic research.
Availability and implementation
The web application is freely available at https://cnv-ClinViewer.broadinstitute.org and the open-source code can be found at https://github.com/LalResearchGroup/CNV-clinviewer.</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>37104749</pmid><doi>10.1093/bioinformatics/btad290</doi><orcidid>https://orcid.org/0000-0002-4217-5277</orcidid><orcidid>https://orcid.org/0000-0003-0546-5141</orcidid><orcidid>https://orcid.org/0000-0003-1268-9995</orcidid><orcidid>https://orcid.org/0000-0001-6127-6308</orcidid><orcidid>https://orcid.org/0000-0001-8698-3770</orcidid><orcidid>https://orcid.org/0000-0002-4435-6610</orcidid><orcidid>https://orcid.org/0000-0002-5173-9636</orcidid><orcidid>https://orcid.org/0000-0002-6833-9049</orcidid><oa>free_for_read</oa></addata></record> |
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| source | PubMed (Medline); Oxford Academic Journals (Open Access) |
| subjects | DNA Copy Number Variations Genome, Human Genomics Humans Original Paper Phenotype Software |
| title | CNV-ClinViewer: enhancing the clinical interpretation of large copy-number variants online |
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