<div dir="ltr">Thanks much Anja! <div><br></div><div>I think Ensembl is a very useful platform for such queries. Am curious for this following query below, could you please let me know how can I do this using the Ensembl platform:</div><div><br></div><div>a) I want to extract the 5' and 3' UTRs from the mRNA of BRCA1 and BRCA2. For instance information 5' & 3' UTR for the refseq geneid "<span style="font-size:inherit;word-spacing:normal;background-color:initial;font-family:Consolas,Monaco,"Andale Mono","Ubuntu Mono",monospace;color:black">NM_007299.3</span>" of BRCA1</div><div><br></div><div><br></div><div>b) Also, find the position of the SNPs (rsIDs) in the 5' and 3' UTRs. For instance information like this: (for the refseq geneid "<span style="background-color:initial;font-family:Consolas,Monaco,"Andale Mono","Ubuntu Mono",monospace;font-size:inherit;word-spacing:normal;color:black">NM_007299.3</span>" of BRCA1)</div><div> </div><div>refseg-geneID mutant-allele position-of-mutation</div><div><span style="color:rgb(0,0,0);font-family:Consolas,Monaco,"Andale Mono","Ubuntu Mono",monospace">NM_007299.3 c to t 400032</span><br></div><div><br></div><div>Thanks much! Please let me know if something is not clear.</div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Sep 21, 2017 at 1:07 PM, Anja Thormann <span dir="ltr"><<a href="mailto:anja@ebi.ac.uk" target="_blank">anja@ebi.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">Hi DK,<div><br></div><div><div>Let me give you some background on where we get our data for allele frequency or genotype frequency annotations from:</div><div><br></div><div>We provide allele frequencies and genotype frequencies (where available) from a set of reference populations provided by projects like 1000 Genomes Project, ESP, gnomAD (supersedes ExAC).</div><div><br></div><div>Only 1000 Genomes provides sample genotypes from which we can compute population genotype frequencies.</div><div><br></div><div>ESP provides population genotype frequencies. But we don't get a break down of genotypes by sample in the population.</div><div><br></div><div>gnomAD only provides allele counts in a population.</div><div><br></div><div>Here is a variant which has annotations from all of the above projects: <a href="http://www.ensembl.org/Homo_sapiens/Variation/Population?db=core;r=1:230709548-230710548;v=rs699;vdb=variation;vf=664" target="_blank">http://www.ensembl.org/Homo_<wbr>sapiens/Variation/Population?<wbr>db=core;r=1:230709548-<wbr>230710548;v=rs699;vdb=<wbr>variation;vf=664</a></div><div><br></div><div>For 1000GENOMES:phase_3:AFR allele frequencies: A: 0.097 G: 0.903 genotype frequencies: A|A: 0.126 A|G: 0.338 G|G: 0.536</div><div>For gnomADe:AFR allele frequencies: A: 0.152 G: 0.848 No genotype frequencies</div><div><br></div><div>Our variation endpoint does not return gnomAD frequencies at the moment. We will include the frequencies for the next release.</div><div><br></div><div>For now I would recommend that you use our VEP endpoint</div><div><a href="https://rest.ensembl.org/documentation/info/vep_id_get" target="_blank">https://rest.ensembl.org/<wbr>documentation/info/vep_id_get</a></div><div>Examples:</div><div><a href="https://rest.ensembl.org/vep/human/id/rs769971095?content-type=application/json" target="_blank">https://rest.ensembl.org/vep/<wbr>human/id/rs769971095?content-<wbr>type=application/json</a></div><div><a href="https://rest.ensembl.org/vep/human/id/rs699?content-type=application/json" target="_blank">https://rest.ensembl.org/vep/<wbr>human/id/rs699?content-type=<wbr>application/json</a></div><div><br></div><div>The VEP makes use of cache files which store allele frequencies for the 1000 Genomes Project super populations (AFR, AMR, EAS, EUR, SAS) and the gnomAD exome data.