The AnnotSV webserver in 2023: updated visualization and ranking
Abstract Much of the human genetics variant repertoire is composed of single nucleotide variants (SNV) and small insertion/deletions (indel) but structural variants (SV) remain a major part of our modified DNA. SV detection has often been a complex question to answer either because of the necessity...
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| Veröffentlicht in: | Nucleic acids research 2023-07, Vol.51 (W1), p.W39-W45 |
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| creator | Geoffroy, Véronique Lamouche, Jean-Baptiste Guignard, Thomas Nicaise, Samuel Kress, Arnaud Scheidecker, Sophie Le Béchec, Antony Muller, Jean |
| description | Abstract
Much of the human genetics variant repertoire is composed of single nucleotide variants (SNV) and small insertion/deletions (indel) but structural variants (SV) remain a major part of our modified DNA. SV detection has often been a complex question to answer either because of the necessity to use different technologies (array CGH, SNP array, Karyotype, Optical Genome Mapping…) to detect each category of SV or to get an appropriate resolution (Whole Genome Sequencing). Thanks to the deluge of pangenomic analysis, Human geneticists are accumulating SV and their interpretation remains time consuming and challenging. The AnnotSV webserver (https://www.lbgi.fr/AnnotSV/) aims at being an efficient tool to (i) annotate and interpret SV potential pathogenicity in the context of human diseases, (ii) recognize potential false positive variants from all the SV identified and (iii) visualize the patient variants repertoire. The most recent developments in the AnnotSV webserver are: (i) updated annotations sources and ranking, (ii) three novel output formats to allow diverse utilization (analysis, pipelines), as well as (iii) two novel user interfaces including an interactive circos view.
Graphical Abstract
Graphical Abstract |
| doi_str_mv | 10.1093/nar/gkad426 |
| format | Article |
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Much of the human genetics variant repertoire is composed of single nucleotide variants (SNV) and small insertion/deletions (indel) but structural variants (SV) remain a major part of our modified DNA. SV detection has often been a complex question to answer either because of the necessity to use different technologies (array CGH, SNP array, Karyotype, Optical Genome Mapping…) to detect each category of SV or to get an appropriate resolution (Whole Genome Sequencing). Thanks to the deluge of pangenomic analysis, Human geneticists are accumulating SV and their interpretation remains time consuming and challenging. The AnnotSV webserver (https://www.lbgi.fr/AnnotSV/) aims at being an efficient tool to (i) annotate and interpret SV potential pathogenicity in the context of human diseases, (ii) recognize potential false positive variants from all the SV identified and (iii) visualize the patient variants repertoire. The most recent developments in the AnnotSV webserver are: (i) updated annotations sources and ranking, (ii) three novel output formats to allow diverse utilization (analysis, pipelines), as well as (iii) two novel user interfaces including an interactive circos view.
Graphical Abstract
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Much of the human genetics variant repertoire is composed of single nucleotide variants (SNV) and small insertion/deletions (indel) but structural variants (SV) remain a major part of our modified DNA. SV detection has often been a complex question to answer either because of the necessity to use different technologies (array CGH, SNP array, Karyotype, Optical Genome Mapping…) to detect each category of SV or to get an appropriate resolution (Whole Genome Sequencing). Thanks to the deluge of pangenomic analysis, Human geneticists are accumulating SV and their interpretation remains time consuming and challenging. The AnnotSV webserver (https://www.lbgi.fr/AnnotSV/) aims at being an efficient tool to (i) annotate and interpret SV potential pathogenicity in the context of human diseases, (ii) recognize potential false positive variants from all the SV identified and (iii) visualize the patient variants repertoire. The most recent developments in the AnnotSV webserver are: (i) updated annotations sources and ranking, (ii) three novel output formats to allow diverse utilization (analysis, pipelines), as well as (iii) two novel user interfaces including an interactive circos view.
