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<H1>[dbsnp-announce] dbSNP Human BUILD 141 (GRCh38 and GRCh37p13)</H1>
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<B>Public announcements regarding dbSNP</B>
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<A HREF="mailto:dbsnp-announce%40ncbi.nlm.nih.gov?Subject=Re%3A%20%5Bdbsnp-announce%5D%20dbSNP%20Human%20BUILD%20141%20%28GRCh38%20and%20GRCh37p13%29&In-Reply-To=%3Cmailman.21129.1400704074.16325.dbsnp-announce%40ncbi.nlm.nih.gov%3E"
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TITLE="[dbsnp-announce] dbSNP Human BUILD 141 (GRCh38 and GRCh37p13)">dbsnp-announce at ncbi.nlm.nih.gov
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<I>Wed May 21 16:27:38 EDT 2014</I>
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<LI>Previous message: <A HREF="000138.html">[dbsnp-announce] RELEASE: dbSNP BUILD 140 (Non-human organisms)
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<PRE>May 21, 2014
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dbSNP Human BUILD 141 (GRCh38 and GRCh37p13)
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dbSNP has released human Build 141 based on the GRCh38 assembly
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(<A HREF="http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26/">http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26/</A>), as well as on the GRCh37.p13 assembly.
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We are providing both assemblies to support those researchers who are still using GRCh37 as well as
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those that are ready to migrate to GRCh38. dbSNP will no longer support annotation on the HuRef and
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the CRA_TCAGchr7v2 assemblies. Instead the addition of mapping to the haploid hydatidiform mole
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(CHM1.1) assembly will be included in the next Build 142 release.
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==================================================================================
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BUILD 141 NOTES:
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* Build Summary: <A HREF="http://www.ncbi.nlm.nih.gov/projects/SNP/snp_summary.cgi?build_id=141">http://www.ncbi.nlm.nih.gov/projects/SNP/snp_summary.cgi?build_id=141</A>
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* Those B138 RS carried into B141 have submitter asserted sequence positions remapped to GRCh37.p13 and
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GRCh38, including all variations from clinical LSDB and ClinVar.
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* Those B138 RS submitted with flanking sequence carried into B141 had their BLAST positions
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verified by SNP as unique (weight 1).
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* Those B138 RS with multiple mapping positions on one or more chromosomes were not included in
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B141. These RS will be analyzed and processed in a subsequent release. The list of rs
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(rs_without_mapping_b141) is available at
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<A HREF="ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/misc/known_issues/b141.">ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/misc/known_issues/b141.</A>
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* Those SS numbers carried over from B138 to B141 will be processed further by dbSNP, given a
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submitter asserted sequence position, and reported in the next human release. It should be
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noted that SS numbers subjected to further processing will include all variations originating
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from clinical LSDB and ClinVar. The next human release will occur in Fall, 2014.
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* Following B138, dbSNP performed a validation of existing submitted SNPs(ss) and their assignment
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into refSNPs(rs). During this validation effort, dbSNP found some ss that were mistakenly clustered
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into rs numbers due to a combination of submission error and mapping ambiguity. dbSNP de-clustered
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these ss from their old rs clusters, and removed the rs number from dbSNP once all of the ss numbers
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were removed from the cluster. A list (rs_declustered.bcp) of de-clustered ss numbers and the
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affected rs numbers is available at
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<A HREF="ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/misc/known_issues/b141/.">ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/misc/known_issues/b141/.</A>
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* Due to assembly differences between GRCh37.p13 and GRCh38, there are differences in mapping
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locations and functional consequence between these two assemblies. A report of the mapping and
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functional consequence differences is available at:
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<A HREF="ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/multi_assembly_support/consequence_change.">ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/multi_assembly_support/consequence_change.</A>
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* There are a set of co-located refSNPs in B141 that will be merged in B142. A list (rs_colocated.bcp)
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of these co-located refSNPs is available at:
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<A HREF="ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/misc/known_issues/b141/">ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/misc/known_issues/b141/</A>
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* There are a number of rs numbers whose genome orientation was flipped between B138 and B141, which
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caused some of these rs numbers to have an extra variant allele in HGVS expression reporting. A
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list of the affected rs numbers (rs_with_changed_orientation.bcp) is available at
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<A HREF="ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/misc/known_issues/b141/.">ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/misc/known_issues/b141/.</A> This issue will be
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corrected in B142.
