Clinical information for TCGA datasets

[Haibe-Kains Benjamin]

Dear developers and maintainers fo the cBioPortal,

First of all, thanks for the great resource you have put together, this is really beneficial for my own research.

I am currently working on a large project where we plan to quantify the contribution of each data type (CNV, gene expression, methylation, ...) for predicting some clinical variable, including survival. We used the 'cgdsr' R package top retrieve the genomic and clinical data. While the genomic data are quite complete, the clinical data seem to be very incomplete. For Breast invasive carcinoma, only disease-free and overall survival are reported; see code below:

## retrieve the breast cancer data
library(cgdsr)
# Create CGDS object
mycgds <- CGDS("http://www.cbioportal.org/public-portal/")
## test the connection

# Get list of cancer studies at server
## get the breast cancer data
mycancerstudy <- getCancerStudies(mycgds)[11, 1]
## get all patient ids
mycaselist <- getCaseLists(mycgds,mycancerstudy)[2, 1]

## get the clinical data
data.clin <- getClinicalData(mycgds, mycaselist)

print(head(data.clin))

When you go through the TCGA data portal, you get much more information and they are publicly available. So my question is, would it be possible to obtain more clinical information through the cBioPortal and especially the 'cgdsr' R package? It would extremely useful for our analysis pipelines.

I am looking forward to hearing back from you.

Best regards,
---
Benjamin Haibe-Kains
Bioinformatics and Computational Genomics Laboratory<http://www.ircm.qc.ca/haibekains>
Institut de Recherches Cliniques de Montréal (IRCM)<http://www.ircm.qc.ca>
110, Avenue des Pins West
Montreal, QC, H2W 1R7
Canada
Université de Montréal<http://www.umontreal.ca> (Département de Biochimie<http://www.biochimie.umontreal.ca/activites-de-recherche/themes-de-recherche-et-professeurs/benjamin-haibe-kains/>)
McGill University (Faculty of Medicine)

[JianJiong Gao]

Dear Benjamin,

Thanks for using the cBioPortal and taking the time to contact us. We
are currently working on a pipeline to importing more TCGA clinical
attributes into the cBioPortal, including patient demographics (age,
gender, and race etc), tumor information (grade and stage, etc),
up-to-date followups, and possibly treatment data. That may take some
time (two months or so). Please stay tuned.

Best,
-JJ

[Haibe-Kains Benjamin]

Great, thanks for your super prompt response. We are happy to hear you are working on this important functionality.

Best,

---
Benjamin Haibe-Kains
Bioinformatics and Computational Genomics Laboratory<http://www.ircm.qc.ca/haibekains>
Institut de Recherches Cliniques de Montréal (IRCM)<http://www.ircm.qc.ca>
110, Avenue des Pins West
Montreal, QC, H2W 1R7
Canada
Université de Montréal<http://www.umontreal.ca> (Département de Biochimie<http://www.biochimie.umontreal.ca/activites-de-recherche/themes-de-recherche-et-professeurs/benjamin-haibe-kains/>)
McGill University (Faculty of Medicine)