Hi Xinwei, We are unable to update hg18 with the build 131 SNPs unless dbSNP provides mappings of those SNPs to the hg18 assembly. However, when dbSNP creates a new build, they map to the latest assembly for each organism.
See the build history page at dbSNP: http://www.ncbi.nlm.nih.gov/SNP/buildhistory.cgi Also compare the build 131 statistics (near the bottom of the page): http://www.ncbi.nlm.nih.gov/SNP/snp_summary.cgi?view+summary=view+summary&build_id=131 To the build 130 statistics: http://www.ncbi.nlm.nih.gov/SNP/snp_summary.cgi?view+summary=view+summary&build_id=130 Finally, here is more information on their build cycle: http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=handbook&part=ch5#ch5.ch5_s4 You could feasibly use the liftOver tool (http://genome.ucsc.edu/cgi-bin/hgLiftOver) to lift SNPs from hg19 to hg18 for your regions of interest, or blat (http://genome.ucsc.edu/cgi-bin/hgBlat) to blat the flanking sequences of SNPs in build 131 to hg18, but this would perhaps lead to misleading results. You will be pleased to know that current and future ENCODE data is in the process of being migrated to hg19. -- Brooke Rhead UCSC Genome Bioinformatics Group On 07/07/10 09:49, She, Xinwei wrote: > Hi, Brooke: > > I really appreciate your detailed explanation, and it does make a lot of > sense. > > However, we use the SNP table from UCSC quite heavily in our research > and we'd also like to use the latest dbSNP update (version 131). The > vast majority of the genome browser's functional tracks that we use, > like ENCODE, transcription regulation and expression, to name a few, > exist only in hg18. Therefore, we can not switch to hg19 at this time. > The data would be much more useful to us and the research community if > the latest dbSNP update could also be applied to hg18. > > I'd really appreciate it if the UCSC team would consider update hg18 > with the latest dbSNP release. > > Xinwei > > -----Original Message----- > From: Brooke Rhead [mailto:[email protected]] > Sent: Tuesday, July 06, 2010 5:48 PM > To: She, Xinwei > Cc: Vanessa Kirkup Swing; [email protected] > Subject: Re: [Genome] dbSNP 131 for hg18? > > Hi Xinwei, > > It is true that UCSC realigns the flanking sequences from dbSNP, but > these realignments are not used to determine genomic location. In fact, > > for each SNP, the realignment is only done between the flanking sequence > > from dbSNP and the genomic region immediately surrounding the location > determined by dbSNP. > > We do this to try to provide useful information in the case where there > is conflicting information about a SNP (for instance, when class is > listed as "single", but the position spans more than one base). > > The genomic coordinates of the SNPs displayed in the Genome Browser come > > directly from dbSNP. > > I hope this is helpful. Please let us know if we can clarify further. > > -- > Brooke Rhead > UCSC Genome Bioinformatics Group > > > She, Xinwei wrote on 7/6/10 1:29 PM: >> Hi, Vanessa: >> >> Thanks for your answer. However, as far as I know, UCSC realigned the >> flanking sequences of SNPs to determine their genomic locations: >> > http://genome.ucsc.edu/cgi-bin/hgc?hgsid=164326263&o=33034697&t=33034698 >> &g=snp131&i=rs7510525 >> >> And that's why I was asking about SNP 131 on hg18, because I'd prefer >> using UCSC's SNP coordinates. >> >> >> Xinwei >> >> -----Original Message----- >> From: Vanessa Kirkup Swing [mailto:[email protected]] >> Sent: Friday, July 02, 2010 6:39 PM >> To: She, Xinwei >> Cc: [email protected] >> Subject: Re: [Genome] dbSNP 131 for hg18? >> >> Dear Xinwei, >> >> We obtain all of our SNP mappings directly from dbSNP, and thus will >> only provide a SNP131 track on hg18 if dbSNP provides the mappings. > The >> other option is to do a lift down using our liftover tool: >> http://genome.ucsc.edu/cgi-bin/hgLiftOver >> >> If you have further questions, please don't hesitate to contact the >> mailing list again. >> >> Vanessa Kirkup Swing >> UCSC Genome Bioinformatics Group >> >> ----- Original Message ----- >> From: "Xinwei She" <[email protected]> >> To: [email protected] >> Sent: Friday, July 2, 2010 10:39:21 AM GMT -08:00 US/Canada Pacific >> Subject: [Genome] dbSNP 131 for hg18? >> >> Hi, there: >> >> It great to see UCSC genome browser has released dbSNP 131 for hg19. >> However, right now vast majority of the functional genomic tracks are >> still in hg18, e.g.. the ENCODE tracks. The genomics community are > still >> mainly working on hg18. I'm just wondering if UCSC has a plan to > release >> dbSNP 131 for hg18, as well? >> >> Xinwei >> >> Notice: This e-mail message, together with any attachments, contains >> information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station, >> New Jersey, USA 08889), and/or its affiliates Direct contact > information >> for affiliates is available at >> http://www.merck.com/contact/contacts.html) that may be confidential, >> proprietary copyrighted and/or legally privileged. It is intended > solely >> for the use of the individual or entity named on this message. 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