Is there a detailed table of patient information available?
In the TECHNICAL WHITE PAPER: CASE QUALIFICATION AND DONOR PROFILES, the table is rather limited and seems to be missing details that were recorded. For instance, it is stated that “the x,y,z coordinates of each located sample were recorded in MNI-ICBM152-T1 template”, yet these coordinates do not feature in any of the patient tables provided; neither in the white paper nor in the browser table at Donor Profiles :: Allen Brain Atlas: Cell Types.
Further, the patient table provided in Berg et al Nature 2021 Table S1 does not include things like seizure history (and btw has some inconsistencies with the Allen cell types DB. For example it lists sample from patient H17.03.13 as “temporal”, whereas the Allen cell types DB has it down as superior frontal gyrus).
I was hoping there would be one central master patient table with all available info for reference.
Thanks for reporting this, we’re looking into the inconsistencies.
Regarding the additional information, in general there is an attempt to capture everything mentioned in the white paper, but it is not always available, and also what’s shared has depended on the project the donor data was used for. Are you particularly interested in the coordinates, or other specific information? For which set of donors?
We can likely put something together to share for your use case, although a complete master list is a challenge due to managing versioning/updates among other issues.
Years of Seizure History. Currently this is missing for the cases in the Human Patch-seq dataset, as this was not published.
Age at epilepsy onset, if recorded.
Specimen sub-brain area (e.g., STG/MTG/ITG for a temporal cortex specimen)
X,Y,Z MNI-ICBM152-T1 coordinates, if indeed available
Please find below a table scoring for which cases I need the above information.
Regarding specimen sub-brain area, I most urgently would like a verdict as to what brain area the specimen came from in these 2 cases:
H17.03.013: Listed as Temporal in Berg et al, but as Superior Frontal Gyrus in Cell types DB.
H17.06.013: Listed as Frontal in Berg et al, but as planum polare (=STG?) in Cell types DB.
(Btw, given the similarity of the donor IDs, could these cases have been switched around between the two tables?)
I very much appreciate any help in this; the completer and more accurate this patient information table becomes, the better we will be able to make use of this incredibly valuable data!