The Children's Hospital of Philadelphia Research Institute provides instrumentation and technical skill through numerous core facilities that service both laboratory and clinical research programs. Providing core facilities to investigators makes research more affordable, convenient, and efficient.

With substantial Hospital support, the Institute has improved and broadened the core facilities available for the Hospital's research community, investing in equipment, services, and other capabilities as well as supporting technical staff. Each year, the Hospital invests millions of dollars in sophisticated research instrumentation for the core facilities, which are lead by scientific or faculty directors and one or more technical directors.

Bioanalytical Core

The Bioanalytical Core Lab specializes in developing and validating robust liquid chromatography/tandem mass spectrometry methods for the analysis of natural products, drugs, and metabolites in various biological samples (blood, DBS, plasma, urine and tissue). The core has extensive experience in method development and validation. Despite the analytical complexity, it approaches every compound with creativity, innovation, and years of scientific knowledge, allowing core personnel to uncover solutions to complex bioanalytical challenges.

The Bioanalytical Core performs method validations, partial validations, cross-matrix validations, or combination of them required to meet project needs. Validation studies are performed in accordance with the US FDA Guidance for Industry, Bioanalytical Method Validation. The core has developed assays for investigational and marketed drugs used for pain, oncology, cardiology and infectious diseases. These assays are typically used to support pediatric drug discovery and development.


The Biorepository Core collects and organizes biospecimens from investigators across the Research Institute. With a capacity for approximately 7 million samples, the facility is designed to house all of the biospecimens available at Children's Hospital, avoiding specimen duplication, preserving precious materials, and providing broad access to data and materials. Initial sample collection focuses on DNA samples, but the facility can also safely store fluids, RNA, tissue samples, and a number of other biospecimens.

Biostatistics and Data Management

The Biostatistics and Data Management Core (BDMC) supports investigators from virtually all subspecialties of pediatric medicine and supports studies ranging from small, narrowly-defined basic science projects to large, multi-site clinical trials and observation studies. The BDMC is staffed by a director, deputy director, and data management/information technology managers, as well as approximately 15 additional staff members representing the disciplines of biostatistics, data management, information technology, and administration.

Center for Applied Genomics Core

The Center for Applied Genomics has an experienced team of researchers analyzing the immense amount of data generated from our high-throughput facility. We have expertise in carrying out large scale NGS, GWAS, CNV, and methylation studies. Currently at CAG, there are 50 active disease projects, both internal and collaborative. We are collaborating with investigators at the Children's Hospital of Philadelphia, the University of Pennsylvania, as well as with international investigators from Croatia, United Kingdom, Denmark and Canada, making our genotyping an international endeavor.

In order to support all data generation, storage, analysis and bioinformatics activities associated with the Center's activities, CAG uses a highly robust and secure system to manage its own data warehousing and analysis needs. Our infrastructure is tailored to support additional hardware dedicated to the biorepository consortium. CAG has taken advantage of this to establish and host a secure, web-enabled server that allows external parties to access the facilities, but is otherwise invisible to all other internet users. This groupware server enjoys the same protection as all other CAG systems, including environmental control in a Tier 3 rated professional hosting facility, 24/7 monitoring, robust TSM based data backup scheme, at least 2x hardware and data redundancy, and support from CAG’s Icelandic IT contractor, Raförninn ehf. with IBM, RedHat, Microsoft, Cisco and Fortigate certified engineers. This highly flexible, fast, and secure system provides all external users with high-quality documentation to their needs. Standard Operating Procedures (SOPs) are prepared and implemented for all new workflows with new customers. All data and results are shared according to the data sharing policy agreements between the CAG and external parties.

If you are interested in collaborating with our Center, you can review the technologies we have available under Our Technology. Alternatively, you can Download Free Software developed at CAG for genomic analyses.

More Information

CAG's external site outlines the services available, a list of the arrays utilized, and a brief description of respective capacities:

For inquiries, please contact co-Director of the Joint Genome Center Brendan Keating, or Research Lab Manager Cecilia Kim.

