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Title:           ClinPrior: an algorithm for diagnosis and novel gene discovery by network-based prioritization
Subject:         Genome Medicine, https://doi.org/10.1186/s13073-023-01214-2
Keywords:        Algorithm;WES/WGS;HPOs;Variant prioritization;Interactome;Hereditary spastic paraplegia;Cerebellar ataxia;Candidate gene
Author:           Agatha Schlüter
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     Item: 
      Title: ClinPrior: an algorithm for diagnosis and novel gene discovery by network-based prioritization
      Children: 
       Item: 
        Title: Abstract 
        Children: 
         Item: 
          Title: Background 
         Item: 
          Title: Methods 
         Item: 
          Title: Results 
         Item: 
          Title: Conclusions 
       Item: 
        Title: Background
       Item: 
        Title: Methods
        Children: 
         Item: 
          Title: ClinPrior: Interactome-driven prioritization method
          Children: 
           Item: 
            Title: Phenotypic score
           Item: 
            Title: Generation of a multilayer interactome network
           Item: 
            Title: Network propagation
           Item: 
            Title: Variant filtering and deleteriousness score
         Item: 
          Title: Patient enrolment and clinical recruitment
       Item: 
        Title: Results
        Children: 
         Item: 
          Title: Benchmarking of ClinPrior using a synthetic WES cohort
         Item: 
          Title: ClinPrior validation on a prospective, real-world discovery cohort of 135 HSPCA families
          Children: 
           Item: 
            Title: Clinical data
           Item: 
            Title: Diagnostic yield of WES and WGS in the HSPCA real-world discovery cohort
         Item: 
          Title: Discovery of novel disease-causing genes through ClinPrior
          Children: 
           Item: 
            Title: RFC1 expansion analysis
           Item: 
            Title: Genetic findings in the HSPCA real-world discovery cohort
           Item: 
            Title: Management implications of a positive genetic diagnosis
           Item: 
            Title: Experimental validation of variants of unknown significance
         Item: 
          Title: ClinPrior generates an expanded network for novel disease gene discovery in HSPCA
       Item: 
        Title: Discussion
       Item: 
        Title: Conclusions
       Item: 
        Title: Anchor 28
       Item: 
        Title: Acknowledgements
       Item: 
        Title: References
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    Keywords: Algorithm;WES/WGS;HPOs;Variant prioritization;Interactome;Hereditary spastic paraplegia;Cerebellar ataxia;Candidate gene
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                           <pdfaProperty:category>external</pdfaProperty:category>
                           <pdfaProperty:description>Mirrors crossmark:CrossmarkDomainExclusive</pdfaProperty:description>
                           <pdfaProperty:name>CrossmarkDomainExclusive</pdfaProperty:name>
                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
                        </rdf:li>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>internal</pdfaProperty:category>
                           <pdfaProperty:description>Mirrors crossmark:DOI</pdfaProperty:description>
                           <pdfaProperty:name>doi</pdfaProperty:name>
                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
                        </rdf:li>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>external</pdfaProperty:category>
                           <pdfaProperty:description>Mirrors crossmark:CrosMarkDomains</pdfaProperty:description>
                           <pdfaProperty:name>CrossMarkDomains</pdfaProperty:name>
                           <pdfaProperty:valueType>seq Text</pdfaProperty:valueType>
                        </rdf:li>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>internal</pdfaProperty:category>
                           <pdfaProperty:description>A name object indicating whether the document has been modified to include trapping information</pdfaProperty:description>
                           <pdfaProperty:name>robots</pdfaProperty:name>
                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
                        </rdf:li>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>internal</pdfaProperty:category>
                           <pdfaProperty:description>ID of PDF/X standard</pdfaProperty:description>
                           <pdfaProperty:name>GTS_PDFXVersion</pdfaProperty:name>
                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
