Background and Literature

Here, we have compiled some important literature related to pediatric CNS brain tumors and computational workflows our group utilizes. Please review.

Consortia

The Children's Brain Tumor Network (CBTN)

The CBTN is a multi-institutional international clinical research consortium which was created to advance therapeutic development for children with central nervous system tumors through the collection and rapid distribution of biospecimens and data. In 2018, the CBTN released WGS and RNA-Seq for ~1,000 tumors for researchers without embargo. Read the CBTN manuscript here.

The Pediatric Neuro-Oncology Consortium (PNOC)

The PNOC is an international consortium dedicated to advancing clinical paradigms and therapy for children and young adults with brain tumors.

Open Source Platforms and Tools

Gabriella Miller Kids First Data Resource Center (GMKF DRC)

We utilize the DNA and RNA sequencing workflows benchmarked and created by the Kids First DRC, which operates at the Children's Hospital of Philadelphia. The code for the workflows can be found in the Kids First GitHub repository with corresponding CWL applications are publicly available within CAVATICA.

OpenPBTA and OpenPedCan

The Open Pediatric Brain Tumor Atlas (OpenPBTA) was a global open-source analysis effort to analyze those first 1,000 PBTA tumors released by the CBTN and the PNOC003 DIPG clinical trial. The OpenPBTA was led and maintained by researchers at CHOP and the Childhood Cancer Data Lab (CCDL) at Alex's Lemonade Stand Foundation. Read the OpenPBTA manuscript here and visit the archived GitHub repository here.

The OpenPBTA was later expanded to include additional pediatric cancer genomic data as well as gene expression data from TCGA and GTEx cohorts through the Open Pediatric Cancer (OpenPedcan) Project. Read the OpenPedCan manuscript here.

OpenScPCA

ALSF supported data generation, deposition, and harmonization of multiple pediatric cancer single cell studies, which are now housed in the Single-cell Pediatric Cancer Atlas Portal. The CCDL created the Open Single-cell Pediatric Cell Atlas (OpenScPCA) analysis project to analyze these data.

CNS Tumor Literature

Pediatric CNS Tumor Classification

The World Health Organization (WHO) introduced "integrated diagnoses" for CNS tumors in 2016, followed by a significant update in 2021. Today, there are still new entities and predispositions being discovered.

Most of these tumors can be classified by running methylation arrays through either the DKFZ classifier or the NCI classifier.

Cancer-specific marker publications

This section is under construction.