CPRIT Pediatric Solid Tumors Comprehensive Data Resource Core
Principal Investigator
Richard Gorlick, M.D.
Overview
The goal of this Cancer Prevention Research Institute of Texas (CPRIT)-funded grant is to establish a bio-repository of longitudinally collected bio-specimens of pediatric brain tumors and sarcomas at initial diagnoses or at recurrence and pre/post-treatment with linked clinical and molecular annotation.
Heat map showing differential gene expression in pediatric brain tumors
Changes in PTEN expression in brain tumor cells prior to treatment
Changes in PTEN expression in brain tumor cells following treatment.
Immunohistochemistry to demonstrate T-cell infiltration in osteosarcoma lung metastases
Samples
Samples can be received from other institutions and analyzed following Institutional Research Board (IRB) approval and establishment of Material Transfer (MTA) and Data Transfer Agreements (DTA). The following sample types will be accepted:
- Formalin fixed paraffin embedded (FFPE)
- Fresh tissue
- Flash frozen cells and tissue
- Blood
- Blood products (serum, plasma, peripheral blood mononuclear cells)
- Bone marrow
- Body fluid (CSF, urine, peritoneal fluid, pleural effusion)
- Buccal swab or saliva
Molecular Analyses and Instrumentation
Genomic and Expression Analyses
- Whole Genome Sequencing (WGS)
- Whole Exome Sequencing (WES)
- RNASeq
Platforms and Instrumentation
- NovaSeq 6000
- Ilumina HiSeq 4000
- Ilumina HiSeq 3000
- Ilumina HiSeq 2000
- Ilumina NextSeq 500
- Ilumina MiSeq
- Ilumina cBot
- Covaris s200
- Blue Pippin
Immune Profiling
Immunohistochemistry (IHC) Multiplex or uniplex using panels of optimized antibodies for the following:
- immune checkpoints
- myeloid derived suppressor cells (MDSCs)
- T cells
Flow Cytometry/Mass Cytometry/Multiplexed Ion Beam Imaging (MIBI) Panels are available for the following:
- T cells
- B cells
- NK cells
- Dendritic cells
- Co-stimulatory and co-inhibitory molecules on T-cells
Functional assessment
- Flow cytometry detection of T cell activation
- ELISPOT
- Neoantigen discovery
- T Cell Receptor (TCR) and B Cell Receptor (BCR) identification
Host factors
- Cytokine analyses
Platforms and Instrumentation
- Meso Scale Discovery (MSD)
- Luminex
- ELISA
- Automated IHC/IF (LeicaTM, Aperio AT2TM, Aperio/GenieTM, GenieTM; VectraTM, Vectra/InformTM, InformTM)
- Immuno fluorescent systems (OpalTM-TSA System for Multiplex Vectra IF, VectraTM (Perkin Elmer, Vectra/InformTM
- MediMachine (disaggregation of tumor tissue)-flow staining Acquisition and Analysis (BD CantoII, BD Fortessa X20)
Epigenetic Analyses
DNA Methylation
- Gene specific and genome-wide methods
- Bisulfite sequencing
- Reduced representation bisulfite sequencing (RRBS)
- Whole Genome Bisulfite Sequencing (WGBS)
- Pyrosequencing DNA methylation analysis (PMA)
High-Throughput ChIP-Seq
- Histone modifications
- Histone H3-K4-me3, Histone H3-K27-me3 (promoters)
- Histone H3-K4-me1, Histone H3-K27-ac (enhancers)
- Histone H3-K36-me3, Histone H3-K79-me2 (gene bodies)
- Histone H3-K9-me3 (heterochromatin)
- Transcription factors (as needed)
Platforms and Instrumentation
- PyroMark Q96ID
- Ilumina HiSeq 3000
- Ilumina NextSeq 500
- Ilumina MISeq
- Ilumina cBot
- Bioruptor Twin Sonicator
- Covaris s200
- Blue Pippin
- Agilent 2100 Bioanalyzer
- Agilent 2200 TapeStation
Proteomic
- High sensitivity LC/MS/MS analysis
- RPPA (tumor tissues and cultured cells)
Platforms and Instrumentation
- High Resolution, Accurate Mass (HRAM) - Orbitrap Fusion Tribrid Mass Spectrometer.
- Matrix –Assisted Laser Desorption Ionization (MALDI) (4700 MALDI TOF/TOF Mass Spectrometer)
- Triple Quadrupoles (TSQ Quantiva Triple Quadrupole Mass Spectrometer)
Contact
Minerva Griffin, M.H.A., C.C.R.P.
Project Director
Pediatrics- Research
UT MD Anderson Cancer Center
Mobile: 713-557-4555
Pager: 713-404-4890
Email: magriffin@mdanderson.org
Xie Yang, Ph.D.
Director, Pediatric Cancer Data Commons
Tel: 214-648-5178
E-mail: Yang.Xie@utsw.edu