                        </rdf:li>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>internal</pdfaProperty:category>
                           <pdfaProperty:description>Conformance level of PDF/X standard</pdfaProperty:description>
                           <pdfaProperty:name>GTS_PDFXConformance</pdfaProperty:name>
                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
                        </rdf:li>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>internal</pdfaProperty:category>
                           <pdfaProperty:description>Company creating the PDF</pdfaProperty:description>
                           <pdfaProperty:name>Company</pdfaProperty:name>
                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
                        </rdf:li>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>internal</pdfaProperty:category>
                           <pdfaProperty:description>Date when document was last modified</pdfaProperty:description>
                           <pdfaProperty:name>SourceModified</pdfaProperty:name>
                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
                        </rdf:li>
                     </rdf:Seq>
                  </pdfaSchema:property>
               </rdf:li>
               <rdf:li rdf:parseType="Resource">
                  <pdfaSchema:namespaceURI>http://crossref.org/crossmark/1.0/</pdfaSchema:namespaceURI>
                  <pdfaSchema:prefix>crossmark</pdfaSchema:prefix>
                  <pdfaSchema:schema>Crossmark Schema</pdfaSchema:schema>
                  <pdfaSchema:property>
                     <rdf:Seq>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>internal</pdfaProperty:category>
                           <pdfaProperty:description>Usual same as prism:doi</pdfaProperty:description>
                           <pdfaProperty:name>DOI</pdfaProperty:name>
                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
                        </rdf:li>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>external</pdfaProperty:category>
                           <pdfaProperty:description>The date when a publication was publishe.</pdfaProperty:description>
                           <pdfaProperty:name>MajorVersionDate</pdfaProperty:name>
                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
                        </rdf:li>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>internal</pdfaProperty:category>
                           <pdfaProperty:description>CrossmarkDomainExclusive</pdfaProperty:description>
                           <pdfaProperty:name>CrossmarkDomainExclusive</pdfaProperty:name>
                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
                        </rdf:li>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>internal</pdfaProperty:category>
                           <pdfaProperty:description>CrossMarkDomains</pdfaProperty:description>
                           <pdfaProperty:name>CrossMarkDomains</pdfaProperty:name>
                           <pdfaProperty:valueType>seq Text</pdfaProperty:valueType>
                        </rdf:li>
                     </rdf:Seq>
                  </pdfaSchema:property>
               </rdf:li>
               <rdf:li rdf:parseType="Resource">
                  <pdfaSchema:namespaceURI>http://prismstandard.org/namespaces/basic/2.0/</pdfaSchema:namespaceURI>
                  <pdfaSchema:prefix>prism</pdfaSchema:prefix>
                  <pdfaSchema:schema>Prism Schema</pdfaSchema:schema>
                  <pdfaSchema:property>
                     <rdf:Seq>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>external</pdfaProperty:category>
                           <pdfaProperty:description>This element provides the url for an article or unit of content. The attribute platform is optionally allowed for situations in which multiple URLs must be specified. PRISM recommends that a subset of the PCV platform values, namely “mobile” and “web”, be used in conjunction with this element. NOTE: PRISM recommends against the use of the #other value allowed in the PRISM Platform controlled vocabulary. In lieu of using #other please reach out to the PRISM group at prism-wg@yahoogroups.com to request addition of your term to the Platform Controlled Vocabulary.</pdfaProperty:description>
                           <pdfaProperty:name>url</pdfaProperty:name>
                           <pdfaProperty:valueType>URI</pdfaProperty:valueType>
                        </rdf:li>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>external</pdfaProperty:category>
                           <pdfaProperty:description>The Digital Object Identifier for the article.