CIRP Driving Simulator

Housed within the Center for Injury Research and Prevention (CIRP) at The Children’s Hospital of Philadelphia Research Institute, the Driving Simulator Core is dedicated to understanding driving behaviors and performance to help improve the safety and health of children, adolescents, and young adults through qualitative and quantitative research. The Driving Simulator Core at CIRP provides the technical and administrative support for conducting simulator-based observational studies.

We offer a high-fidelity, fixed-base driving simulator with a rich audio and visual environment for conducting research that features:

  • a three-channel open cockpit configuration with a driver’s seat
  • an integrated advanced, lightweight eye-tracking system
  • a video-based data visualization program for processing simulator data
  • specialty programming to analyze eye-tracking data

We also offer a one-channel, desktop version with a game control console that also features eye-tracking capabilities. Both driving simulators feature customizable programming to replicate controlled scenarios typical in the driving environment, such as dynamic traffic behaviors, pedestrians, distractions, time of day, and weather to fit the needs of researchers.

CIRP researchers are using the driving simulator to help improve the assessment of driving skills, to better understand how drivers’ behaviors and emotions can affect driving performance, and to develop predictive algorithms to increase driving skills. Another recent study is using the driving simulator to evaluate web-interventions and curriculum for parent-supervised practice driving for teens. For more information on Teen Driver Safety Research conducted at CIRP, visit

Clinical Research Support Office

The Clinical Research Support Office (CRSO) assists in the start-up, execution and completion of clinical research projects, in compliance with local and federal requirements. The office maintains a staff of well-trained study coordinators and project managers who can be assigned to support any type of clinical research studies at Children's Hospital. The CRSO Navigator is available to assist/guide investigators with any questions that arise during the design, start up, and execution of their clinical studies. The CRSO also is also available to assist investigators with budget preparation, IRB submissions, and IND and IDE applications to the Food and Drug Administration The CRSO maintains a highly trained staff with expertise on good clinical practices of clinical research, which ensures that study teams comply with all relevant regulatory requirements.

The CRSO works with faculty on industry- and investigator-initiated clinical research projects; provides full and part time nurse and no nurse study coordinators and project managers; and facilitates contact between principal investigators and sponsors or contract research organizations interested in conducting trials at the Hospital.

Clinical Viral Vector

The Clinical Vector Core utilizes a patented vector production technology and a highly efficient purification process that utilizes combined column and gradient centrifugation-based process steps. This system has manufactured clinical grade AAV vectors that have demonstrated excellent safety in several clinical studies.

Flow Cytometry

The Flow Cytometry Core offers access to high performance flow cytometry equipment and analysis software, individualized training for researchers interested in operating analyzers and cell sorters, as well as full service flow cytometry assays and cell sorting. The staff is available to assist investigators with the design and implementation of a variety of polychromatic flow cytometry applications. Custom flow cytometry assays for basic and clinical research studies are available upon request. The cell sorters existing in the lab can be used with a wide range of sample types, from microparticles to whole organisms (C. elegans, zebrafish).

Healthcare Analytics

The Healthcare Analytics Unit (HAU) serves as a resource for Hospital investigators using administrative data to address research questions by providing expertise in analysis data creation, statistical programming, advanced analysis, study design, and sample size calculation. The HAU is a core service unit of two centers in the CHOP Research Institute – the Center for Pediatric Clinical Effectiveness (CPCE) and PolicyLab. CPCE performs clinical epidemiology, health services, and community-based research to elucidate the best practices in the diagnosis, prognosis, and management of pediatric disease. PolicyLab researchers are methodological experts in the disciplines of epidemiology, health services research, program evaluation, and ethics.

High Throughput Sequencing

The High-Throughput Sequencing Core at Children’s Hospital and the Beijing Genomics Institute have formed a collaborative genome center called BGI@CHOP. Together, these elements for the 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, whole exome, RNA-SEQ, and ChIP-SEQ.

Human Pluripotent Stem Cell Core

The human embryonic stem cell/induced pluripotent Stem Cell (hESC/iPSC) Core generates control and patient-specific iPSC lines by cellular reprogramming using current technologies. The core has a training course in cell maintenance and growth, specialized differentiation protocols for disease modeling and drug screening, and quality-control reagents for the Children’s Hospital and University of Pennsylvania academic communities. The facility maintains five NIH-approved human ESC lines and has generated more than 60 disease-specific iPSC lines.

