Hi,
Unless I missed some information or file, I have some problems making the correspondences between the genetic data file of batch 1 (anm_batch1_hg19.fam, [syn4259682](https://www.synapse.org/#!Synapse:syn4259682)) and the clinical data file (AddNeuroMed_BasicVariables.csv, [syn4984917](https://www.synapse.org/#!Synapse:syn4984917))
For batch2 genetic data (anm_batch_2_hg19.fam, [syn4259685](https://www.synapse.org/#!Synapse:syn4259685)) ), I have no problem and I can find all Ids present in the fam file in the clinical file (except for 2 but maybe this is expected). But for batch1 (anm_batch_1_hg19.fam, [syn4259682](https://www.synapse.org/#!Synapse:syn4259682)), there is no correspondence at all. By looking closely at the ID format, I may have found some rules to make the correspondence. While it is said that clinical Entity IDs are on the format site, dx and subject ID (e.g : KPOADC001 = KPO (Kuopio) ADC (Alzheimer's disease) 001 (unique subject id)) it is not the case for fam file IDs. It seems that fam IDs are composed of site, first letter of dx (A for ADC, M for MCI and C for CTL), and subject ID without the first leading 0. If this is correct, so the correspondence can be found. For example, for all 3 different status :
- THSA0010 (fam) could be THSADC010 (clinical) ?
- KPOC0025 (fam) could be KPOCTL025 (clinical) ?
- LDZM0005 (fam) could be LDZMCI005 (clinical) ?
Could you confirm that ?
If this is correct, there are still some unresolved IDs for those prefixed by LND (LND site) because the first letter of diagnosis is missing. and because it seems that their subject ID was not split across status. For example, LND0021 could be either LNDADC021, LNDMCI021 or LNDCTL021 but I don't think it is the case because we can have subject IDs > 80 (e.g LND0137) which is not the case for LND samples in the clinical file (there is no such LNDADC137 or LNDMCI137 or LNDCTL137). While all LND samples from fam file seem to be coded as cases, we could conclude that they are not control, but since MCI are also coded as cases in the fam file, we don't know his real status (MCI vs AD). If this is correct, how could we have their clinical data ?
Thanks in advance,
Best,
Created by bgrenier Thank you for this update.
Do you have a rough estimation on when the data will be available ?
Thank you in advance,
Best, The data contributor is in the process of uploading a new version of the data to correct this issue. Request to join the [AMP-AD_DataReleaseUpdates](https://www.synapse.org/#!Team:3372003) team to be alerted when the data is available
Drop files to upload
Id correspondence between genetic data and clinical data page is loading…