Hello
Do any data sources other than dbSNP record information about allele frequencies for SNPs. I'm also interested to know other sources that provide the dbSNP information (e.g. ensembl variation database). I've looked in the obvious candidates such as HGMD and OMIN but it is possible i have overlooked something.
thanks
try hapmap : http://hapmap.ncbi.nlm.nih.gov/downloads/frequencies/?N=D
although dbSNP has indeed records of allele frequencies, HapMap would be probably the best place right now to query such information as it has been conceived to do so. the CEPH data may also be interesting, but have in mind that 1000 Genomes will probably be the best place in a very close future to do so, and with higher variation coverage (approximately 4 or even 5 times more).
[self-promoting mode: ON] and as I always mention when a population genetics question is posted here, you can give it a go to our in-house development called SPSmart, which allows combining different population based sources of course not to compete with the previously mentioned resources, but to flexibilize up to particular populations certain types of queries.
Another source is JSNP, the Japanese Single Polymorphism Nucleotide database. I don't use this so often and only when working with Asian populations, but I have found it useful on occasion.
HapMap is useful because it has data from phase II and onward that often are not in dbSNP. (Good point, Pierre)
There are likely numerous sources for allele frequency data which are not readily available or obvious. For example, we have analyzed some 200+ SNPs in a Puerto Rican population; see papers by Mattei et al and Lai et al. These data could go into NCBI and likely dbSNP (because there is a mechanism at NCBI to submit population allele frequency data), but we have not taken the time to do such. Many other groups certainly can offer the same excuse.
Thus, one option would be to identify those published articles describing allele frequencies in a population very similar to yours and to capture the data into your own local, workable database.
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i'm going to award you the tick because of the word flexibilize!
hahaha... your critical assessment capacity has definitely been flexibilized! unfortunately I find myself making up "new english words" too often (they sound so good that I can't help it!), so thank you for the review.
@Jorge Amigo: Your SPSmart is exactly what I need for my analysis. I wonder about the newest 1000G SNP data. Will you include this in the next time?
I've been unfortunately very busy during this last academic year ending up my thesis, but updating the entire SPSmart framework (mainly 1000genomes and dbSNP, but right now I'm evaluating the possibility to include the recently released 427 samples from Complete Genomics) is currently on the top-3 items of my to-do list. keep an eye on the RSS feed.