Question
Question Posted 10/28/14:
Merging the ADNI_PTID_WGS_Sample_Correspondence with the ADNIMERGE table (by PTID = ADNI_PTID), I do not find the announced numbers of sequenced patients by disease category, according to http://adni.loni.usc.edu/data-samples/genetic-data/ :
"818 ADNI participants:
128 with AD,
415 with MCI,
267 controls and
8 of uncertain diagnosis"
The counts I observe are quite different:
Sequenced
No Yes Sum
Diagnostic
1 0 1
AD 248 40 288
CN 136 264 400
EMCI 71 223 294
LMCI 307 226 533
SMC 73 0 73
Sum 836 753 1589
Could you please help me understanding where this discrepancy comes from ?
Many thanks in advance !
Merging the ADNI_PTID_WGS_Sample_Correspondence with the ADNIMERGE table (by PTID = ADNI_PTID), I do not find the announced numbers of sequenced patients by disease category, according to http://adni.loni.usc.edu/data-samples/genetic-data/ :
"818 ADNI participants:
128 with AD,
415 with MCI,
267 controls and
8 of uncertain diagnosis"
The counts I observe are quite different:
Sequenced
No Yes Sum
Diagnostic
1 0 1
AD 248 40 288
CN 136 264 400
EMCI 71 223 294
LMCI 307 226 533
SMC 73 0 73
Sum 836 753 1589
Could you please help me understanding where this discrepancy comes from ?
Many thanks in advance !
Response posted 11/03/14 by Sungeun Kim:
As you know, the ADNI is an ongoing study and subject's diagnosis can change over time. The number of samples in each diagnosis was collected when the ADNI WGS project was planned. So, you should not think of these numbers as the final sample size for each diagnosis. Depending on which time point you are interested in, the number of samples in each diagnosis will change.
Response posted 11/03/14 by Jérôme Dauvillier:
Thank you for your kind answer.
I did imagine that part of the differences could be accounted for by changes of diagnosis between baseline and the time the WGS was launched.
But I guess this would not explain why, out of the 809 PTIDs listed in ADNI_PTID_WGS_Sample_Correspondence.xlsx table, the following 23 PTIDs are not found in a very recent version (30.10.2014) of the ADNIMERGE table, would it?
"002_s_4654" "003_s_0981" "007_s_4568" "007_s_4637" "009_s_4543" "013_s_4580" "014_s_4615" "016_s_4584" "021_s_4558" "023_s_4241" "023_s_4502" "037_s_4432" "041_s_4629" "052_s_4626" "068_s_0210" "072_s_4610" "073_s_4614" "094_s_4560" "109_s_4531" "128_s_4603" "128_s_4609" "128_s_4653" "137_s_4520"
I did imagine that part of the differences could be accounted for by changes of diagnosis between baseline and the time the WGS was launched.
But I guess this would not explain why, out of the 809 PTIDs listed in ADNI_PTID_WGS_Sample_Correspondence.xlsx table, the following 23 PTIDs are not found in a very recent version (30.10.2014) of the ADNIMERGE table, would it?
"002_s_4654" "003_s_0981" "007_s_4568" "007_s_4637" "009_s_4543" "013_s_4580" "014_s_4615" "016_s_4584" "021_s_4558" "023_s_4241" "023_s_4502" "037_s_4432" "041_s_4629" "052_s_4626" "068_s_0210" "072_s_4610" "073_s_4614" "094_s_4560" "109_s_4531" "128_s_4603" "128_s_4609" "128_s_4653" "137_s_4520"
Response posted 11/03/14 by Sungeun Kim:
We do not know why those individuals do not appear in the ADNIMERGE table, but if you look at "Roster.csv" to find RID mappted to PTID and "DXSUM_PDXCONV_ADNIALL.csv", then you should be able to find their diagnosis.
Response posted 11/03/14 by Jérôme Dauvillier:
It turns out that the PTIDs that could not be matched are misspelled in the ADNI_PTID_WGS_Sample_Correspondence table: they have an 'S' character in lowercase instead of uppercase... Could you ask people who package the WGS data to fix this bug ?
The return link to send you this reply was also misspelled: adni.loni.us.edu instead of adni.loni.usc.edu ...
The return link to send you this reply was also misspelled: adni.loni.us.edu instead of adni.loni.usc.edu ...
