{"id":4412,"date":"2018-02-04T21:05:44","date_gmt":"2018-02-04T21:05:44","guid":{"rendered":"http:\/\/www.cytognomix.com\/?p=4412"},"modified":"2018-02-04T21:06:23","modified_gmt":"2018-02-04T21:06:23","slug":"oct-1-2017-comment-on-pubmed-pmid-28949076-rules-and-tools-to-predict-the-splicing-effects-of-exonic-and-intronic-mutations-in-pubmed-commons-internet-bethesda-md-national-library-of-medic","status":"publish","type":"post","link":"https:\/\/www.cytognomix.com\/?p=4412","title":{"rendered":"Oct. 1, 2017. Comment on PubMed PMID 28949076: Rules and tools to predict the splicing effects of exonic and intronic mutations. In: PubMed Commons [Internet]. Bethesda (MD): National Library of Medicine; 2017 Sep 26"},"content":{"rendered":"<p><a id=\"ui-ncbipopper-10\" role=\"button\" href=\"https:\/\/www.ncbi.nlm.nih.gov\/myncbi\/peter.rogan.1\/comments\/\" class=\"broken_link\">Peter Rogan<\/a><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/28949076#cm28949076_74191\">2017 Oct 01 8:57 p.m.<\/a><\/p>\n<div data-md=\"We would like to alert readers to the fact that information theory-based splicing mutation analysis has been used  to analyze a wide range of variants (in\/dels and SNVs) that affect splicing in introns and exons in peer reviewed studies. These tools have been used analyze mutations that alter branchpoint recognition and within introns in peer reviewed studies. The Automated Splice Site and Exon Definition Analysis server, ASSEDA (&lt;PMID:23348723&gt;) analyzes mutations at branchpoints, within intronic sequences, at cryptic splice sites, and at splicing regulatory protein binding sites (&quot;enhancer\/silencer&quot; sequences).  We have also published the Shannon pipeline (&lt;PMID:23499923&gt;), which carries out mutation analysis affecting splicing (and transcription factor binding sites; &lt;PMID:27899659&gt;) on a genome scale. Veridical is software validates splicing mutations found with the Shannon pipeline (or any other program) with RNASeq data from the same individual (&lt;PMID: 24741438&gt;, &lt;PMID:25394353&gt;).&lt;\/p&gt;\n&lt;p&gt;Our previous review article extensively describes the use of these tools for splicing mutation analysis by many other research groups, besides ourselves (&lt;PMID:25717368&gt;).\"><\/p>\n<p>We would like to alert readers to the fact that information theory-based splicing mutation analysis has been used to analyze a wide range of variants (in\/dels and SNVs) that affect splicing in introns and exons in peer reviewed studies. These tools have been used analyze mutations that alter branchpoint recognition and within introns in peer reviewed studies. The Automated Splice Site and Exon Definition Analysis server, ASSEDA (<a title=\"Prediction of mutant mRNA splice isoforms by information theory-based exon definition.\" href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/23348723\/\">Mucaki EJ, 2013<\/a>) analyzes mutations at branchpoints, within intronic sequences, at cryptic splice sites, and at splicing regulatory protein binding sites (&#8220;enhancer\/silencer&#8221; sequences). We have also published the Shannon pipeline (<a title=\"Interpretation, stratification and evidence for sequence variants affecting mRNA splicing in complete human genome sequences.\" href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/23499923\/\">Shirley BC, 2013<\/a>), which carries out mutation analysis affecting splicing (and transcription factor binding sites;\u00a0<a title=\"Discovery and validation of information theory-based transcription factor and cofactor binding site motifs.\" href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/27899659\/\">Lu R, 2017<\/a>) on a genome scale. Veridical is software validates splicing mutations found with the Shannon pipeline (or any other program) with RNASeq data from the same individual (<a title=\"Validation of predicted mRNA splicing mutations using high-throughput transcriptome data.\" href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/24741438\/\">Viner C, 2014<\/a>,\u00a0<a title=\"Splicing mutation analysis reveals previously unrecognized pathways in lymph node-invasive breast cancer.\" href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/25394353\/\">Dorman SN, 2014<\/a>).<\/p>\n<p>Our previous review article extensively describes the use of these tools for splicing mutation analysis by many other research groups, besides ourselves (<a title=\"Interpretation of mRNA splicing mutations in genetic disease: review of the literature and guidelines for information-theoretical analysis.\" href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/25717368\/\">Caminsky N, 2014<\/a>).<\/p>\n<\/div>\n","protected":false},"excerpt":{"rendered":"<p>Peter Rogan2017 Oct 01 8:57 p.m. We would like to alert readers to the fact that information theory-based splicing mutation analysis has been used to analyze a wide range of variants (in\/dels and SNVs) that affect splicing in introns and exons in peer reviewed studies. These tools have been used analyze mutations that alter branchpoint [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":[],"categories":[6],"tags":[],"_links":{"self":[{"href":"https:\/\/www.cytognomix.com\/index.php?rest_route=\/wp\/v2\/posts\/4412"}],"collection":[{"href":"https:\/\/www.cytognomix.com\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.cytognomix.com\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.cytognomix.com\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.cytognomix.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=4412"}],"version-history":[{"count":2,"href":"https:\/\/www.cytognomix.com\/index.php?rest_route=\/wp\/v2\/posts\/4412\/revisions"}],"predecessor-version":[{"id":4414,"href":"https:\/\/www.cytognomix.com\/index.php?rest_route=\/wp\/v2\/posts\/4412\/revisions\/4414"}],"wp:attachment":[{"href":"https:\/\/www.cytognomix.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=4412"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.cytognomix.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=4412"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.cytognomix.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=4412"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}