{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T11:43:44Z","timestamp":1753875824999,"version":"3.41.2"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2022,5,5]],"date-time":"2022-05-05T00:00:00Z","timestamp":1651708800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,9,20]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Evaluation of phenotype-driven gene prioritization approaches for Mendelian diseases could facilitate the software development and method selection for the workflow configuration and clinical practice. In our original article, the performance of 10 well-recognized causal-gene prioritization methods was benchmarked using 305 cases from the deciphering developmental disorders (DDD) project and 209 in-house cases via a relatively unbiased methodology. The evaluation results showed that LIRICAL and AMELIE were two of the best methods in our benchmark experiments, and the possible integrative approach of these two methods may enhance the diagnostic efficiency. However, some methodological critiques were raised by the authors of Exomiser and PhenIX, so we revisited our benchmarking studies to answer their comments in this letter.<\/jats:p>","DOI":"10.1093\/bib\/bbac181","type":"journal-article","created":{"date-parts":[[2022,4,22]],"date-time":"2022-04-22T11:10:04Z","timestamp":1650625804000},"source":"Crossref","is-referenced-by-count":4,"title":["Revisiting benchmark study for response to methodological critiques of \u2018Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases\u2019"],"prefix":"10.1093","volume":"23","author":[{"given":"Xiao","family":"Yuan","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6218-1885","authenticated-orcid":false,"given":"Peng","family":"Zhang","sequence":"additional","affiliation":[]}],"member":"286","published-online":{"date-parts":[[2022,5,5]]},"reference":[{"key":"2022092013202323300_ref1","article-title":"Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases","volume":"23","author":"Yuan","year":"2022","journal-title":"Brief Bioinform"},{"key":"2022092013202323300_ref2","doi-asserted-by":"crossref","first-page":"2004","DOI":"10.1038\/nprot.2015.124","article-title":"Next-generation diagnostics and disease-gene discovery with the Exomiser","volume":"10","author":"Smedley","year":"2015","journal-title":"Nat Protoc"},{"key":"2022092013202323300_ref3","doi-asserted-by":"crossref","first-page":"252ra123","DOI":"10.1126\/scitranslmed.3009262","article-title":"Effective diagnosis of genetic disease by computational phenotype analysis of the disease-associated genome","volume":"6","author":"Zemojtel","year":"2014","journal-title":"Sci Transl Med"},{"key":"2022092013202323300_ref4","doi-asserted-by":"crossref","first-page":"1073","DOI":"10.1038\/nprot.2009.86","article-title":"Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm","volume":"4","author":"Kumar","year":"2009","journal-title":"Nat Protoc"},{"key":"2022092013202323300_ref5","doi-asserted-by":"crossref","first-page":"248","DOI":"10.1038\/nmeth0410-248","article-title":"A method and server for predicting damaging missense mutations","volume":"7","author":"Adzhubei","year":"2010","journal-title":"Nat Methods"},{"key":"2022092013202323300_ref6","doi-asserted-by":"crossref","first-page":"575","DOI":"10.1038\/nmeth0810-575","article-title":"MutationTaster evaluates disease-causing potential of sequence alterations","volume":"7","author":"Schwarz","year":"2010","journal-title":"Nat Methods"},{"key":"2022092013202323300_ref7","doi-asserted-by":"crossref","first-page":"877","DOI":"10.1016\/j.ajhg.2016.08.016","article-title":"REVEL: an ensemble method for predicting the pathogenicity of rare missense variants","volume":"99","author":"Ioannidis","year":"2016","journal-title":"The Am J Hum Genet"},{"key":"2022092013202323300_ref8","doi-asserted-by":"crossref","first-page":"510","DOI":"10.1038\/s41467-020-20847-0","article-title":"MVP predicts the pathogenicity of missense variants by deep learning","volume":"12","author":"Qi","year":"2021","journal-title":"Nat Commun"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/23\/5\/bbac181\/45937633\/bbac181.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/23\/5\/bbac181\/45937633\/bbac181.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,9,20]],"date-time":"2022-09-20T17:24:33Z","timestamp":1663694673000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/doi\/10.1093\/bib\/bbac181\/6580907"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,5,5]]},"references-count":8,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2022,9,20]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbac181","relation":{},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"type":"print","value":"1467-5463"},{"type":"electronic","value":"1477-4054"}],"subject":[],"published-other":{"date-parts":[[2022,9]]},"published":{"date-parts":[[2022,5,5]]},"article-number":"bbac181"}}