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create-pptc-pdx-corplots

create-pptc-pdx-oncoprints

As part of an overall strategy for improving therapies for childhood cancers, the PPTC seeks to develop models for the types of tumors that will be encountered in early phase clinical testing by establishing patient derived xenografts (PDXs) from high-risk childhood cancers refractory to current standard of care treatments. Genomic profiling of these models is required to enable PPTC investigators to develop robust "responder hypotheses" when drug activity is observed. With funding provided by Alex's Lemonade Stand Foundation, we genomically characterize a major subset of 286 PDX models. We use whole exome sequencing, transcriptome sequencing, and SNPArray to characterize the tumor models. The focus on DNA and RNA sequencing data mirrors the current standard practice in most clinical diagnostics lab that use these technologies to detect the spectrum of targetable mutations, gene amplifications, and gene fusion events relevant to preclinical drug development.

create-pptc-pdx-pie

Pie chart for Figure 1 of Manuscript

epigenomics-data-descriptor

gmkf-nbl-fusion-analysis

Fusion analysis for GMKF Neuroblastoma

immunoprofile_shinyapp

Shiny app for immunoprofiling across pediatric and adult tumors

maftools

Summarize, Analyze and Visualize MAF files from TCGA or in house studies.

mosse-lab-tools

Various QoL tools and script snippets to aid researchers in the Mosse lab

nbl-cell-line-rna-seq

pdx-classification

Applying Machine Learning Ras, NF1, and TP53 Classifiers to PDX model gene expression

pdx-mouse-subtraction

pptc-pdx-classifier-analysis

pptc-pdx-copy-number-and-svs

Indel and Breakpoints plots

pptc-pdx-ethnicity-inference

Ethnicity inference for Pediatric Preclinical Testing Consortium (PPTC) patient-derived xenograft models

pptc-pdx-mut-sigs

pptc-pdx-rna-seq-clustering

pptc-pdx-tmb

pptx-pdx-fusion-analysis

Fusion pipeline and figures

scrap

selective Cross Reactive Antigen Presentation

scrap_commandline

selective Cross Reactive Antigen Presentation (command line version)

tad_pathways_pipeline

Pipeline to implement a "TAD_Pathways" analysis. Discover candidate genes based on association signals in TADs