Hi Teresita, I am asking one of our engineers to look at your allele frequencies question, but I can answer your question about Common vs. Flagged SNPs.
The Common SNPs and Flagged SNPs are not expected to be mutually exclusive. There are longer explanations on the track controls pages (click on the blue track names in the Variation and Repeats section on the main Genome Browser page: http://genome.ucsc.edu/cgi-bin/hgTracks). From the Flagged SNPs page: "Only SNPs flagged as clinically associated by dbSNP, mapped to a single location in the reference genome assembly, and *not* known to have a minor allele frequency of at least 1%, are included in this subset." From the Common SNPs page: "Only SNPs that have a minor allele frequency of at least 1% and are mapped to a single location in the reference genome assembly are included in this subset. ... The selection of SNPs with a minor allele frequency of 1% or greater is an attempt to identify variants that appear to be reasonably common in the general population. Taken as a set, common variants should be less likely to be associated with severe genetic diseases due to the effects of natural selection, following the view that deleterious variants are not likely to become common in the population." Also, if you scroll down to the description of "Miscellaneous Attributes (dbSNP)" under "Interpreting and Configuring the Graphical Display" you will see these two descriptions: "Clinically Associated - SNP is in OMIM/OMIA and/or at least one submitter is a Locus-Specific Database. This does not necessarily imply that the variant causes any disease, only that it has been observed in clinical studies. Appears in OMIM/OMIA - SNP is mentioned in Online Mendelian Inheritance in Man for human SNPs, or Online Mendelian Inheritance in Animals for non-human animal SNPs. Some of these SNPs are quite common, others are known to cause disease; see OMIM/OMIA for more information." I hope this answers your first question. We will get back to you with an answer to your other question. -- Brooke Rhead UCSC Genome Bioinformatics Group On 04/28/11 12:14, Teresita Diaz De Ståhl wrote: > Hello UCSC, > > > > I would appreciate if you can provide me some help... I have some problems > trying to get the correct information on minor allele frequency. > > If I understand correctly > > * Common SNPs (132): uniquely mapped variants that appear in at least 1% > of the population > * Flagged SNPs (132): uniquely mapped variants, excluding Common SNPs, > that have been flagged by dbSNP as "clinically associated" > * Mult. SNPs (132): variants that have been mapped to more than one > genomic location > > > > * Common SNPs (132) and Flagged SNPs (132) should be mutually exclusive > that is as "clinically associated" SNPs are not "common" and common SNPs are > not flagged as "clinically associated". But when I download the information > for rs169547 (only as an example) I went through the Table browser and I > choose CommonSNP(132), > http://genome.ucsc.edu/cgi-bin/hgTables?db=hg19&position=chr13:32929380-32929390&hgsid=193533287 > > > > * I get the results that I send you in the attached file.. > > > > * This SNP is flagged as clinically associated....why? I downloaded > through the common SNPs? > > > > * Then I get 3 frequencies for 3 alleles: G,A,C, > 0.963316,0.033403,0.003281, > > > > * Is the minor allele freq 0.003281? for C? > > > However in db132 > http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?searchType=adhoc_search&type=rs&rs=rs169547 > this SNP has a MAF/MinorAlleleCount: T=0.025/32 and for T. Is the minor > allele T or C? > > Am I looking at the wrong columns? I would appreciate if you can help me to > get into the right track... > Thanks > > Kind regards /Teresita > > > > > > Teresita Díaz de Ståhl, PhD., Assoc. Prof. > > Department of Oncology-Pathology > > Cancer Center Karolinska, CCK R8:04 > > Karolinska Institutet > > SE-171 76 Stockholm, Sweden > > +46-8-517 721 35 (office) > > E-mail: [email protected] > > > > > > -----Original Message----- > From: Brooke Rhead [mailto:[email protected]] > Sent: den 28 april 2011 01:29 > To: Teresita Diaz De Ståhl > Cc: [email protected] > Subject: Re: [Genome] minor allele frequency > > > > Hello Teresita, > > > > Allele frequencies are now included in our SNP tables (this was not true > prior to dbSNP build 132). So, if you download the snp132 table from here: > > > > http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/ > > > > (the filename is snp132.txt.gz), you will get allele frequencies. Note that > this file is quite large, so you will probably want to use one of the > alternate methods for downloading described at the top of that page. > > > > The table schema is shown here: > > http://genome.ucsc.edu/cgi-bin/hgTables?db=hg19&hgta_group=varRep&hgta_track=snp132&hgta_table=snp132&hgta_doSchema=describe+table+schema > > > > Note that not all SNPs include allele frequency data. > > > > You might also be interested to know that we now provide 4 separate SNP > tracks, described in our announcement here: > > http://genome.ucsc.edu/goldenPath/newsarch.html#041811.2 > > (and also described on the SNP track descriptions in the Genome Browser). > > > > If you have further questions, please feel free to contact us again at > [email protected]<mailto:[email protected]>. > > > > -- > > Brooke Rhead > > UCSC Genome Bioinformatics Group > > > > > > On 04/27/11 07:41, Teresita Diaz De Ståhl wrote: > >> Hi, > > >> I wonder if it is possible to download the db132 including data of > >> minor allele frequency for each SNP. Thanks in advance for some tips > >> how to do it. > > >> Kind regards > > >> Teresita > > >> Teresita Díaz de Ståhl, PhD > > >> _______________________________________________ > >> Genome maillist - [email protected]<mailto:[email protected]> > >> https://lists.soe.ucsc.edu/mailman/listinfo/genome >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
