Biorepository

CBTTC Biorepository at The Children’s Hospital of Philadelphia

The CHOP Biorepository core collects and organizes biospecimens from CBTTC investigators. With a capacity for approximately 8.6 million samples, the facility is designed to serve all of the CBTTC’s biobanking needs, avoiding specimen duplication, preserving precious materials, and providing broad access to data and materials. Initial sample collection has focused on DNA samples; however, additional resources are in place (-80oC freezers and liquid N2 storage) to safely store fluids, RNA, tissue samples, cells, and a number of other biospecimens. The CBTTC at CHOP is collaborating with the CHOP biorepository to facilitate the operational launch of the facility. The biorepository uses Nautilus and the eHonestBroker to manage the specimen inventories.

Tissue Storage and Requests

CHOP CBTTTC biorepository
State-of-the-art bio repository at the CBTTC Operations Center, The Children’s Hospital of Philadelphia

General questions regarding prioritization of biospecimen use from the CHOP biorepository are handled by appropriate tissue banking committees consisting of users and experts. The tissue committees determine which materials should be deposited, the appropriate storage conditions, the proposed period of storage, and prioritization of access. The tissue committees also receive and consider petitions from outside groups for deposits and access to materials. The CBTTC Scientific Committee reviews all CBTTC specimen requests providing the CHOP biorepository with approval releases.

Facility

The Biorepository is located in a 2956 sqft temperature controlled, card access facility on the A-Level of the CHOP Colket Translational Research Building (CTRB) in Philadelphia, Pennsylvania. The heart of the Biorepository Core is the REMP Mid-size Store (MSS). The store holds up to 17,472 plates (96 or 384 well or matrix tube format, 1.7-6.7 million samples) in a carefully monitored -20°C temperature and humidity-controlled environment. The REMP MSS operates with four redundant cooling systems; however, only two of the cooling units are needed at any given time to maintain the store’s temperature. Electrical power is ensured through the CTRB’s emergency power system. A UPS backup is also on-line to bridge the two systems during an electrical emergency and the facility is equipped with a wireless system for monitoring equipment status.

REMP Sample Management System

The REMP stores and retrieves samples by use of a sophisticated robotic system that travels up and down the central corridor on a rail system. Racks of plates and trays are stored in shelves on both sides of the store. The robot is capable of scanning barcodes, cherry-picking tubes, and running automated sample consolidation routines during downtime to maximize storage efficiency. The REMP MSS keeps track of sample location within the store itself through an integrated sample administration system and an Oracle database. Samples and plates are tracked within REMP via 1D and 2D barcodes. Currently, the Biorepository is also outfitted to accommodate liquid N2 storage for up to 400,000 samples and -80oC storage for up to 1.2 million samples.

Sequencing Facilities

Beijing Genomics Institute (BGI) at CHOP

BGI
The Illumina HiSeq 2000 platform provides genomic sequencing capabilities to the CBTTC

The CBTTC utilizes the expertise of the BGI@CHOP Joint Genome Center to research the genetic and molecular characterization of specific tumor subtypes. The Children’s Hospital of Philadelphia and the Beijing Genomics Institute (BGI) formed a collaborative genome center entitled BGI@CHOP in 2011 while strengthening their partnership in January 2013 to focus on the facilitation of the CBTTC mission and vision. BGI@CHOP is a state-of-the-art High-throughput Sequencing (HTS) core with increased capacity, expertise, and analytical resources for conducting next-generation sequencing studies.

The HTS Core provides automated library construction and high-quality, high-throughput sequencing services for whole genome and whole exome, targeted sequencing, Transcriptome, and digital expression profiling (RNA-SEQ), gene regulation and epigenetic analysis (ChIP-SEQ), small RNA discovery (smRNA-SEQ), and multiplex sequencing (multiple samples in one lane) using the Illumina HiSeq 2000 platform. This partnership will ensure the highest quality data while reducing expenditures and analyses time to facilitate CBTTC pediatric brain tumor research worldwide.