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<p class="MsoNormal"><span lang="EN-US">Hi all,<br>
<br>
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Not sure if this is the right contact point for a bioinformatics bug (we have a support ticket open via Fabienne Maurer but I’ve heard progress is limited).<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">I’m writing this with some potential critical implications. Our lab techs were using Ensembl to extract gene sequences for designing Sanger primers to validate variants in the parents of our pre-natal patients. I’m not
sure if we are alone in the world to do the primer design this way or if it is just us.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Starting sometime after December 28<sup>th</sup> (first fault detection on Jan 15<sup>th</sup>), the rich text format (RTF) output from the main ensemble website is no longer displaying any variant coloration when you
apply MAF filtering (potentially with release 111? Maybe dbSNP related?).<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Usually, we remove highlighting from variants with a minor allele frequency (MAF) of less than 0.01% to avoid rare variants so we can solely visualize the common polymorphisms. Otherwise, we risk designing a primer which
could provide a false-negative result for a patient/parent (i.e. if one of the primers fail to anneal due to inherent variation in the population).<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Currently when the MAF < 0.01% filter is applied all “coloration/highlighting” (i.e. a proxy for MAF) for the variants is NOT output to the RTF file.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Luckily, I’m aware of the Ensembl archives and this was able to solve our immediate problem.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">However, in case anyone else is using a similar method I think it would be good to fix the underlying issue.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Steps to reproduce:<br>
<br>
<o:p></o:p></span></p>
<ol style="margin-top:0cm" start="1" type="1">
<li class="MsoListParagraph" style="margin-left:0cm;mso-list:l0 level1 lfo3"><span lang="EN-US">Visit transcript exon page.<o:p></o:p></span>
<ol style="margin-top:0cm" start="1" type="a">
<li class="MsoListParagraph" style="margin-left:0cm;mso-list:l0 level2 lfo3"><span lang="EN-US">Working : http://jul2023.archive.ensembl.org/Homo_sapiens/Transcript/Exons?db=core;g=ENSG00000075624;r=7:5526409-5563902;t=ENST00000646664<o:p></o:p></span></li><li class="MsoListParagraph" style="margin-left:0cm;mso-list:l0 level2 lfo3"><span lang="EN-US">Broken: http://ensembl.org/Homo_sapiens/Transcript/Exons?db=core;g=ENSG00000075624;r=7:5526409-5563902;t=ENST00000646664<o:p></o:p></span></li></ol>
</li><li class="MsoListParagraph" style="margin-left:0cm;mso-list:l0 level1 lfo3"><span lang="EN-US">Click ‘Download Sequence’ (just below
<o:p></o:p></span></li><li class="MsoListParagraph" style="margin-left:0cm;mso-list:l0 level1 lfo3"><span lang="EN-US">Set ‘File format’ to RTF (Word-compatible)<o:p></o:p></span></li><li class="MsoListParagraph" style="margin-left:0cm;mso-list:l0 level1 lfo3"><span lang="EN-US">For the option ‘Hide variants by frequency (MAF)’ set it to ‘Hide rare, MAF < 0.01%’
<o:p></o:p></span></li><li class="MsoListParagraph" style="margin-left:0cm;mso-list:l0 level1 lfo3"><span lang="DE-CH">Click ‘Download’<o:p></o:p></span></li></ol>
<p class="MsoNormal"><span lang="DE-CH"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">If you start with 1a you get a sequence with highlighted variants based on MAF (with the rare ones excluded, i.e. un-highlighted)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">If you start with 1b you don’t have any significant highlighting.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Note that if you don’t apply step 4 you get all the highlighting for all variants regardless of MAF (which still works for both 1a and 1b) – suggesting its related to the filtering.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">I tried on multiple OS, browsers, computers, ensembl-mirrors, and the issue seems to stem from the v111 release.<br>
<br>
Hope this helps.<br>
<br>
Thanks,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Ben<o:p></o:p></span></p>
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