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Pay it Forward!

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The Treehouse Childhood Cancer Initiative is a research arm of the UCSC Genomics Institute. We enable the sharing of pediatric cancer genomic data using tools developed by our Genomics Institute colleagues. We use shared data to analyze a child’s tumor against both child and adult patient cancer tumors using a “pan cancer” or cross-comparison gene expression analysis. Our goal is to identify situations where an an approved drug, often an adult drug, is predicted to work on a child with cancer.

As part of our research, we have gathered a compendium of RNA gene expression data which we have made available for download and visualization. Please let us know if there is an additional format or tool that would make it easier for you to use our data.
 

Visualize

The UCSC Cluster Browser interactively displays samples in the Treehouse dataset positioned according to their RNA profiles. Users can color the samples based on dataset features like Disease. This browser quickly shows samples clustered using the t-SNE algorithm and best shows relationships among larger groups.

UCSC Xena allows users to explore the Treehouse dataset, finding correlations and trends within and across genomic and phenotypic variables. Users can interactively add, remove, and rearrange arbitrary slices of data including genes, transcripts and other dataset features. This example shows that neuroblastoma, in comparison to other pediatric cancers, has a much stronger ALK gene expression and younger patient population.

The UCSC TumorMap interactively displays samples in the Treehouse dataset positioned according to their RNA profiles. Users can color the samples based on dataset features like Disease. This browser shows samples clustered using the OpenOrd algorithm and best separates smaller groups. (See “TumorMap: Exploring the Molecular Similarities of Cancer Samples in an Interactive Portal.” Cancer Research November 2017)

Download

Go to our cohort page on the UCSC Xena Functional Genomics Browser to download our Public Expression Dataset.

Over 11, 000 samples are available for download along with clinical data including age, gender, and disease type. Our samples are derived from partner clinical sites and publicly available repositories, including TARGET and TCGA.

Pipeline

We are committed to data sharing and encourage you to be part of this sharing network. Our data was processed with the RNA-Seq pipeline developed by the UC Santa Cruz Computational Genomics lab. The pipeline is available for general use; the source code is hosted on GitHub at BD2KGenomics/toil-rnaseq and a Dockerized version is available at UCSC-Treehouse/pipelines. If you use our data, and have data of your own, pay it forward by running this pipeline and sharing back. We will add these results to our public compendium of expression data, with a credit to your contribution. By doing so, your samples and those of other partner sites will contribute to an ever-improving virtuous cycle of data sharing, ensuring that each participant’s data pays it forward to future participants!

Thank You!

We are grateful to all our supporters and clinical partners (see below, and on our Acknowledgments page). Without them, we would not be able to accomplish this important work.

Thank you to all who are sharing data. A special shout out to the St. Baldrick’s Foundation and the California Initiative to Advance Precision Medicine, not only for supporting Treehouse but for their commitment to data sharing and their efforts to advance responsible data sharing.

With support from

California Initiative to Advance Precision MedicineSt. Baldrick's FoundationUnravel pediatric cancerTeam G Childhood Cancer Foundation

With thanks to our clinical and research partners

Stanford MedicineCHOC Children'sUCSF Benioff Children's HospitalsBC Children's HospitalSt. Jude Children’s Research Hospital

Data Usage Policy

If you use our data, please acknowledge the Treehouse Childhood Cancer Initiative as the source of the data.

If you use our pipeline to process your data, we would appreciate it if you share the results with us, so it can be added to the public database. Just send us an email and we’ll get in touch to arrange the data transfer. Our goal is to benefit researchers and pediatric patients everywhere through access to data.