Hello! I was looking at data stored in BigQuery associated with AMP PD releases and I only found genomics data related to WGS, but couldn’t find specific data related to Illumina or NeuroX SNP arrays. Is this type of data available in AMP PD platform? I obtained it directly from PPMI and PDBP, but wanted to know if it is also present there and I missed it
Do you mean data sequenced on an Illumina array? If so, I think GP2 data in AMP is sequenced on Illumina: Genomic Data | AMP-PD.
I don’t have the right access to be able to confirm unfortunately, but maybe @vdardov can help?
The WGS data available through AMP PD is generated by using an Illumina sequencing platform, but there is no SNP array data. From my understanding, you are able to bioinformatically extract SNPs from WGS data using something like PLINK, although this is not my area of expertise, so someone more familiar with WGS data (@hirotaka) , please comment.
In terms of GP2 data, I am not seeing anything in the data release notes that mentions SNP arrays. The SNP array data might indeed only be available directly through PPMI and PDBP as you have observed.
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Thank you for your answer! Yeah, I was definetely interested in the array data itself, as my working group is using this type of data. As per my knowledege, as you said, I think the SNP array data are only present individually in both datasets, but not directly in AMP PD.
I think thee newest release has an array data on NeuroBooster for some of the samples from the PPMI participants.
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