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Open Pediatric Brain Tumor Atlas Team Introduces Genomic Data Collection, Analytical Tools

In a paper appearing in Cell Genomics, researchers from the Pacific Pediatric Neuro-Oncology Consortium, the Children's Brain Tumor Network, Children's Hospital of Philadelphia, Alex's Lemonade Stand Foundation, and elsewhere describe an open-source pediatric brain tumor atlas and analysis platform that currently houses whole-genome sequence, exome sequence, RNA-seq, and other data for 1,074 pediatric tumors and 22 patient-derived cell lines, along with 40 open-source analytical modules to assess the genomic data. The resulting resource, known as OpenPBTA, builds on a 2018 release of raw data from the Pediatric Brain Tumor Atlas (PTBA), the team writes. In their new study, the authors used OpenPBTA to track down genetic variants with potential diagnostic, prognostic, and therapeutic ties, including TP53 losses linked to poorer-than-usual overall survival patterns in children with ependymomas or a certain form of glioma. "We created the OpenPBTA as an open, real-time, reproducible analysis framework to genomically characterize pediatric brain tumors, bringing together basic and translational researchers, clinicians and data scientists," they write, adding that "the OpenPBTA has enabled a framework to support real-time integration of clinical trials subjects … allowing researchers and clinicians to link tumor biology to translational impact through clinical decision support during tumor board discussions."

The Scan

Positive Framing of Genetic Studies Can Spark Mistrust Among Underrepresented Groups

Researchers in Human Genetics and Genomics Advances report that how researchers describe genomic studies may alienate potential participants.

Small Study of Gene Editing to Treat Sickle Cell Disease

In a Novartis-sponsored study in the New England Journal of Medicine, researchers found that a CRISPR-Cas9-based treatment targeting promoters of genes encoding fetal hemoglobin could reduce disease symptoms.

Gut Microbiome Changes Appear in Infants Before They Develop Eczema, Study Finds

Researchers report in mSystems that infants experienced an enrichment in Clostridium sensu stricto 1 and Finegoldia and a depletion of Bacteroides before developing eczema.

Acute Myeloid Leukemia Treatment Specificity Enhanced With Stem Cell Editing

A study in Nature suggests epitope editing in donor stem cells prior to bone marrow transplants can stave off toxicity when targeting acute myeloid leukemia with immunotherapy.