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<p class="MsoNormal">Hi,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></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.<o:p></o:p></p>
<p class="MsoNormal">I was hoping VEP could provide this information since it provides information about variants.<o:p></o:p></p>
<p class="MsoNormal">The data that I downloaded from COSMIC includes the following fields (or importance here):<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Pubmed ID 15138567<o:p></o:p></p>
<p class="MsoNormal"><span style="background:yellow;mso-highlight:yellow">COSMIC Mutation ID 45724</span><o:p></o:p></p>
<p class="MsoNormal">CDS Mutation Syntax c.253_254delCC<o:p></o:p></p>
<p class="MsoNormal">AA Mutation Syntax p.P85fs*63<o:p></o:p></p>
<p class="MsoNormal">Gene Name TP53<o:p></o:p></p>
<p class="MsoNormal">Accession Number ENST00000269305<o:p></o:p></p>
<p class="MsoNormal">COSMIC Sample ID 1399473<o:p></o:p></p>
<p class="MsoNormal">Samp gene mutated y<o:p></o:p></p>
<p class="MsoNormal">Entrez Gene ID 7157<o:p></o:p></p>
<p class="MsoNormal">Swissprot ID P04637 ---> See if can get the protein sequence from here<o:p></o:p></p>
<p class="MsoNormal">Ensembl Gene ID ENSG00000141510<o:p></o:p></p>
<p class="MsoNormal">COSMIC Study ID blank (nothing)<o:p></o:p></p>
<p class="MsoNormal">Genomic Coordinates (GRCh38) 17:7676115-7676116<o:p></o:p></p>
<p class="MsoNormal">CDS Mutation Type Deletion<o:p></o:p></p>
<p class="MsoNormal">CDS Mutation Start 253<o:p></o:p></p>
<p class="MsoNormal">CDS Mutation Stop 254<o:p></o:p></p>
<p class="MsoNormal">AA Mutation Type Deletion - Frameshift<o:p></o:p></p>
<p class="MsoNormal">AA Mutation Start 85<o:p></o:p></p>
<p class="MsoNormal">AA Mutation Stop 85<o:p></o:p></p>
<p class="MsoNormal">Somatic status Variant of unknown origin<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I tried to get results from VEP using the following 3 formats for this frameshift mutation:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">TP53:c.253_254delCC<o:p></o:p></p>
<p class="MsoNormal">- this gave an error<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">17:c.253_254delCC<o:p></o:p></p>
<p class="MsoNormal">- this returned nothing<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">ENST00000269305:c.253_254delCC<o:p></o:p></p>
<p class="MsoNormal">- this returned a table of results with a large number of results.<o:p></o:p></p>
<p class="MsoNormal">(screenshot below)<o:p></o:p></p>
<p class="MsoNormal"><img width="204" height="127" id="Picture_x0020_1" src="cid:image001.jpg@01D26B42.6EAF4700"><o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></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.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Why am I am getting different results for the same variant passed in different formats (all HGVS)?<o:p></o:p></p>
<p class="MsoNormal">Is VEP well suited for what I am trying to do?<o:p></o:p></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.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thank you,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">- Pankaj<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span style="font-size:7.0pt;font-family:"Verdana","sans-serif"">-----------------------------<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.0pt;font-family:"Verdana","sans-serif"">Pankaj Agarwal, M.S<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.0pt;font-family:"Verdana","sans-serif"">Bioinformatician<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.0pt;font-family:"Verdana","sans-serif"">Data Analyst<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.0pt;font-family:"Verdana","sans-serif"">Applied Therapeutics<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.0pt;font-family:"Verdana","sans-serif"">Div. of Surgical Sciences<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.0pt;font-family:"Verdana","sans-serif"">Dept. of Surgery<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.0pt;font-family:"Verdana","sans-serif"">Duke University<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.0pt;font-family:"Verdana","sans-serif"">M: 919-244-6389<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.0pt;font-family:"Verdana","sans-serif"">O: 919-681-2251<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.0pt;font-family:"Verdana","sans-serif""><a href="mailto:p.agarwal@duke.edu"><span style="color:blue">p.agarwal@duke.edu</span></a><o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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