ADNI AD case/control

[Shikta Das]

Hi All, 

I am trying to make ADNI AD case/control column for a GWAS. Please can anyone help me? I am lost in the sea of the data files. 

Cheers

Shikta 

[illor...@gmail.com]

Before anything, I would like to warn you about the labels:

AD is actually "probable AD", which to my knowledge means that after some tests, they decided that the person has Alzheimer's Disease.

Two further notes on that:

• First, the clinical diagnosis is not as accurate as the definite autopsy confirmation of AD.
• Second, regarding Alzheimer's Disease, if it is your target, it is thought to begin as many as 20 years or so before symptoms are visible, with changes in the brain that are unnoticeable to the person affected. This, in turn, means that people labelled as MCI (Mild Cognitive Impairment) or NC (Normal Cognitive) might actually be in an early stage of AD.
  

Combining the two previous points, you can see how hard it would be to pick a target and say that they are (and will be) free from AD, thus serving as "control".

The database keeps track of a series of subjects that get tested every so often, and some of them (unfortunately) move on from NC to MCI and to AD.

Perhaps you could make some assumptions and take subjects of advanced age that still keep being labelled as NC, for controls, and subjects that are labelled as AD as such.

About the data sets, the "TADPOLE_D1_D2.csv" is probably the one you might be looking for, since it is the one that the organisers ever-so-kindly prepared for researchers.
Additionally, "TADPOLE_D1_D2_Dict.csv" contains the explanation for the different columns or features.

I hope I could be of help. I made some assumptions on your actual goals to answer this, so if I didn't fully understand the question, please feel free to provide further details.

Cheers,

Isaac Llorente

NIC-VICOROB research intern

[Razvan Marinescu]

Isaac explained the caveats with diagnosis quite well. 

Regarding a particular column, you can use column "DX" (column BC Excel) in TADPOLE_D1_D2.csv, from the TADPOLE Challenge zip file. It contains diagnosis as either NL (cognitively normal), MCI or Dementia.  

Raz

[Shikta Das]

Thank you so much for your comments, really appreciate it. 

Just a question about D1_D2.csv : Does it have the maximum sample size? Or have there been any exclusions on the list? 

Can I join D3 as well? I need to make one file for ADNI1, ADNIGO and ADNI3

Kind regards

Shikta 

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Kind Regards

Dr. Shikta Das

Discovery Genetics Project Leader

C4X Discovery Ltd

shikt...@c4xdiscovery.com

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[illor...@gmail.com]

Dear Dr Shikta Das ,

For the first question (exclusions), I prefer to let the organisers answer, although this might help:
"D1: The TADPOLE standard training set draws on longitudinal data from the entire ADNI history. The data set
contains a set of measurements for every individual that has provided data to ADNI in at least two separate visits
(diff erent dates) across three phases of the study: ADNI1, ADNI GO, and ADNI2." []

Regarding the second question, D3 information is already included in the D1-D2 csv. Quoting the organisers:

" D3 - The TADPOLE cross-sectional prediction set contains a single (most recent) time point and a limited set of variables from each rollover individual (same set of individuals as D2) ".

[source: https://tadpole.grand-challenge.org/Details/]

Kind regards,

Isaac Llorente
NIC-VICOROB research intern