The DOI may also be used as the dc:identifier. If used as a dc:identifier, the URI form should be captured, and the bare identifier should also be captured using prism:doi. If an alternate unique identifier is used as the required dc:identifier, then the DOI should be specified as a bare identifier within prism:doi only. If the URL associated with a DOI is to be specified, then prism:url may be used in conjunction with prism:doi in order to provide the service endpoint (i.e. the URL). </pdfaProperty:description>
                           <pdfaProperty:name>doi</pdfaProperty:name>
                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
                        </rdf:li>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>external</pdfaProperty:category>
                           <pdfaProperty:description>ISSN for an electronic version of the issue in which the resource occurs. Permits publishers to include a second ISSN, identifying an electronic version of the issue in which the resource occurs (therefore e(lectronic)Issn. If used, prism:eIssn MUST contain the ISSN of the electronic version.</pdfaProperty:description>
                           <pdfaProperty:name>issn</pdfaProperty:name>
                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
                        </rdf:li>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>internal</pdfaProperty:category>
                           <pdfaProperty:description>Volume number</pdfaProperty:description>
                           <pdfaProperty:name>volume</pdfaProperty:name>
                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
                        </rdf:li>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>internal</pdfaProperty:category>
                           <pdfaProperty:description>Issue number</pdfaProperty:description>
                           <pdfaProperty:name>number</pdfaProperty:name>
                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
                        </rdf:li>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>internal</pdfaProperty:category>
                           <pdfaProperty:description>Starting page</pdfaProperty:description>
                           <pdfaProperty:name>startingPage</pdfaProperty:name>
                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
                        </rdf:li>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>internal</pdfaProperty:category>
                           <pdfaProperty:description>Ending page</pdfaProperty:description>
                           <pdfaProperty:name>endingPage</pdfaProperty:name>
                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
                        </rdf:li>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>external</pdfaProperty:category>
                           <pdfaProperty:description>The aggregation type specifies the unit of aggregation for a content collection. Comment PRISM recommends that the PRISM Aggregation Type Controlled Vocabulary be used to provide values for this element. Note: PRISM recommends against the use of the #other value currently allowed in this controlled vocabulary. In lieu of using #other please reach out to the PRISM group at info@prismstandard.org to request addition of your term to the Aggregation Type Controlled Vocabulary. </pdfaProperty:description>
                           <pdfaProperty:name>aggregationType</pdfaProperty:name>
                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
                        </rdf:li>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>external</pdfaProperty:category>
                           <pdfaProperty:description>Title of the magazine, or other publication, in which a resource was/will be published. Typically this will be used to provide the name of the magazine an article appeared in as metadata for the article, along with information such as the article title, the publisher, volume, number, and cover date. Note: Publication name can be used to differentiate between a print magazine and the online version if the names are different such as “magazine” and “magazine.com.”</pdfaProperty:description>
                           <pdfaProperty:name>publicationName</pdfaProperty:name>
                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
                        </rdf:li>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>external</pdfaProperty:category>
                           <pdfaProperty:description>Copyright</pdfaProperty:description>
                           <pdfaProperty:name>copyright</pdfaProperty:name>
                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
                        </rdf:li>
                     </rdf:Seq>
                  </pdfaSchema:property>
               </rdf:li>
               <rdf:li rdf:parseType="Resource">
                  <pdfaSchema:namespaceURI>http://ns.adobe.com/pdf/1.3/</pdfaSchema:namespaceURI>
                  <pdfaSchema:prefix>pdf</pdfaSchema:prefix>
                  <pdfaSchema:schema>Adobe PDF Schema</pdfaSchema:schema>
                  <pdfaSchema:property>
                     <rdf:Seq>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>internal</pdfaProperty:category>
                           <pdfaProperty:description>A name object indicating whether the document has been modified to include trapping information</pdfaProperty:description>
                           <pdfaProperty:name>Trapped</pdfaProperty:name>
                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
                        </rdf:li>
                     </rdf:Seq>
                  </pdfaSchema:property>
               </rdf:li>
               <rdf:li rdf:parseType="Resource">
                  <pdfaSchema:namespaceURI>http://ns.adobe.com/xap/1.0/mm/</pdfaSchema:namespaceURI>
                  <pdfaSchema:prefix>xmpMM</pdfaSchema:prefix>
