BioConductor/AnnotationHub loading of dbSNP from NCBI seems broken - how to work around?

Question

[curtish]

Folks,

I'm trying to get ethnic-specific MAF for a set of SNPs inside R (relatively novice R user).

So, I searched BioConductor's AnnotationHub for human, dbsnp, etc and found AH47013.

However, when I tried to load it

library(AnnotationHub)
ah = AnnotationHub()
# launch interactive dataset query interface
d <- display(ah)
AH47013 <- ah[["AH47013"]] # load dbSNP 141
warnings()

that showed that it was failing to load https://annotationhub.bioconductor.org/fetch/52464

which is actually a redirect to

ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b141_GRCh37p13/VCF/common_all.vcf.gz

which no longer exists and has been replaced with dbSNP144:

ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b144_GRCh37p13/VCF/common_all_20150605.vcf.gz

So, the questions are :

• how does AnnotationHub get updated?
• how do I work around this in the mean time?
• was there a different resource or a better way to get this done in BioConductor?
  • (yes, we've found SNPsnap server @ Broad, but want to do this locally in R)

Thanks!

Curtis

[Giovanni M Dall'Olio]

This is a good question and I also tried to use AnnotationHub without success. I believe this should be done through the SNPLocs data packages, however the most recent package has not been updated since dnSNP144 (we are now at dbSNP146).

Answer 1

[cpad0112]

Do you have corresponding dbSNP IDs (for your variants) ? If so, you can use biomart to get MAF.

rsnps package queries SNAP server. Example code and output is given below:

> LDSearch('rs2836443')
Querying SNAP...
Querying NCBI for up-to-date SNP annotation information...
Done!
$rs2836443
       Proxy       SNP Distance RSquared DPrime GeneVariant     GeneName
3  rs2836443 rs2836443        0    1.000  1.000    INTRONIC C21orf24,ERG
2  rs2836442 rs2836443     -234    0.966  1.000    INTRONIC C21orf24,ERG
4  rs2836445 rs2836443     1420    0.873  1.000    INTRONIC C21orf24,ERG
1 rs11910637 rs2836443    -2495    0.873  1.000    INTRONIC C21orf24,ERG
                                                                                                                                                                    GeneDescription
3 Putative uncharacterized protein C21orf24. [Source:Uniprot/SWISSPROT;Acc:Q6XXX2], Transcriptional regulator ERG (Transforming protein ERG). [Source:Uniprot/SWISSPROT;Acc:P11308]
2 Putative uncharacterized protein C21orf24. [Source:Uniprot/SWISSPROT;Acc:Q6XXX2], Transcriptional regulator ERG (Transforming protein ERG). [Source:Uniprot/SWISSPROT;Acc:P11308]
4 Putative uncharacterized protein C21orf24. [Source:Uniprot/SWISSPROT;Acc:Q6XXX2], Transcriptional regulator ERG (Transforming protein ERG). [Source:Uniprot/SWISSPROT;Acc:P11308]
1 Putative uncharacterized protein C21orf24. [Source:Uniprot/SWISSPROT;Acc:Q6XXX2], Transcriptional regulator ERG (Transforming protein ERG). [Source:Uniprot/SWISSPROT;Acc:P11308]
  Major Minor   MAF NObserved Chromosome_NCBI Marker_NCBI Class_NCBI Gene_NCBI
3     T     G 0.417       120              21   rs2836443        snp       ERG
2     A     G 0.425       120              21   rs2836442        snp       ERG
4     G     A 0.450       120              21   rs2836445        snp       ERG
1     A     G 0.450       120              21  rs11910637        snp       ERG
  Alleles_NCBI Major_NCBI Minor_NCBI MAF_NCBI  BP_NCBI
3          G/T          T          G   0.2444 38499351
2          A/G          A          G   0.3890 38499117
4          A/G          G          A   0.2546 38500771
1          A/G          A          G   0.2638 38496856