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Pediatric Oncology

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The Johns Hopkins NF1 Biospecimen Repository

Neurofibromatosis type 1 (NF1) is a common genetic disorder caused by mutations in NF1 and characterized by a predisposition to the development of nerve sheath tumors, including dermal neurofibromas, plexiform neurofibromas (PN), and malignant peripheral nerve sheath tumors (MPNST). Currently, surgery is the only treatment option for patients with NF who have symptomatic PN. Progress developing nonsurgical therapy for PN has been limited by a number of factors including a limited number of cell culture based and animal models of PN, and limited access of investigators to primary PN tissue from patients with NF1. Although progress is being made in the development and utilization of animal models and cell culture models, the limited availability of primary patient tissue remains unaddressed.

The Comprehensive Neurofibromatosis Center at Johns Hopkins serves a large volume of patients affected by NF1.  We have an IRB-approved research study for banking NF1-associated tumors including plexiform neurofibromas, MPNST, and blood fractions from patients with NF1.  The goal of this project is to establish a comprehensively annotated biorepository of tissue and blood fractions for use in NF1 research.  Tumors included in our biospecimen bank include: cutaneous neurofibroma, diffuse infiltrating neurofibroma, plexiform neurofibroma, atypical neurofibroma, and MPNST.  Our goal is to increase availability of these tissues to the NF1 research community through scientific resource and data sharing.

Tissue is collected according to Standard Operating Procedure on the day of surgery. Tissue banking procedures are in accordance with NCI Best Practices for all banking efforts. H&E of each banked sample is reviewed by the study neuro-pathologist for quality control. Banked specimens undergo comprehensive genomic characterization using RNAseq and whole exome sequencing (WES), and data are available through Synapse. A fully annotated clinical database accompanies the bank, and includes NF1-associated symptoms and findings, tumor characteristics, and outcome data.

Banked samples are available to the NF1 research community upon review of a scientific proposal.

A current inventory of available specimens can be found here.

  • MPNST – genomics:  Each PN and MPNST specimen (including frozen, xenografts, cell lines, and blood normal) in our biospecimen repository has been sequenced using WES and RNAseq.  These data are being made publicly available through a collaboration between NTAP and Sage Bionetworks.
  • MPNST – characterization of novel PDX (with Wash U.):  In collaboration with Dr. Angela Hirbe at Wash U., we are characterizing the genomic and phenotypic profile of patient derived xenografts (PDX) of MPNST, in order to expand the number of available models in the field of MPNST research.

Samples in our repository include:

  • Flash frozen tissue
  • Viably frozen tissue
  • Slides from paraffin embedded tissue
  • Viably frozen cells
  • Clinical information for NF1 physical signs and symptoms
  • Cell lines
  • Patient derived xenografts

How to Request Specimens:
Investigators interested in requesting specimens for their research can complete a specimen request form found here.  Completed forms should be sent to Dr. Pratilas (cpratil1@jhmi.edu) and cc: Kai Pollard (mkai1@jhmi.edu). Each request will be reviewed by an internal scientific review committee and investigators will be notified of a decision within approximately two weeks.

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