Dear all,
I have two questions regarding https://doi.org/10.7303/syn3157238.
1. This study has 2099 subjects but 313,530 SNPs. What is the reason for relatively fewer identified SNPs compared to other studies like ADNI and GWAS studies? For instance rs11690153 in chromosome 2 associated with BIN1 seems to be missing (10^-11 ad gwas p-value)
2. The position information of the SNPs does not seem to match GRCh37 or GRCh38. Am I reading this correctly?
Thanks in advance.
Created by rrajesh Dear Abby,
Thanks for your prompt response! Hi there, I'm not sure why there are relatively fewer SNPs identified in this study, but it is one of the earliest data contributions to the AD portal. I'm also not sure about the concordance between these SNP data and the GRCh37/38 builds -- there doesn't appear to be any information on that in the study methods or in the 2009 paper referenced. I suggest contacting Dr. Steven Youngkin at the Mayo Clinic, who was the PI on the LOADGWAS project. Someone in his lab may be able to shed some light on these questions!