Hi, about syn21126462,
(1) for file names,
"P??????????????.gz" denotes "AD carrying TREM2-R62H";
"AD??????????????.gz" denotes "AD carrying TREM2-CV";
"C??????????????.gz" denotes "controls";
Do they?
(2) How to label these samples? I related these data with metadata (that is, syn3191087) by individualID, I found "ceradsc" is used to label these samples not by "braaksc", is that so?
Many thanks.
Created by xinxingwu I got it and will try it. Many thanks. Hi @xinxingwu , again I believe that since these samples are from ROSMAP specimens, the original classification is based on the cogdx variable in the metadata. However, since this study is looking specifically at different TREM2 variants, and I don't see any information about which TREM2 variant each sample carries, our metadata may be incomplete. I'm going to investigate this further.
In the meantime, most ROSMAP individuals have genomic variant information available (either SNParray or WGS), which you could potentially use to identify TREM2 variants. ROSMAP variant data is here: syn17008936. The biospecimen metadata file syn21323366 will also help you map individualIDs you are interested in to specimens that have WGS or SNParray data (use the "assay" column).
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What do the file names denote? and How to label samples? page is loading…