Metabolomics Core

The Metabolomic Core provides investigators with a resource that facilitates the analysis of major metabolic pathways in humans, animals, and in vitro systems. The analytical repertoire includes the measurement – both in vivo and in vitro – of flux through major pathways of intermediary metabolism, including glycolysis, the tricarboxylic acid cycle, the oxidation of fatty acids and amino acids, the urea cycle and protein synthesis and degradation; determination of in vivo metabolic rate in freely moving organisms; and determination of selected drugs and/or drug metabolites with triple-stage quadruple mass spectrometry.


The CHOP Microbiome Center was established in 2015 within the PennCHOP Microbiome Program to meet the growing needs of the Penn and CHOP communities in the field of microbiome research. The Program’s mission is to develop microbiome-based strategies that generate biomarkers or therapeutics to improve health and treat disease.

NMR/Microimaging Services

NMR/Microimaging Services at Children’s Hospital feature a 400 MHz (9.4Tesla) high-resolution wide-bore spectrometer equipped with a HP computer. The system can perform most of the traditional high-resolution NMR experiments as well as microimaging of specimens and small models. The services are available not only to Children’s Hospital investigators but also to investigators affiliated with large center program or private research institutions.

Nucleic Acid PCR

The Nucleic Acid PCR Core Facility provides a centralized source for specialized services, technical expertise and reagents to support investigators’ molecular biology needs. These services include Sanger DNA sequencing, small-scale next-generation sequencing and library assistance, fluorescent fragment analysis (MLPA and microsatellite analysis), microarrays, real-time PCR, oligonucleotide ordering, and sample quality control assessment.


The Pathology Core Laboratory provides basic histopathology, research immunohistochemistry, tissue microarray, and laser capture microdissection services to researchers at Children's Hospital and within the surrounding academic community.

The core offers a full range of histopathology services including tissue processing, embedding, and cutting, for both paraffin and frozen tissue. The core also performs most standard stains as well as immunohistochemistry, antibody workup, fluorescence, in situ hybridization and TUNEL. Tissue microarrays can be constructed, and sophisticated imaging instrumentation is available for virtual microscopy and image analysis. Specialized software is available to image and analyze tissue microarrays, and to manage and store array data.

Protein Core

The Protein and Proteomics Core Facility at Children’s Hospital addresses the overwhelming need for the technological resources to identify, produce, and characterize new proteins. The facility provides a variety of services for investigators at CHOP, the University of Pennsylvania , and outside institutions. These services include producing and characterizing proteins, investigating protein-protein interactions, and characterizing whole proteomes. Some services are provided on a user-operated, sign-up basis, while others are performed as full-service by the dedicated facility personnel.

Research Viral Vector

The Research Viral Vector Core: As part of The Center for Cellular and Molecular Therapeutics, the Research Vector Core (RVC) has expanded its capacity to provide infrastructure support for investigators interested in using viral vectors in their research model systems.

Shipping Core

The Research Institute's Shipping Core is a "fee for service" core facility that is available for shipment of hazardous substances for all Research Institute faculty and staff. The Shipping Core provides comprehensive shipping services including: packaging, labeling, shipping and tracking of hazardous materials shipments; identification and procurement of any necessary shipping permits; training and certification of labs whose PIs have chosen to ship their own packages as "Certified Shippers"; and providing shipping supplies to "Certified Shippers" at cost.

Translational Core Laboratory (TCL)

The Translational Core Laboratory (TCL) at CHOP provides a variety of services ranging from sample collection to laboratory testing. We support investigators at both CHOP and UPENN for patient-orientated research as well as preclinical studies.

Web Services

The Research IS Web Services Core designs and supports web sites for investigators, labs, studies, Core Facilities, Affinity Groups, outreach programs, and Centers of Emphasis, as well as providing web development for Research Administration. The team develops a variety of client-side and database-driven web applications, including search and data gathering functionality, custom login and access restriction, and more. Web Services posts new content and site updates daily as part of their service to internal clients. In addition, the team provides development support to, and day-to-day administration of, Institute-wide web presences, including the Research Institute public website, the Research Institute intranet and the Share (Wiki) collaborative environment.