Hi,
I want to look at the odds ratios and P-values of the 17 priority SNPs available under Tier 1. However, I am unable to find the source file or a manuscript on PubMed which could provide these. I have found various manuscripts which quote some SNPs which overlap with the 17 priority SNPs, but not all. So, I wanted to know to if someone could point me in the right direction or help me understand where to locate the source. Thank you!
Hi Muhammad,
If you’re referring to where to find these within Fox DEN, these are in the ‘Genetic’ table of the explorer and can be downloaded directly or through the monthly data cuts.
If you’re referring to the provenance of the data, these were generated as part of the Fox Insight Genetic Sub-study (FIGS) conducted in partnership with 23andMe. Once logged in, there is additional genotyping and documentation information which can be found here: Fox Login Page .
The sub-study section of this paper describes how the data were generated in greater detail: Fox Insight at 5 years - a cohort of 54,000 participants contributing longitudinal patient-reported outcome, genetic, and microbiome data relating to Parkinson’s disease | Scientific Data.
Hope this helps, let me know if you have any other questions!
Josh
Hi Joshua,
Thank you for responding! I was able to find these 17 SNPs in FOX DEN and have also gone through the sub-study documentation for genetic data. However, I am looking for something different.
Perhaps a better way to phrase my question would be to ask why these 17 SNPs are called priority SNPs. Maybe the answer is that these SNPs have been found to be associated with PD. If yes, then this was likely determined using a regression analysis by comparing controls and cases, or similar.
If yes, then where can I access this particular statistical data? Is this available in a MJFF publication or document? Or this information is based on other publications, because of which these 17 SNPs are called “priority“ SNPs?
I want to know what the odds are of finding each of these SNPs in an individual with PD, and at what level of significance.
Thank you!
Hi Muhammad,
My recollection is that these were selected as variants of interest by scientific staff at the time of release while we put administrative processes in places and made platform improvements to safeguard study participant privacy ahead of releasing the full genotyping data for each member of the sub-study; there isn’t any such regression that was done to my knowledge, but I can inquire and update this thread if I hear otherwise.
For your latter question, I would suggest consulting the genetic platform annotations in the sub-study documentation, which includes expected call rate by genotyping array (the platform_version variable indicates which array was used for which participant, there are several, but the majority on v5).
Hope this helps, let me know if you have any other questions!
Hi, wanted to check-in with information that may or may not be helpful. There’s a paper which was published in Nature which also lists the 23&Me team as an author: A meta-analysis of genome-wide association studies identifies 17 new Parkinson’s disease risk loci | Nature Genetics
Initially, I thought that maybe this is the paper which discovered the 17 priority SNPs since the MJFF genetic data is gathered alongside 23&Me, if I am not wrong. However, I was disappointed to find out that out of 17 SNPs, only rs2280104 is present in Table 2.
I wanted to share regardless, incase this is helpful and leads somewhere.
