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<div style="font-family:sans-serif"><div style="white-space:normal"><p dir="auto">Hi Andrius,</p>
<p dir="auto">I'm not sure that I explained the LRG project clearly. The goal is to create standard, stable references sequences appropriate for clinical reporting. This is necessary because both transcript annotation and the underlying genome sequence change over time. Without effective standards, variants reported in HGVS nomenclature, but missing information such as genome assembly or transcript version, can become ambiguous over time. Interpretation and reinterpretation of variants into classifications such as benign or pathogenetic also requires stable location information, which is what LRGs provide.</p>
<p dir="auto">It is also important to note that LRG sequences are just one part of our larger toolkit supporting interpretation of genome variation.</p>
<p dir="auto">Regardless, I think best to take further discussion off this list. Please feel free to contact me directly.</p>
<p dir="auto">Thanks,<br>
Paul </p>
<br><p dir="auto">On 9 Oct 2017, at 17:07, Andrius Baskys, MD, PhD wrote:</p>
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<blockquote style="border-left:2px solid #777; color:#777; margin:0 0 5px; padding-left:5px"><div id="9EEC19D5-BE8B-45BC-87D7-29D1F82386AE"><div dir="auto">Hello Paul,<br></div>
<div dir="auto">Thank you very much for your comments and information. I noticed from the description you send me that 'Community' who provides you with a feedback does not include practicing physicians, or someone who could use this information to diagnose and treat diseases in real life. I think that is a mistake and it hampers the implentation of your effort into clinical practice, which is the ultimate goal.<br></div>
<div dir="auto">Hope you will find my comments useful.<br></div>
<div dir="auto">Kind regards,<br></div>
<div dir="auto">Andrius<br><br></div>
<div dir="auto"><!-- tmjah_g_1299s -->Andrius Baskys, MD, PhD<!-- tmjah_g_1299e --><br></div>
<div dir="auto"><!-- tmjah_g_1299s -->Newport Beach, CA 92658 USA<!-- tmjah_g_1299e --><br></div>
<div dir="auto"><!-- tmjah_g_1299s -->Ph. 877-483-2071<!-- tmjah_g_1299e --><br></div>
<div dir="auto"><!-- tmjah_g_1299s -->Intl. +1 626-239-8378<!-- tmjah_g_1299e --><br></div>
<div dir="auto"><!-- tmjah_g_1299s -->Fax 877-953-8777<!-- tmjah_g_1299e --></div>
<div class="gmail_quote" >On Oct 9, 2017, at 8:35 AM, Paul Flicek <<a href="mailto:flicek@ebi.ac.uk" target="_blank">flicek@ebi.ac.uk</a>> wrote:<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div style="font-family:sans-serif"><div style="white-space:normal"><p dir="auto">Hi Andrius,</p>
<p dir="auto">The LRG project works extensively with the community to create transcripts suitable for variant reporting. The LRG sequences and their component transcripts are standards specifically designed for clinical use cases, but the LRG project does not interpret variants.</p>
<p dir="auto">Our curators work to ensure that transcripts with clinical relevance are annotated accurately and that they meet the requirements of diagnostic laboratories, LSDB curators and other users.</p>
<p dir="auto">For more information, we have published a couple of papers describing the project including the most recent one in 2014: <a href="http://europepmc.org/articles/PMC3965024" style="color:#3983C4">http://europepmc.org/articles/PMC3965024</a>. There is also information at <a href="http://www.lrg-sequence.org" style="color:#3983C4">http://www.lrg-sequence.org</a>.</p>
<br><p dir="auto">Paul</p>
<br><p dir="auto">On 9 Oct 2017, at 15:56, Andrius Baskys, MD, PhD wrote:</p>
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<blockquote style="border-left:2px solid #777; color:#777; margin:0 0 5px; padding-left:5px"><div id="5025AAB5-3BC4-457F-AA58-9B76FFDDB28A"><div text="#000000" bgcolor="#FFFFFF"><div dir="auto">Hi Emily,<br><br></div>
<div dir="auto">I admire the amazing work that Ensembl is doing and use it in my practice as much as possible. However, i noticed your adverts for a bioinformatician to review "clinically relevant" transcripts and wonder how would a person who never treated a patient determine what is clinically relevant? Or is clinical knowledge irrelevant?<br><br></div>
<div dir="auto">Just curious.<br><br></div>
<div dir="auto">Kind regards,<br></div>
<div dir="auto">Andrius<br><br></div>
<div dir="auto"><!-- tmjah_g_1299s -->Andrius Baskys, MD, PhD<!-- tmjah_g_1299e --><br></div>
<div dir="auto"><!-- tmjah_g_1299s -->1133 Camelback Street #9287<!-- tmjah_g_1299e --><br></div>
<div dir="auto"><!-- tmjah_g_1299s -->Newport Beach, CA 92658 USA<!-- tmjah_g_1299e --><br></div>
<div dir="auto"><!-- tmjah_g_1299s -->Ph. 877-483-2071<!-- tmjah_g_1299e --><br></div>
<div dir="auto"><!-- tmjah_g_1299s -->Intl. +1 626-239-8378<!-- tmjah_g_1299e --><br></div>
<div dir="auto"><!-- tmjah_g_1299s -->Fax 877-953-8777<!-- tmjah_g_1299e --></div>
<div class="gmail_quote">On Oct 9, 2017, at 1:07 AM, Emily Perry <<a href="mailto:emily@ebi.ac.uk" target="_blank">emily@ebi.ac.uk</a>> wrote:<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Hi All<br>
<br>
We have a couple of jobs advertised:<br>
<a class="moz-txt-link-freetext" href="http://www.ensembl.info/jobs/">http://www.ensembl.info/jobs/</a><br>
<br>
<b>Bioinformatician – GENCODE</b><br>
We’re looking for a bioinformatician to review clinically relevant
consensus GENCODE and RefSeq transcripts for the CREST project.
We’re looking for degrees in genetics or biological sciences with
experience in Perl and genomics. Closes 21st October.<br>
<br>
<b>Scientific curator – LRG</b><br>
We’re looking for a scientific curator to work on the Locus
Reference Genomic project, curating clinically relevant gene
annotation. We’re looking for degrees in genetics or biological
sciences with understanding of genetic variation and genomics.
Closes 12th November.<br>
<br>
All the best<br>
<br>
Emily<br>
<pre class="moz-signature" cols="72">--
Dr Emily Perry (Pritchard)
Ensembl Outreach Project Leader
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge
CB10 1SD
UK </pre>
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