661 lines
42 KiB
HTML
661 lines
42 KiB
HTML
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<div class="search"><form method="get" action="/snp/"><div class="search_form"><label for="database" class="offscreen_noflow">Search database</label><select id="database"><optgroup label="Recent"><option value="snp" selected="selected">SNP</option><option value="nuccore">Nucleotide</option><option value="books">Books</option><option value="refseq" class="last">RefSeq</option></optgroup><optgroup label="All"><option value="gquery">All Databases</option><option value="assembly">Assembly</option><option value="biocollections">Biocollections</option><option value="bioproject">BioProject</option><option value="biosample">BioSample</option><option value="books">Books</option><option value="clinvar">ClinVar</option><option value="cdd">Conserved Domains</option><option value="gap">dbGaP</option><option value="dbvar">dbVar</option><option value="gene">Gene</option><option value="genome">Genome</option><option value="gds">GEO DataSets</option><option value="geoprofiles">GEO Profiles</option><option value="gtr">GTR</option><option value="ipg">Identical Protein Groups</option><option value="medgen">MedGen</option><option value="mesh">MeSH</option><option value="nlmcatalog">NLM Catalog</option><option value="nuccore">Nucleotide</option><option value="omim">OMIM</option><option value="pmc">PMC</option><option value="protein">Protein</option><option value="proteinclusters">Protein Clusters</option><option value="protfam">Protein Family Models</option><option value="pcassay">PubChem BioAssay</option><option value="pccompound">PubChem Compound</option><option value="pcsubstance">PubChem Substance</option><option value="pubmed">PubMed</option><option value="snp">SNP</option><option value="sra">SRA</option><option value="structure">Structure</option><option value="taxonomy">Taxonomy</option><option value="toolkit">ToolKit</option><option value="toolkitall">ToolKitAll</option><option value="toolkitbookgh">ToolKitBookgh</option></optgroup></select><div class="nowrap"><label for="term" class="offscreen_noflow" accesskey="/">Search term</label><div class="nowrap"><input type="text" name="term" id="term" title="Search SNP" value="" class="jig-ncbiclearbutton jig-ncbiautocomplete" data-jigconfig="isEnabled:false,disableUrl:'NcbiSearchBarAutoComplCtrl'" autocomplete="off" data-sbconfig="ds:'no',pjs:'no',afs:'yes'" /></div><button id="search" type="submit" class="button_search nowrap" cmd="go">Search</button></div></div><input type="hidden" name="p$a" id="p$a" /><input type="hidden" name="p$l" id="p$l" value="PAFAppLayout" /><input type="hidden" name="p$st" id="p$st" value="snp" /><input name="SessionId" id="SessionId" value="CE8B5AF87C7FFCB1_0191SID" disabled="disabled" type="hidden" /><input name="Snapshot" id="Snapshot" value="/projects/staticsites/snp/snpdoc@1.10" disabled="disabled" type="hidden" /></form><ul class=" inline_list searchlinks"><li>
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<a href="/snp/advanced">Advanced</a>
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</li></ul></div>
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</div>
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<div class="nav_and_browser">
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</div>
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<!-- was itemctrl -->
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<div class="container">
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<div id="maincontent" class="content col twelve_col last">
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<div class="col1">
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<h1 id="entrez-snp-20-updates"><strong>Entrez SNP (2.0) Updates:</strong></h1>
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<div class="toc">
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<ul>
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<li><a href="#update05252020">May 26, 2020 - New Features....</a><ul>
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<li><a href="#1-search-dbsnp-using-hgvs">1. Search dbSNP using HGVS**</a></li>
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<li><a href="#2-snps-with-alfa-frequency">2. SNPs with ALFA frequency**</a><ul>
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<li><a href="#all-snps-with-alfa-frequency-can">All SNPs with ALFA frequency can be retrieved using an Entrez filter.</a></li>
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<li><a href="#user-byalfa-facet-under-validate">User 'by-ALFA' facet under 'Validate Status' Filters.</a></li>
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<li><a href="#click-on-the-alfa-link-of-each-r">Click on the 'ALFA' link of each RefSNP to view frequency by population.</a></li>
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</ul>
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</li>
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</ul>
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</li>
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<li><a href="#update02202020">February 5, 2020 - Support for GRCh37 position search and reporting</a></li>
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<li><a href="#update09292019">September 29, 2019 - dbSNP 2.0 General Updates</a><ul>
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<li><a href="#no-change-to-the-web-search-http">No change to the web search https://www.ncbi.nlm.nih.gov/snp</a></li>
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<li><a href="#web-result-display-changes">Web Result Display changes</a></li>
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<li><a href="#eutils-changes">Eutils changes</a></li>
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</ul>
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</li>
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<li><a href="#dbsnp-tutorials">dbSNP Tutorials</a></li>