</div><div><br></div><div>Please find a list of our populations, their short names and descriptions here:</div><div><a href="http://www.ensembl.org/info/genome/variation/data_description.html#populations" target="_blank">http://www.ensembl.org/info/<wbr>genome/variation/data_<wbr>description.html#populations</a></div><div><br></div><div>The VEP provides annotations from:</div><div>gnomADe:ALL - All gnomAD exomes individuals</div><div>gnomADe:AFR - African/African American</div><div>gnomADe:AMR - Admixed American</div><div>gnomADe:ASJ - Ashkenazi Jewish</div><div>gnomADe:EAS - East Asian</div><div>gnomADe:FIN - Finnish</div><div>gnomADe:NFE - Non-Finnish European</div><div>gnomADe:OTH - Other</div><div>gnomADe:SAS - South Asian</div><div>1000GENOMES:phase_3:AFR African</div><div>1000GENOMES:phase_3:AMR American</div><div>1000GENOMES:phase_3:EAS East Asian</div><div>1000GENOMES:phase_3:EUR European</div><div>1000GENOMES:phase_3:SAS South Asian</div><div><br></div><div>The populations use the following names in the vep endpoints:</div><div> - for example for gnomADe:NFE: gnomad_nfe_maf and gnomad_nfe_allele</div><div> - for example for 1000GENOMES:phase_3:AFR: afr_maf and afr_allele</div><div><br></div><div>We have a post vep endpoint which allows you to send a list of variant IDs for annotation. <a href="https://rest.ensembl.org/documentation/info/vep_id_post" target="_blank">https://rest.<wbr>ensembl.org/documentation/<wbr>info/vep_id_post</a></div><div><br></div><div><div>I hope that helps you with your use case.</div><span class="HOEnZb"><font color="#888888"><div><br></div><div>Anja</div></font></span></div><div><div class="h5"><div><br></div><div><br></div><div><blockquote type="cite"><div>On 20 Sep 2017, at 22:05, deepak kumar <<a href="mailto:deepak.k.choubey@gmail.com" target="_blank">deepak.k.choubey@gmail.com</a>> wrote:</div><br class="m_-1526393040704610493Apple-interchange-newline"><div><div dir="ltr">Hi Anja,<div><br></div><div>Thank you so much for the reply. It certainly helped me to get to the right direction of my query. However, could you please help me understand a few queries regarding the same:</div><div><br></div><div>To start of with, I find the "Rest API" a very clean approach to get variant information.</div><div><br></div><div>a) My aim is to find if a SNP (rsID let say <span style="font-family:Times;font-size:inherit">rs769971095</span>) share populations, or in other words, if this rsID mutation can be found in more than one population. From the links you provided I see that I can find an answer but am confused between "population allele frequency" and "population genotype frequency". To fulfill my aim, data for this rsID should be taken from "population allele frequency" or "population genotype frequency"?</div><div><br></div><div>b) The population name given in the "example output" of the "Rest API" are in short form like 'AMR', 'SAS' etc. Could you please let me know how can i retrieve the full population name for a given rsID?</div><div><br></div><div>Thanks much!</div><div>DK</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Sep 19, 2017 at 7:22 PM, Anja Thormann <span dir="ltr"><<a href="mailto:anja@ebi.ac.uk" target="_blank">anja@ebi.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">Hi DK,<div><br></div><div>you have a few options of getting allele frequencies for a variant.</div><div><br></div><div>You can use</div><div> - our perl API: <a href="http://www.ensembl.org/info/docs/api/variation/variation_tutorial.html#alleles" target="_blank">http://www.ensembl.org/in<wbr>fo/docs/api/variation/variatio<wbr>n_tutorial.html#alleles</a> (to get you started)</div><div> - our REST API: <a href="https://rest.ensembl.org/documentation/info/variation_id" target="_blank">https://rest.ensembl.org/<wbr>documentation/info/variation_i<wbr>d</a> (to get you started)</div><div> - the VEP: <a href="https://www.ensembl.org/info/docs/tools/vep/script/vep_options.html" target="_blank">https://www.ensembl.org/i<wbr>nfo/docs/tools/vep/script/vep_<wbr>options.html</a> It will allow you to annotate your input variants with frequency data if available</div><div><br></div><div>Please feel free to contact us again if you have any questions regarding the above approaches.</div><div><br></div><div>Kind regards,</div><div>Anja</div><div><br></div><div><br><div><blockquote type="cite"><div><div class="m_-1526393040704610493h5"><div>On 19 Sep 2017, at 16:06, deepak kumar <<a href="mailto:deepak.k.choubey@gmail.com" target="_blank">deepak.k.choubey@gmail.com</a>> wrote:</div><br class="m_-1526393040704610493m_5289383583780598652Apple-interchange-newline"></div></div><div><div><div class="m_-1526393040704610493h5"><div dir="ltr">Dear ALL,<div><br></div><div><span style="color:rgb(51,51,51);font-family:sans-serif;font-size:13px"> I have been looking for a way to find "which nsSNP (with rs ID number like rs769971095) belong to what population(s), and if possible