                  <pdfaSchema:schema>XMP Media Management Schema</pdfaSchema:schema>
                  <pdfaSchema:property>
                     <rdf:Seq>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>internal</pdfaProperty:category>
                           <pdfaProperty:description>UUID based identifier for specific incarnation of a document</pdfaProperty:description>
                           <pdfaProperty:name>InstanceID</pdfaProperty:name>
                           <pdfaProperty:valueType>URI</pdfaProperty:valueType>
                        </rdf:li>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>internal</pdfaProperty:category>
                           <pdfaProperty:description>The common identifier for all versions and renditions of a document.</pdfaProperty:description>
                           <pdfaProperty:name>DocumentID</pdfaProperty:name>
                           <pdfaProperty:valueType>URI</pdfaProperty:valueType>
                        </rdf:li>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>internal</pdfaProperty:category>
                           <pdfaProperty:description>The common identifier for all versions and renditions of a document.</pdfaProperty:description>
                           <pdfaProperty:name>OriginalDocumentID</pdfaProperty:name>
                           <pdfaProperty:valueType>URI</pdfaProperty:valueType>
                        </rdf:li>
                     </rdf:Seq>
                  </pdfaSchema:property>
               </rdf:li>
               <rdf:li rdf:parseType="Resource">
                  <pdfaSchema:namespaceURI>http://www.aiim.org/pdfa/ns/id/</pdfaSchema:namespaceURI>
                  <pdfaSchema:prefix>pdfaid</pdfaSchema:prefix>
                  <pdfaSchema:schema>PDF/A ID Schema</pdfaSchema:schema>
                  <pdfaSchema:property>
                     <rdf:Seq>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>internal</pdfaProperty:category>
                           <pdfaProperty:description>Part of PDF/A standard</pdfaProperty:description>
                           <pdfaProperty:name>part</pdfaProperty:name>
                           <pdfaProperty:valueType>Integer</pdfaProperty:valueType>
                        </rdf:li>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>internal</pdfaProperty:category>
                           <pdfaProperty:description>Amendment of PDF/A standard</pdfaProperty:description>
                           <pdfaProperty:name>amd</pdfaProperty:name>
                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
                        </rdf:li>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>internal</pdfaProperty:category>
                           <pdfaProperty:description>Conformance level of PDF/A standard</pdfaProperty:description>
                           <pdfaProperty:name>conformance</pdfaProperty:name>
                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
                        </rdf:li>
                     </rdf:Seq>
                  </pdfaSchema:property>
               </rdf:li>
               <rdf:li rdf:parseType="Resource">
                  <pdfaSchema:schema>Springer Nature ORCID Schema</pdfaSchema:schema>
                  <pdfaSchema:namespaceURI>http://springernature.com/ns/xmpExtensions/2.0/</pdfaSchema:namespaceURI>
                  <pdfaSchema:prefix>sn</pdfaSchema:prefix>
                  <pdfaSchema:property>
                     <rdf:Seq>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:name>authorInfo</pdfaProperty:name>
                           <pdfaProperty:valueType>Bag AuthorInformation</pdfaProperty:valueType>
                           <pdfaProperty:category>external</pdfaProperty:category>
                           <pdfaProperty:description>Author information: contains the name of each author and his/her ORCiD (ORCiD: Open Researcher and Contributor ID). An ORCiD is a persistent identifier (a non-proprietary alphanumeric code) to uniquely identify scientific and other academic authors.</pdfaProperty:description>
                        </rdf:li>
                     </rdf:Seq>
                  </pdfaSchema:property>
                  <pdfaSchema:valueType>
                     <rdf:Seq>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaType:type>AuthorInformation</pdfaType:type>
                           <pdfaType:namespaceURI>http://springernature.com/ns/xmpExtensions/2.0/authorInfo/</pdfaType:namespaceURI>
                           <pdfaType:prefix>author</pdfaType:prefix>
                           <pdfaType:description>Specifies the types of author information: name and ORCID of an author.</pdfaType:description>
                           <pdfaType:field>
                              <rdf:Seq>
                                 <rdf:li rdf:parseType="Resource">
                                    <pdfaField:name>name</pdfaField:name>
                                    <pdfaField:valueType>Text</pdfaField:valueType>
                                    <pdfaField:description>Gives the name of an author.</pdfaField:description>
                                 </rdf:li>
                                 <rdf:li rdf:parseType="Resource">
                                    <pdfaField:name>orcid</pdfaField:name>
                                    <pdfaField:valueType>URI</pdfaField:valueType>
                                    <pdfaField:description>Gives the ORCID of an author.</pdfaField:description>
                                 </rdf:li>
                              </rdf:Seq>
                           </pdfaType:field>
                        </rdf:li>
                     </rdf:Seq>
                  </pdfaSchema:valueType>
               </rdf:li>
            </rdf:Bag>
         </pdfaExtension:schemas>
      </rdf:Description>
   </rdf:RDF>
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