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<li><a href="#additional-resources">Additional Resources</a></li>
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</ul>
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</div>
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<h2 id="update05252020">May 26, 2020 - New Features....</h2>
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<h3 id="1-search-dbsnp-using-hgvs">1. Search dbSNP using HGVS**</h3>
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<p>Example: <a href="/snp/?term=NM_000237.3%3Ac.1421C%3EG+NG_013007.1%3Ag.7147G%3EA">NM_000237.3:c.1421C>G OR NG_013007.1:g.7147G>A</a> </p>
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<h3 id="2-snps-with-alfa-frequency">2. SNPs with ALFA frequency**</h3>
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<h4 id="all-snps-with-alfa-frequency-can">All SNPs with ALFA frequency can be retrieved using an Entrez filter.</h4>
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<p>Example: <a href="https://www.ncbi.nlm.nih.gov/snp/?term=all%5Bsb%5D+AND+by+alfa%5BValidation%5D">all[sb] AND by alfa[Validation]</a> </p>
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<h4 id="user-byalfa-facet-under-validate">User 'by-ALFA' facet under 'Validate Status' Filters.</h4>
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<p><img src="/core/assets/snp/docs/entrez/alfa_filter.jpg" alt="By-ALFA" /></p>
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<h4 id="click-on-the-alfa-link-of-each-r">Click on the 'ALFA' link of each RefSNP to view frequency by population.</h4>
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<p><img src="/core/assets/snp/docs/entrez/RS_ALFA_Details.JPG" alt="RS_ALFA-link" /></p>
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<h2 id="update02202020">February 5, 2020 - Support for GRCh37 position search and reporting</h2>
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<p>dbSNP web search (https://www.ncbi.nlm.nih.gov/snp/) and eUtils eSearch, eFetch, and eSummary now supports both GRCh38 and GRCh37(new) coordinates. The POSITION_GRCH37 field have been added to the <a href="https://www.ncbi.nlm.nih.gov/snp/docs/entrez_help/">guide</a> of all available terms. </p>
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<p><strong>Example</strong>: Search rs1000000038 using the GRCh38 and GRCh37 fields POSITION and POSITION_GRCH37, respectively </p>
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<p>GRCh38 -</p>
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<p><a href="https://www.ncbi.nlm.nih.gov/snp/?term=62587167%5BPOSITION%5D+AND+8%5BCHR%5D">https://www.ncbi.nlm.nih.gov/snp/?term=62587167%5BPOSITION%5D+AND+8%5BCHR%5D</a></p>
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<p><a href="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=snp&term=62587167%5BPOSITION%5D+AND+8%5BCHR%5D">https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=snp&term=62587167%5BPOSITION%5D+AND+8%5BCHR%5D</a></p>
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<p>GRCh37 -</p>
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<p><a href="https://www.ncbi.nlm.nih.gov/snp/?term=63499726%5BPOSITION_GRCH37%5D+AND+8%5BCHR%5D">https://www.ncbi.nlm.nih.gov/snp/?term=63499726%5BPOSITION_GRCH37%5D+AND+8%5BCHR%5D</a></p>
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<p><a href="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=snp&term=63499726%5BPOSITION_GRCH37%5D+AND+8%5BCHR%5D">https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=snp&term=63499726%5BPOSITION_GRCH37%5D+AND+8%5BCHR%5D</a></p>
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<p>dbSNP eUtils eFetch and eSummary XML report GRCh37 positions in the previous assembly field CHRPOS_PREV_ASSM along with chromosome positions (CHRPOS) the variant positions on the latest assembly (GRCh38). </p>
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<p>Example: <a href="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=snp&retmode=xml&id=328">https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=snp&retmode=xml&id=328</a></p>
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<p>GRCh38:</p>
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<pre><code class="language-xml"><CHRPOS>8:19962213</CHRPOS>
|
|
</code></pre>
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<p>GRCh37:</p>
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<pre><code class="language-xml"><CHRPOS_PREV_ASSM>8:19819724</CHRPOS_PREV_ASSM>
|
|
</code></pre>
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<p>Visit the resources below for additional information.</p>
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<p>Search guide - <a href="https://www.ncbi.nlm.nih.gov/snp/docs/entrez_help/">https://www.ncbi.nlm.nih.gov/snp/docs/entrez_help/</a></p>
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<p>eUtils tutorials - <a href="https://github.com/ncbi/dbsnp/tree/master/tutorials">https://github.com/ncbi/dbsnp/tree/master/tutorials</a></p>
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<p>Please send your comments and suggestions to (snp-admin@ncbi.nlm.nih.gov).</p>
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<hr />
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<h2 id="update09292019">September 29, 2019 - dbSNP 2.0 General Updates</h2>
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<p>Notifications:
|
|
As previously announced on April 19, 2018, dbSNP Entrez currently only houses human data. In addition, the Entrez and eUtils report formats RS docsum, XML, ASN.1, FASTA, and FLAT format will no longer be available. dbSNP Entrez eUtils will transition to a new single compact eSummary format, the spec and sample data are below. Please contact snp-admin@ncbi.nlm.nih.gov if you have any comments or concerns.</p>
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<h3 id="no-change-to-the-web-search-http">No change to the web search <a href="https://www.ncbi.nlm.nih.gov/snp">https://www.ncbi.nlm.nih.gov/snp</a></h3>