what gender"? I came to know about the Ensembl "population genetics" for the variants. </span><br></div><div><span style="color:rgb(51,51,51);font-family:sans-serif;font-size:13px"><br></span></div><div><p style="box-sizing:border-box;margin:0px 0px 10px;color:rgb(102,102,102);font-family:sans-serif;font-size:13px">I found the respective population genetics info for 2 rsIDs; rs559632360 & rs769971095</p><p style="box-sizing:border-box;margin:0px 0px 10px;color:rgb(102,102,102);font-family:sans-serif;font-size:13px">For "rs769971095" the super-population it shows is: ALL, AFR, AMR, ASJ, EAS, FIN, NFE, OTH, SAS. </p><p style="box-sizing:border-box;margin:0px 0px 10px;color:rgb(102,102,102);font-family:sans-serif;font-size:13px">For "rs559632360" the super-population it shows is: ALL, AFR, AMR, EAS, SAS, EUR.</p><p style="box-sizing:border-box;margin:0px 0px 10px;color:rgb(102,102,102);font-family:sans-serif;font-size:13px"><br></p><p style="box-sizing:border-box;margin:0px 0px 10px;color:rgb(102,102,102);font-family:sans-serif;font-size:13px">For rs559632360 rsID, it also shows population genetics from "1000 Genomes Project Phase 3 & gnomAD exomes" along with "subpopulation" information, whereas, for rs769971095 it shows only "gnomAD exomes" population genetics.</p><p style="box-sizing:border-box;margin:0px 0px 10px;color:rgb(102,102,102);font-family:sans-serif;font-size:13px"><a rel="nofollow" href="http://grch37.ensembl.org/Homo_sapiens/Variation/Population?db=core;r=3:12625875-12626875;v=rs769971095;vdb=variation;vf=135759093" style="box-sizing:border-box;background:transparent;color:rgb(66,139,202);text-decoration-line:none" target="_blank">http://grch37.ensembl.org/Homo<wbr>_sapiens/Variation/Population?<wbr>db=core;r=3:12625875-12626875;<wbr>v=rs769971095;vdb=variation;<wbr>vf=135759093</a></p><p style="box-sizing:border-box;margin:0px 0px 10px;color:rgb(102,102,102);font-family:sans-serif;font-size:13px"><a rel="nofollow" href="http://grch37.ensembl.org/Homo_sapiens/Variation/Population?db=core;r=3:12632759-12633759;v=rs559632360;vdb=variation;vf=92299087#population_freq_SAS" style="box-sizing:border-box;background:transparent;color:rgb(66,139,202);text-decoration-line:none" target="_blank">http://grch37.ensembl.org/Homo<wbr>_sapiens/Variation/Population?<wbr>db=core;r=3:12632759-12633759;<wbr>v=rs559632360;vdb=variation;<wbr>vf=92299087#population_freq_<wbr>SAS</a></p><p style="box-sizing:border-box;margin:0px 0px 10px;color:rgb(102,102,102);font-family:sans-serif;font-size:13px">Does this mean that for "rs769971095" there is no "1000 genomes project phase 3" data available? </p><p style="box-sizing:border-box;margin:0px 0px 10px;color:rgb(102,102,102);font-family:sans-serif;font-size:13px">I am interested to know if these two rsIDs belong to one population, so, can it be said that these rsIDs share same population? If yes, what population they share? It would be great if I could know how to make a reasonable interpretation for this.</p><p style="box-sizing:border-box;margin:0px 0px 10px;color:rgb(102,102,102);font-family:sans-serif;font-size:13px">Also, I need to do this for many rsIDs, could you please let me know how this process can be automated? Where, I can generate results like this:</p><p style="box-sizing:border-box;margin:0px 0px 10px;color:rgb(102,102,102);font-family:sans-serif;font-size:13px"><br></p><p style="box-sizing:border-box;margin:0px 0px 10px;color:rgb(102,102,102);font-family:sans-serif;font-size:13px"><b>rsID Super-Population with allele frequencies Sub-population</b></p><p style="box-sizing:border-box;margin:0px 0px 10px;color:rgb(102,102,102);font-family:sans-serif;font-size:13px">rs769971095 ALL, AFR, AMR, ASJ, EAS, FIN, NFE, OTH, SAS. .......etc</p><p style="box-sizing:border-box;margin:0px 0px 10px;color:rgb(102,102,102);font-family:sans-serif;font-size:13px">rs559632360 ALL, AFR, AMR, EAS, SAS, EUR ......etc </p><p style="box-sizing:border-box;margin:0px 0px 10px;color:rgb(102,102,102);font-family:sans-serif;font-size:13px"><br></p><p style="box-sizing:border-box;margin:0px 0px 10px;color:rgb(102,102,102);font-family:sans-serif;font-size:13px"><br></p><p style="box-sizing:border-box;margin:0px 0px 10px;color:rgb(102,102,102);font-family:sans-serif;font-size:13px">Thanks much! DK</p></div></div></div></div>
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