Question: SNP not found on any SNP arrays
0
gravatar for mcumeh
3.9 years ago by
mcumeh0
United States
mcumeh0 wrote:

Hi all,

I am trying to analyze a SNP in ERBB2 that may be associated with breast cancer. What I would like to do is show that presence of the SNP has a higher occurrence in cancer vs. normal patients. I started my analysis by trying to analyze publicly available data sets from the TCGA and NCBI GEO, however when I download the list of probes for the SNP arrays, my SNP of interest is not found. I've looked at multiple types of Affymeterix SNP arrays as well as some Illumina but I can't find the SNP in any of the files. I know the SNP does exist because it comes up in dbSNP, and the UCSC and Ensembl genome browsers.

Has anyone else run into this problem? I am not sure if the SNP is mislabeled on the arrays, or if there is just no probe towards that SNP. If this is the case, are there other ways to find a correlation between the presence of a SNP and breast cancer? I have considered going back to the whole genome sequencing data and seeing if I can determine the presence of the SNP that way. 

Any help would be greatly appreciated.

Thank you

Maxine

snp snp arrays • 1.1k views
ADD COMMENTlink modified 3.9 years ago by Jason Chen10 • written 3.9 years ago by mcumeh0
0
gravatar for Jason Chen
3.9 years ago by
Jason Chen10
United States
Jason Chen10 wrote:

What SNP is it? If it is very rare and non exonic it will probably not be found on any of the arrays. If it's relatively common then you could try imputation (see for example BEAGLE https://faculty.washington.edu/browning/beagle/beagle.html or IMPUTE2 https://mathgen.stats.ox.ac.uk/impute/impute_v2.html)

ADD COMMENTlink written 3.9 years ago by Jason Chen10
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