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<h3 id="web-result-display-changes">Web Result Display changes</h3>
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<p><strong>1. Removed flanking sequences</strong></p>
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<p><strong>2. Removed Allele Origin</strong></p>
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<p><strong>3. Removed Geneview</strong></p>
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<p><strong>4. Added Variant Type</strong> - Variant types <a href="/snp/docs/RefSNP_about/#variation-type">supported</a>. </p>
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<p><strong>5. Added Alleles</strong> - The alleles are always reported in the forward <a href="/core/assets/snp/docs/RefSNP_orientation_updates.pdf">orientation</a> with respect to the latest assembly version (ie. GRCh38.p13).</p>
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<p><strong>6. Added additional Functional Consequences</strong> - All consequences based on RefSeq are reported, not just most severe as reported in old version. </p>
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<p><strong>7. Added additional Population Frequency</strong> - Allele frequency from different projects are added in addition to the previously reported Global MAF that was based on the 1000 Genomes Project.</p>
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<p><img src="/core/assets/snp/docs/entrez/Entrez_2.0_display_changes.jpg" alt="refsnp changes example" /></p>
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<h3 id="eutils-changes">Eutils changes</h3>
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<p><strong>1. Deprecated eUtils reports</strong> - RS docsum, XML, ASN.1, FASTA, and FLAT are deprecated and no longer supported.</p>
|
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|
|
<p><strong>2. Added eUtils RefSNP JSON report (beta)</strong> - Use efetch to retrieve dbSNP new JSON object (<a href="https://api.ncbi.nlm.nih.gov/variation/v0/var_service.yaml">schema</a>) containing comprehensive RefSNP content and for convenient integration into <a href="https://www.ncbi.nlm.nih.gov/books/NBK25500/">eUtils</a> workflows. This beta service is still in testing mode so please limit your request to 1-3 RSID/second. Alternative, you can use the Variation Service <a href="https://api.ncbi.nlm.nih.gov/variation/v0/">API</a> directly with additional functions including variant normalization using RSID, <a href="https://www.ncbi.nlm.nih.gov/variation/notation/">SPDI</a>, HGVS, or VCF format and remapping. Complete downloads of dbSNP (+660M RS) are also available on the FTP site in <a href="https://ftp.ncbi.nih.gov/snp/latest_release/JSON">JSON</a> or <a href="https://ftp.ncbi.nih.gov/snp/latest_release/VCF">VCF</a> formats. </p>
|
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|
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<p>efetch example: </p>
|
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|
|
<pre><code class="language-bash">curl -X GET "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=snp&id=268,328&retmode=text&rettype=json"
|
|
</code></pre>
|
|
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|
|
|
<p><strong>3. Updated eSummary XML</strong> - The single XML eSummary report is available with the changes listed (1-5) above. A sample <a href="https://github.com/ncbi/dbsnp/blob/master/specs/eSummary.xml">report</a> and <a href="https://github.com/ncbi/dbsnp/blob/master/specs/eSummary.xsd">schema</a> are available on GitHub.</p>
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|
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|
|
<p>eSummary example: <a href="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=snp&id=268,328">https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=snp&id=268,328</a></p>
|
|
|
|
|
|
<pre><code class="language-bash">curl -X GET "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=snp&id=268,328"
|
|
</code></pre>
|
|
|
|
|
|
<p>Users should migrate to the new default eSummary 2.0 version above. The older 1.0 version will be deprecated later this year but is still made available during the transition period. The old 1.0 version can be requested by adding the version number (version=1.0) as shown below.
|
|
<a href="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=snp&id=268,328&version=1.0">https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=snp&id=268,328&version=1.0</a></p>
|
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|
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<h2 id="dbsnp-tutorials">dbSNP Tutorials</h2>
|
|
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|
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<p>Tutorial are available on <a href="https://github.com/ncbi/dbsnp/tree/master/tutorials">GitHub</a>.</p>
|
|
|
|
|
|
<ul>
|
|
<li>
|
|
<p><a href="/snp/docs/eutils_help/">eUtils</a></p>
|
|
</li>
|
|
<li>
|
|
<p><a href="https://github.com/ncbi/dbsnp/tree/master/tutorials/Variation%20Services">NCBI Variation Services</a></p>
|
|
</li>
|
|
<li>
|
|
<p><a href="https://github.com/ncbi/dbsnp/tree/master/tutorials">Parsing RS JSON</a></p>
|
|
</li>
|
|
</ul>
|
|
|
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|
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<h2 id="additional-resources">Additional Resources</h2>
|
|
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|
|
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<ul>
|
|
<li>
|
|
<p><a href="/snp/docs/RefSNP_about/">About RefSNP(rs)</a></p>
|
|
</li>
|
|
<li>
|
|
<p><a href="https://ncbiinsights.ncbi.nlm.nih.gov/2017/07/07/dbsnp-redesign-supports-future-data-expansion/">dbSNP Redesign</a></p>
|
|
</li>
|
|
<li>
|
|
<p><a href="https://www.biorxiv.org/content/10.1101/537449v3">SPDI Publication</a></p>
|
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</li>
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</ul>
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