Graphical Abstract
Graphical Abstract</description><subject>Artificial Intelligence</subject><subject>Computer Science</subject><subject>Genome</subject><subject>Genome, Human</subject><subject>High-Throughput Nucleotide Sequencing</subject><subject>Humans</subject><subject>INDEL Mutation</subject><subject>Polymorphism, Single Nucleotide</subject><subject>Restriction Mapping</subject><subject>Sequence Analysis, DNA</subject><subject>Web Server Issue</subject><subject>Whole Genome Sequencing</subject><issn>0305-1048</issn><issn>1362-4962</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2023</creationdate><recordtype>article</recordtype><sourceid>TOX</sourceid><sourceid>EIF</sourceid><recordid>eNp9kc9PwjAYhhujEURP3s1ORmMmX3-Mdl6UEBUTEg-i16bbOqiODtsNo3-9Q5CoB09N2qfPm-97ETrEcI4hpl2rXHfyojJGeluojWmPhCzukW3UBgpRiIGJFtrz_hkAMxyxXdSinOBeFEMbXY2nOuhbW1YPT8GbTrx2C-0CYwMChF4E9TxTlc6ChfG1KsyHqkxpA2WzwCn7YuxkH-3kqvD6YH120OPN9XgwDEf3t3eD_ihMGeNVyEWTrYWOVS4U1SnNecKIEAnOSZIqhtM0olGWcQ6JiAlwqjCLswRYTnORcNpBlyvvvE5mOku1rZwq5NyZmXLvslRG_n6xZion5UJioASALw2nK8P0z79hfySXd9BsBzNGFrhhT9Zprnytta_kzPhUF4Wyuqy9JAILiFj8pT1boakrvXc637gxyGVBsilIrgtq6KOfY2zY70Ya4HgFlPX8X9MnL1uY8A</recordid><startdate>20230705</startdate><enddate>20230705</enddate><creator>Geoffroy, Véronique</creator><creator>Lamouche, Jean-Baptiste</creator><creator>Guignard, Thomas</creator><creator>Nicaise, Samuel</creator><creator>Kress, Arnaud</creator><creator>Scheidecker, Sophie</creator><creator>Le Béchec, Antony</creator><creator>Muller, Jean</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>1XC</scope><scope>VOOES</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0002-7682-559X</orcidid><orcidid>https://orcid.org/0000-0002-4149-0857</orcidid></search><sort><creationdate>20230705</creationdate><title>The AnnotSV webserver in 2023: updated visualization and ranking</title><author>Geoffroy, Véronique ; Lamouche, Jean-Baptiste ; Guignard, Thomas ; Nicaise, Samuel ; Kress, Arnaud ; Scheidecker, Sophie ; Le Béchec, Antony ; Muller, Jean</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c447t-78141e8e9af8a3ec3f7b4288b1f2bca41cc535dd770b892073a149db04f3f8b73</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2023</creationdate><topic>Artificial Intelligence</topic><topic>Computer Science</topic><topic>Genome</topic><topic>Genome, Human</topic><topic>High-Throughput Nucleotide Sequencing</topic><topic>Humans</topic><topic>INDEL Mutation</topic><topic>Polymorphism, Single Nucleotide</topic><topic>Restriction Mapping</topic><topic>Sequence Analysis, DNA</topic><topic>Web Server Issue</topic><topic>Whole Genome Sequencing</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Geoffroy, Véronique</creatorcontrib><creatorcontrib>Lamouche, Jean-Baptiste</creatorcontrib><creatorcontrib>Guignard, Thomas</creatorcontrib><creatorcontrib>Nicaise, Samuel</creatorcontrib><creatorcontrib>Kress, Arnaud</creatorcontrib><creatorcontrib>Scheidecker, Sophie</creatorcontrib><creatorcontrib>Le Béchec, Antony</creatorcontrib><creatorcontrib>Muller, Jean</creatorcontrib><collection>Oxford Journals Open Access Collection</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>Hyper Article en Ligne (HAL)</collection><collection>Hyper Article en Ligne (HAL) (Open Access)</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Nucleic acids research</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Geoffroy, Véronique</au><au>Lamouche, Jean-Baptiste</au><au>Guignard, Thomas</au><au>Nicaise, Samuel</au><au>Kress, Arnaud</au><au>Scheidecker, Sophie</au><au>Le Béchec, Antony</au><au>Muller, Jean</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>The AnnotSV webserver in 2023: updated visualization and ranking</atitle><jtitle>Nucleic acids research</jtitle><addtitle>Nucleic Acids Res</addtitle><date>2023-07-05</date><risdate>2023</risdate><volume>51</volume><issue>W1</issue><spage>W39</spage><epage>W45</epage><pages>W39-W45</pages><issn>0305-1048</issn><eissn>1362-4962</eissn><abstract>Abstract
Much of the human genetics variant repertoire is composed of single nucleotide variants (SNV) and small insertion/deletions (indel) but structural variants (SV) remain a major part of our modified DNA. SV detection has often been a complex question to answer either because of the necessity to use different technologies (array CGH, SNP array, Karyotype, Optical Genome Mapping…) to detect each category of SV or to get an appropriate resolution (Whole Genome Sequencing). Thanks to the deluge of pangenomic analysis, Human geneticists are accumulating SV and their interpretation remains time consuming and challenging. The AnnotSV webserver (https://www.lbgi.fr/AnnotSV/) aims at being an efficient tool to (i) annotate and interpret SV potential pathogenicity in the context of human diseases, (ii) recognize potential false positive variants from all the SV identified and (iii) visualize the patient variants repertoire. The most recent developments in the AnnotSV webserver are: (i) updated annotations sources and ranking, (ii) three novel output formats to allow diverse utilization (analysis, pipelines), as well as (iii) two novel user interfaces including an interactive circos view.
Graphical Abstract
Graphical Abstract</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>37216590</pmid><doi>10.1093/nar/gkad426</doi><orcidid>https://orcid.org/0000-0002-7682-559X</orcidid><orcidid>https://orcid.org/0000-0002-4149-0857</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | Artificial Intelligence Computer Science Genome Genome, Human High-Throughput Nucleotide Sequencing Humans INDEL Mutation Polymorphism, Single Nucleotide Restriction Mapping Sequence Analysis, DNA Web Server Issue Whole Genome Sequencing |
| title | The AnnotSV webserver in 2023: updated visualization and ranking |
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