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==================================================================================
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REPORTING, SEARCH, AND DOWNLOADS NOTES:
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Reporting on RefSNP:
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The refSNP page will report the positions of variations on both the GRCh38
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assembly and the GRCh37.p13 assembly.
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The Variation Reporter (<A HREF="http://www.ncbi.nlm.nih.gov/variation/tools/reporter">http://www.ncbi.nlm.nih.gov/variation/tools/reporter</A> ):
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The Variation Reporter does not yet take query locations on GRCh38 but will remain on GRCh37. Support for
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submissions and reporting on both GRCh37 and GRCh38 will be released by the end of May, 2014. For
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more information on the Variation Reporter, see:
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<A HREF="http://www.ncbi.nlm.nih.gov/variation/tools/reporter/docs/help.">http://www.ncbi.nlm.nih.gov/variation/tools/reporter/docs/help.</A>
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Entrez Search:
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Although B141 maps to both GRCh38 and GRCh37p13, Entrez SNP is indexed with GRCh38
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positions and annotations only.
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FTP Downloads:
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The FTP directory structure for B141 is available at: <A HREF="ftp://ftp.ncbi.nih.gov/snp">ftp://ftp.ncbi.nih.gov/snp</A>
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/release-notes/Build141/ b141_human_ftp_directory_change.txt
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=================================================================================
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GENERAL NOTES:
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1) The dbSNP Handbook was updated on April 3, 2014 with new content and important dbSNP policy
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revisions: <A HREF="http://www.ncbi.nlm.nih.gov/books/NBK174586/">http://www.ncbi.nlm.nih.gov/books/NBK174586/</A>
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2) The dbSNP VCF submission instructions
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were updated to add support for reporting allele frequencies and for the submission of asserted
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variant locations for organisms without assemblies:
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<A HREF="http://www.ncbi.nlm.nih.gov/projects/SNP/docs/dbSNP_VCF_Submission.pdf">http://www.ncbi.nlm.nih.gov/projects/SNP/docs/dbSNP_VCF_Submission.pdf</A>
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3) The Genotype Search is no longer available. The Genotype Search site
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(<A HREF="http://www.ncbi.nlm.nih.gov/projects/SNP/snp_gf.cgi">http://www.ncbi.nlm.nih.gov/projects/SNP/snp_gf.cgi</A>), however, has a list of alternative download
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services in its place. Watch the Genotype Search site for announcements about the new Genotype
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Service that will be available later this year.
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4) A preview version of the new Variation Viewer for human is available here
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(<A HREF="http://www.ncbi.nlm.nih.gov/variation/view">http://www.ncbi.nlm.nih.gov/variation/view</A>) . Variation Viewer will eventually replace VarVu
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(<A HREF="http://www.ncbi.nlm.nih.gov/sites/varvu?gene=4023&rs=328">http://www.ncbi.nlm.nih.gov/sites/varvu?gene=4023&rs=328</A>) and dbSNP GeneView Page (<A HREF="http://www.ncbi.">http://www.ncbi.</A>
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nlm.nih.gov/projects/SNP/snp_ref.cgi?showRare=on&chooseRs=coding&go=Go&locusId=1287) with integrate
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contents from dbSNP, dbVar, and clinVar and a more robust search system. You can get started by
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watching the video "NCBI Variation Viewer Introduction" Video or visiting the FAQ or Help page.
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Please contact us if you have questions or would like to provide feedback.
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YouTube Video: <A HREF="https://www.youtube.com/watch?v=rnWZ9MFBwUM">https://www.youtube.com/watch?v=rnWZ9MFBwUM</A>
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Help Page: <A HREF="http://www.ncbi.nlm.nih.gov/variation/view/help/">http://www.ncbi.nlm.nih.gov/variation/view/help/</A>
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FAQ: <A HREF="http://www.ncbi.nlm.nih.gov/variation/view/faq/">http://www.ncbi.nlm.nih.gov/variation/view/faq/</A>
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Contact <A HREF="http://www.ncbi.nlm.nih.gov/mailman/listinfo/dbsnp-announce">snp-admin at ncbi.nlm.ncbi.nih.gov</A> if you have any questions or concerns.
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dbSNP Production Team
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National Center for Biotechnology Information (NCBI)
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National Library of Medicine National Institutes of Health
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</PRE>
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