<div dir="ltr">Hi Pankaj,<div><br></div><div>There's an error in one of your HGVS inputs, but apart from this I see the expected results for all three notations.</div><div><br></div><div>The correct one for the chromosomal location should be:</div><div><br></div><div>17:g.7676115_7676116delGG<br></div><div><br></div><div>You must use "g." for chromosomal coordinates, and provide the sequence on the forward strand, so GG instead of CC. I've attached a screenshot of the results I get when I use the instant VEP function on this input.</div><div><br></div><div>You will see many results because the TP53 gene has a large number of alternate transcripts [1]. You may ask VEP to select one of these by choosing the option "Select one selected consequence per variant" in the "Restrict results" field of the Filtering section on the VEP web interface.</div><div><br></div><div>Regards</div><div><br></div><div>Will McLaren</div><div>Ensembl Variation</div><div><br></div><div>[1] : <a href="http://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000141510;r=17:7661779-7687550">http://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000141510;r=17:7661779-7687550</a></div><div><br></div><div><img src="cid:ii_ixst0jkt0_1598d13218d4e083" width="559" height="406"><br><br></div><div><br></div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On 10 January 2017 at 18:07, Pankaj Agarwal <span dir="ltr"><<a href="mailto:p.agarwal@duke.edu" target="_blank">p.agarwal@duke.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<p class="MsoNormal">Hi,<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">I have downloaded a set of frameshift mutations from COSMIC using Biomart. My goal is to get the protein sequence of the transcript starting from the location of the frameshift mutation.<u></u><u></u></p>
<p class="MsoNormal">I was hoping VEP could provide this information since it provides information about variants.<u></u><u></u></p>
<p class="MsoNormal">The data that I downloaded from COSMIC includes the following fields (or importance here):<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Pubmed ID 15138567<u></u><u></u></p>
<p class="MsoNormal"><span style="background:yellow">COSMIC Mutation ID 45724</span><u></u><u></u></p>
<p class="MsoNormal">CDS Mutation Syntax c.253_254delCC<u></u><u></u></p>
<p class="MsoNormal">AA Mutation Syntax p.P85fs*63<u></u><u></u></p>
<p class="MsoNormal">Gene Name TP53<u></u><u></u></p>
<p class="MsoNormal">Accession Number ENST00000269305<u></u><u></u></p>
<p class="MsoNormal">COSMIC Sample ID 1399473<u></u><u></u></p>
<p class="MsoNormal">Samp gene mutated y<u></u><u></u></p>
<p class="MsoNormal">Entrez Gene ID 7157<u></u><u></u></p>
<p class="MsoNormal">Swissprot ID P04637 ---> See if can get the protein sequence from here<u></u><u></u></p>
<p class="MsoNormal">Ensembl Gene ID ENSG00000141510<u></u><u></u></p>
<p class="MsoNormal">COSMIC Study ID blank (nothing)<u></u><u></u></p>
<p class="MsoNormal">Genomic Coordinates (GRCh38) 17:7676115-7676116<u></u><u></u></p>
<p class="MsoNormal">CDS Mutation Type Deletion<u></u><u></u></p>
<p class="MsoNormal">CDS Mutation Start 253<u></u><u></u></p>
<p class="MsoNormal">CDS Mutation Stop 254<u></u><u></u></p>
<p class="MsoNormal">AA Mutation Type Deletion - Frameshift<u></u><u></u></p>
<p class="MsoNormal">AA Mutation Start 85<u></u><u></u></p>
<p class="MsoNormal">AA Mutation Stop 85<u></u><u></u></p>
<p class="MsoNormal">Somatic status Variant of unknown origin<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">I tried to get results from VEP using the following 3 formats for this frameshift mutation:<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">TP53:c.253_254delCC<u></u><u></u></p>
<p class="MsoNormal">- this gave an error<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">17:c.253_254delCC<u></u><u></u></p>
<p class="MsoNormal">- this returned nothing<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">ENST00000269305:c.253_254delCC<u></u><u></u></p>
<p class="MsoNormal">- this returned a table of results with a large number of results.<u></u><u></u></p>
<p class="MsoNormal">(screenshot below)<u></u><u></u></p>
<p class="MsoNormal"><img width="204" height="127" id="m_2047190566092784800Picture_x0020_1" src="cid:image001.jpg@01D26B42.6EAF4700"><u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Please note that the results do include the COSMIC Mutation ID that is same as the one that I have for this variant.<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Why am I am getting different results for the same variant passed in different formats (all HGVS)?<u></u><u></u></p>
<p class="MsoNormal">Is VEP well suited for what I am trying to do?<u></u><u></u></p>
<p class="MsoNormal">Could you please suggest other ways I can get the a single NT or protein sequence for the unique frameshift mutation that I am using for the query.<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Thank you,<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">- Pankaj<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><span style="font-size:7.0pt;font-family:"Verdana","sans-serif"">-----------------------------<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:7.0pt;font-family:"Verdana","sans-serif"">Pankaj Agarwal, M.S<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:7.0pt;font-family:"Verdana","sans-serif"">Bioinformatician<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:7.0pt;font-family:"Verdana","sans-serif"">Data Analyst<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:7.0pt;font-family:"Verdana","sans-serif"">Applied Therapeutics<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:7.0pt;font-family:"Verdana","sans-serif"">Div. of Surgical Sciences<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:7.0pt;font-family:"Verdana","sans-serif"">Dept. of Surgery<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:7.0pt;font-family:"Verdana","sans-serif"">Duke University<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:7.0pt;font-family:"Verdana","sans-serif"">M: <a href="tel:(919)%20244-6389" value="+19192446389" target="_blank">919-244-6389</a><u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:7.0pt;font-family:"Verdana","sans-serif"">O: <a href="tel:(919)%20681-2251" value="+19196812251" target="_blank">919-681-2251</a><u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:7.0pt;font-family:"Verdana","sans-serif""><a href="mailto:p.agarwal@duke.edu" target="_blank"><span style="color:blue">p.agarwal@duke.edu</span></a><u></u><u></u></span></p>
<p class="MsoNormal"><u></u> <u></u></p>
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