Treehouse Childhood Cancer Initiative

[gwaybio]

New, publicly available dataset of 11,078 RNAseq + clinical childhood cancer tumors.

Xena data

Blog Post

This will open up a lot of analysis opportunities - exciting it is now available!

[dhimmel]

Nice! It looks like the release includes:

• RNASeq gene expression data
• Clinical information: Age, gender, and disease

But mutation data is not available? Or @gwaygenomics is mutation data available elsewhere, do we know?

[gwaybio]

Mutation data is available as sequencing but is under controlled access - not sure if there are plans on making mutation calls available.

On a closer inspection, it looks like most of the samples are the same TCGA tumors. There are 732 TARGET tumors and 549 Treehouse tumors.

Here's the TARGET tumor breakdown:

Tumor	Count
acute myeloid leukemia	224
acute lymphoblastic leukemia	194
neuroblastoma	162
wilms tumor	123
clear cell sarcoma of the kidney	11
clear cell carcinoma of the kidney	2

A more thorough clinical data exploration in this notebook

[gwaybio]

Update - It looks like some variant calls are available in the [target data matrix](looks like some mutation data are available as MAF calls).

including:

1. ALL (ftp://caftpd.nci.nih.gov/pub/OCG-DCC/TARGET/ALL/WXS/Phase2/L3/mutation/)
2. AML (ftp://caftpd.nci.nih.gov/pub/OCG-DCC/TARGET/AML/WXS/L3/mutation/BCM/VerifiedSomatic/)
3. NBL (ftp://caftpd.nci.nih.gov/pub/OCG-DCC/TARGET/NBL/WXS/L3/mutation/Broad/VerifiedSomatic/)
4. WT (ftp://caftpd.nci.nih.gov/pub/OCG-DCC/TARGET/WT/WXS/L3/mutation/BCM/VerifiedSomatic/)

[dhimmel]

@gwaygenomics are there any files with mutation calls for specific samples or are all the mutation datasets just summaries?

[gwaybio]

are there any files with mutation calls for specific samples or are all the mutation datasets just summaries?

Yes, the data are there for specific samples