Detailed patient donor details table available?


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.

Any help would be much appreciated!

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.

Hi Tom, thank you very much for your reply.

The info I was hoping to get is the following:

  1. Years of Seizure History. Currently this is missing for the cases in the Human Patch-seq dataset, as this was not published.
  2. Age at epilepsy onset, if recorded.
  3. Specimen sub-brain area (e.g., STG/MTG/ITG for a temporal cortex specimen)
  4. 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!

Patient info table:

AIB Donor ID Cortex Sub brain Region Years of Seizure History Age at epilepsy onset x,y,z MNI-ICBM152-T1
H15.03.006 Temporal X X
H15.06.016 Frontal X X
H15.06.017 Temporal X X
H15.06.018 Temporal X X
H16.03.001 Temporal X X
H16.03.002 Temporal X X
H16.03.003 Frontal X X
H16.03.005 Temporal X X
H16.03.006 Temporal X X
H16.03.007 Temporal X X
H16.03.008 Temporal X X
H16.03.009 Parietal X X
H16.03.010 Temporal X X
H16.03.011 Temporal X X
H16.06.002 Temporal X X
H16.06.003 Temporal X X
H16.06.004 Temporal X X
H16.06.006 Frontal X X
H16.06.007 Frontal X X
H16.06.008 Temporal X X
H16.06.009 Temporal X X
H16.06.010 Temporal X X
H16.06.011 Temporal X X
H16.06.012 Frontal X X
H16.06.013 Temporal X X
H17.03.002 Temporal X X
H17.03.005 Temporal X X
H17.03.006 Temporal X X X
H17.03.007 Temporal X X
H17.03.008 Temporal X X
H17.03.009 Temporal X X
H17.03.010 Temporal X X
H17.03.011 Temporal X X
H17.03.012 Frontal X X
H17.03.013 Temporal SFG? - PLZ VERIFY X X
H17.03.014 Temporal X X X
H17.03.015 Temporal X X X X
H17.03.016 Temporal X X X
H17.06.003 Temporal X X
H17.06.004 Parietal X X
H17.06.005 Temporal X X
H17.06.006 Temporal X X
H17.06.007 Frontal X X
H17.06.009 Temporal X X
H17.06.012 Temporal X X
H17.06.013 Frontal PLP? - PLZ VERIFY X X
H17.06.015 Temporal X X X
H17.06.016 Frontal X X X X
H17.26.001 Temporal X X X X
H17.26.002 Temporal X X X X
H17.26.003 Temporal X X X
H17.26.004 Temporal X X X X
H17.26.005 Frontal X X X
H18.03.002 Frontal X X X X
H18.03.003 Temporal X X X X
H18.03.004 Temporal X X X
H18.03.005 Temporal X X X
H18.03.006 Parietal X X X
H18.03.007 Temporal X X X
H18.03.008 Temporal X X X
H18.03.009 Temporal X X X
H18.03.010 Temporal X X X
H18.03.012 Temporal X X X
H18.03.313 Temporal X X X
H18.03.314 Temporal X X X
H18.03.315 Temporal X X X
H18.03.316 Temporal X X X
H18.03.317 Temporal X X X
H18.03.318 Temporal X X X
H18.03.319 Temporal X X X
H18.03.320 Temporal X X X
H18.03.322 Temporal X X X
H18.03.323 Frontal X X X
H18.06.001 Frontal X X X
H18.06.004 Temporal X X X
H18.06.005 Temporal X X X
H18.06.358 Frontal X X X
H18.06.359 Frontal X X X
H18.06.362 Frontal X X X
H18.06.363 Temporal X X X
H18.06.365 Frontal X X X
H18.06.366 Temporal X X X
H18.06.367 Temporal X X X
H18.06.368 Temporal X X X
H18.06.371 Temporal X X X
H18.25.001 Temporal X X X X
H18.26.001 Parietal X X X X
H18.26.002 Temporal X X X X
H18.26.403 Frontal X X X
H18.26.404 Temporal X X X
H18.26.405 Temporal X X X
H18.28.001 Temporal X X X X
H18.28.009 Frontal X X X X
H18.28.010 Frontal X X X X
H18.28.012 Temporal X X X X
H18.28.013 Frontal X X X X
H18.28.015 Frontal X X X X
H18.28.017 Frontal X X X X
H18.28.018 Temporal X X X X
H18.28.019 Temporal X X X X
H18.28.020 Temporal X X X X
H18.28.025 Temporal X X X X
H18.28.026 Temporal X X X X
H18.29.124 Temporal X X X X
H18.29.125 Temporal X X X X
H18.29.126 Frontal X X X X
H18.29.127 Parietal X X X X
H18.29.134 Temporal X X X X
H19.03.301 Temporal X X X
H19.03.302 Temporal X X X
H19.03.304 Temporal X X X
H19.03.305 Temporal X X X
H19.28.001 Frontal X X X X
H19.28.003 Occipital X X X X
H19.28.004 Frontal X X X X
H19.28.005 Temporal X X X X
H19.28.007 Occipital X X X X
H19.29.142 Frontal X X X X

Dear Tom, any chance you or one of your colleagues can provide an update regarding the above? Thanks