API access vs Website survive differences

[Rafi Danino]

Hello,

I am interested in extracting information about the survival of all patients across 225 studies "These studies are manually curated and include both TCGA and non-TCGA datasets, with no overlapping samples"

Only patients who get treatment (all types of cancer).

As an example  I want to focus on patients who have MTAP  with HOMDEL (deletion).

My main points of interest are:

1. The number of patients with an overall survival (OS) status of 0.
2. The number of patients with an overall survival (OS) status of 1.

To achieve this, I used an API-based approach with the following steps:

1. Retrieve all treatments and their associated patients, along with study IDs.
2. Use the fetchDiscreteCopyNumbersInMolecularProfileUsingPOST function.
3. For each patient, compile a list of genes with alterations.
4. Sum the patients with MTAP HOMDEL who fall into two survival groups: status 0 and status 1.

The results I obtained for MTAP were as follows:

• OS status 0: 226 patients
• OS status 1: 337 patients

However, when I interactively used the website, selecting the same 225 studies and focusing on MTAP in the CNA-genes, I obtained different results:

• MTAP - HOMDEL: 1920 patients (OS(0)-760, OS(1)-936)

 

Can you explain the possibility for this significant difference between these two approaches

[Nikolaus Schultz]

Hi,

Apologies for the late response. You mention that you used available treatment data as a filter - is it possible that you only applied the filter when using the API but not when using the website? 

Niki.

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