Clinical & Specimen Data

biorepository_8The Children’s Brain Tumor Tissue Consortium has enrolled more than 2,050 subjects and contains over 21,000 tubes of specimens, all highly annotated with clinical data and available for request by researchers across the world.  These achievements are the result of the hard work and dedication of the CBTTC Institutional Members including Children’s Hospital of Philadelphia (CHOP), Children’s Hospital of Pittsburgh of UPMC, Seattle Children’s Hospital, Ann & Robert H. Lurie Children’s Hospital of Chicago, Meyer Children’s Hospital (Florence, Italy), UCSF Benioff Children’s Hospital, Lucile Packard Children’s Hospital Stanford, Bristol-Meyers Squibb Children’s Hospital at Robert Wood Johnson University Hospital, Children’s National Health System, Weill Cornell Pediatric Brain & Spine Center,  Joseph M. Sanzari Children’s Hospital at Hackensack University Medical Center, Children’s Hospital of Orange County: CHOC Children’s, University of California Santa Cruz: Treehouse Childhood Cancer Initiative, The Beijing Tiantan Hospital Neurosurgery Center (Beijing, China), Genebank (Beijing Genomics Institute – Shenzhen, China) and the dedication and support of the Children’s Brain Tumor Foundation, the International Licensing Industry Merchandisers’ Association, countless volunteers and dedicated donors. The commitments of these partnerships and others being forged will only further ensure the shared vision to identify better testing, treatments, and outcomes for children diagnosed with these devastating diseases.


Specimen Collection

All  specimens collected by the CBTTC are considered a gift from our donors and their families. The specimen and accessioning process follows a detailed workflow to ensure that donated biospecimens are preserved for later use by researchers.  With this in mind, we make sure to collect our specimens and store them with the utmost care. With standardized best practice across multiple institutions, we hope to build a foundation to allow for faster, more effective scientific breakthroughs.

specimen-collection-process-chart

Process Overview

Blood is collected from patients to be used as a non-tumor control. The genomic data generated from blood samples can be compared to the genetic information of the tumor to identify the occurrence of specific mutations . Tissue samples are collected from a surgery or biopsy and immediately are flash-frozen using liquid nitrogen vapor. This process preserves the integrity of the tissue DNA/RNA, which will be extracted for scientific projects such as whole genome or RNA sequencing. Tissue in freezing media is extracted at the time of surgery and placed in media for cryopreservation and for use in cell line generation.

The tissue samples are sent via courier to the CBTTC Operations Center, where , after tissue is flash frozen and some tissue is placed in freezing media, fresh tissue (not frozen) is brought to the lab and immediately processed as cell lines. Cell lines are used for many different types of studies, in vitro and in vivo.

Specimen Accessioningtubes

Each month, CBTTC member institutions ship biospecimens for processing at the CBTTC’s operations center. All specimens are packaged and shipped with dry ice to maintain specimen quality and minimize degradation of DNA or RNA due to thawing.  Specimens are accessioned into Nautilus, a laboratory information management system (LIMS).  Each submitted specimen is placed inside a tube and labeled with a unique 2D-barcode.  The barcodes are scanned into in LIMS and assigned a specific location within the biorepository. Additional information including weight, volume and any abnormalities are recorded within the specimen’s profile.

Specimen Requests

Requests for specimens are submitted through an online form to the CBTTC operations staff. Each request is thoroughly reviewed for accuracy before being sent to the Scientific Committee for approval. Examples of requests include specimens for whole genome sequencing, RNA sequencing and cell line studies.

The Scientific Committee is comprised of experts in pediatric brain tumor research from each member institution of the CBTTC. Proposed projects are reviewed by each institution for approval.  This process ensures that the specimens at the CBTTC are only used for scientifically valid projects. Project data from an approved request is typically available within one-year following the receipt of specimens. All data generated by specimens from the bank becomes a part of the bank as well. The collected data is stored for use in future approved projects to help identify new treatments for pediatric brain tumors.

Data Access Agreement

The CBTTC supports data sharing and collaborative discovery through CBTTC-supported portals/platforms, NIH-supported portals/platforms, or other public platforms with approved security and patient privacy protection. The CBTTC adheres to NIH guidelines for genomic data sharing and follows the longstanding principles of rapid data release as articulated in the Bermuda and Ft. Lauderdale agreements with no pre-established data embargo periods on quality controlled data. Because the volume of human genomic and phenotypic data contained in the CBTTC is substantial and, in some instances, potentially sensitive (e.g., data related to the presence or risk of developing particular diseases or conditions and information regarding family relationships or ancestry), data must be shared in a manner consistent with the research participants’ informed consent, and the confidentiality of the data and the privacy of participants must be protected. As such, access to human genomic data will be provided fully to research investigators who, along with their institutions, have certified their agreement with the expectations and terms of access detailed below.

 

Download the CBTTC Data Access Agreement

 

Frequently Asked Questions

Can multiple investigators request the same biospecimen?

This depends largely on investigator interest in the samples. However, there are safeguards in place to make sure we know how much tissue is remaining and if a request could potentially deplete a biospecimen.

 

What data is returned to the CBTTC from a project?

All data generated from CBTTC specimens must be returned to the CBTTC. Raw data is expected back in real time and all other data at the completion of the project.

 

Can I control who sees the data from my project?

Please refer to the separate Data Access Agreement. The expectation is that all raw data be released to CBTTC via the Cavatica platform in real-time. The individual investigator will inform the decision on when the data can be made available.

 

How long will it take CBTTC Operations to review my request?

The time it takes to review a request is largely dependent on the size and the complexity of the request. Please see the specimen request timeline for more information.

 

Can I get tissue for a project?

Unless absolutely necessary for the scientific purpose proposed, no tissue will be given out directly from the bank. All extractions will be performed by the biorepository core at CHOP and all cell lines will be generated by the CBTTC Cell Line Engineer.

 

How is DNA/RNA extracted?

The following process is used for extractions: Qiagen AllPrep DNA/RNA/miRNA method is used for processing. In this method there is no treatment of the DNA with RNase. The RNA samples do undergo a DNAse treatment

Other info about DNA/RNA: The Tissue RNA samples are dissolved in water.

The Tissue DNA samples are in TE (10mM Tris/1 mM EDTA pH8.0)

Blood DNA samples are in TE