CHOP Biobank: Unlocking the Secrets to Childhood Health and Disease

CHOP is in the unique position to have biobanking represent its diverse patient community, including those not typically contacted for research and apparently healthy neuro-typical children without chronic disease.

mccannn [at] chop.edu (By Nancy McCann)

Imagine a world where we can identify disease markers specific to pediatric illnesses; find patterns between medical history, cellular findings, and diseases; and develop new treatments and diagnostic tools. That's the potential power of the Children's Hospital of Philadelphia Biobank.

The CHOP Biobank is an institutional resource that gathers biospecimens (a source of genomic data) and health information from electronic medical records (a source of phenotypic data) from CHOP patients and relatives, enabling CHOP researchers to collaborate more easily and ultimately understand causes, influences, and outcomes of disease.

"Think of the CHOP Biobank as a reservoir of knowledge helping us to unravel the mysteries of childhood health and disease," said David Stokes, PhD, the director of the CHOP Biorepository Resource Center (BioRC), which processes and stores the specimens collected by the CHOP Biobank and other biobanking studies conducted at CHOP.

As a disease-agnostic, institution-wide biobank that aligns operations with other established biobanking efforts across CHOP, the CHOP Biobank provides a robust biorepository and data set for the entire CHOP community to access. CHOP is in the unique position to have biobanking represent its diverse patient community, including those not typically contacted for research and apparently healthy neuro-typical children without chronic disease.

Susan Furth, MD, PhD

"By weaving together the existing biobanking initiatives and the CHOP Biobank, we'll make this quilt of opportunity for our best science to come forward so we can bring this wealth of data back to demystify disease, understand patient's unique signature of disease, and then find new ways to diagnose and treat disease and improve the outcomes for children," said Susan Furth, MD, PhD, executive vice president and chief scientific officer of CHOP Research Institute.

Why Pediatric Biobanks Are Needed for Child Health Research Breakthroughs

Despite the critical need for pediatric biospecimens and data to be included in biobanking efforts, most U.S. biobanks are adult focused — children are generally left out or underrepresented.

Cutting-edge research in child health today requires biobanking of pediatric biological samples, such as blood and tissue along with associated health information. Diseases that affect children are often more diverse and more rare than adult diseases. And childhood-presenting conditions more often have a genetic contribution to them than diseases that affect adults.

It's also important to gain information on how a child typically grows and develops by including samples from healthy children in the biobanking efforts to function as controls that are age matched. Yet controls for children under the age of 5, which is the largest period of growth and development in children, are nearly absent from biobanks.

Kate Driesbaugh, PhD

"It's essential to build these large pediatric study populations for the discovery of disease markers, looking for genomic correlations, and developing new treatment options and tools for quicker diagnoses," said Kate Driesbaugh, PhD, manager of the CHOP Biobank.

The CHOP Biobank is a central part of the CHOP Omics and Big Data Initiative, with the vision to lead in developing new omics-based diagnostics and therapeutics for children and for CHOP to be the destination of choice for the diagnosis and treatment of complicated diseases using omics technology. The principal investigator of the CHOP Biobank is Lisa Guay-Woodford, MD, senior advisor for Clinical and Translational Research Initiatives. Faculty co-leads Daniel Rader, MD, and Yi Xing, PhD, along with a committee of faculty and staff from across the Institute, help guide the vision and strategy.

First Steps: Consent and Participation

The CHOP Biobank is open to all CHOP patients. Participation is voluntary and includes children who are receiving specialized care for medical conditions as well as apparently healthy children. Eligibility also includes biological relatives of CHOP patients, which can help build better genomic studies.

Participation will last for as long as the patient is followed at CHOP but will not involve any special study visits. The data and samples collected will be stored as a resource for future research. Participants can withdraw at any time.

CHOP Biobank: Making Breakthroughs Together. Access the video transcript

To acquire consent for collecting biospecimens, traditional methods like in-person meetings with study coordinators and talking to a patient's family on the phone are conducted. But to reach a wider portion of the CHOP patient population, the CHOP Biobank can recruit and educate through the MyCHOP patient portal and possibly other channels, in partnership with Epic Research, Epic Digital and Technology Services, and the Recruitment Enhancement Core, enabling the Biobank team to do both targeted recruitment of interesting cohorts who researchers would like to contact, as well as heterogeneous recruitment to reach a broader population.

Lisa Guay-Woodford, MD

"We're focusing on using clinical samples that already exist for a patient," Dr. Guay-Woodford said, such as residual samples like leftover blood from clinical testing or discarded tissue from a clinical procedure. "Most importantly, we can access this throughout the patient's clinical care at CHOP."

Consent also gives access to the patient's associated electronic medical records.

"This allows us to marry a patient's genomic data and their phenotypic data to create this large repository," Dr. Driesbaugh said, "providing CHOP researchers with a robust institution-wide biobank that represents the CHOP community."

With a single research protocol incorporating all appropriate consent and review processes for a fully informed patient cohort, the CHOP Biobank will be able to streamline biospecimen and data collection and study enrollment, allowing researchers to conduct their studies more quickly. Investigators will be able to easily access de-identified data, and identifiable data will be available with Institutional Review Board approval. Recontact with participants is also allowable under the consent to do further follow-up research.

Journey of a Biospecimen

The consent is signed. The specimen is collected. Then what happens to it? How will it help future research?

Enter the CHOP BioRC, a CHOP Core facility whose mission is to procure, store, distribute, and process precious biosamples following best practices and guidelines. With a capacity for approximately three million samples, the facility serves all of CHOP's biobanking needs, helping to avoid specimen duplication and providing organized data and materials.

The first stop for any specimen, but in this case let's say it's residual blood from a patient's complete blood count (CBC), is the laboratory information management system (LIMS). This system barcodes and tracks all specimens in terms of type and when they were collected, allowing for effective management of samples and associated data.

The CHOP BioRC procures, stores, distributes, and processes biosamples following best practices and guidelines

"LIMS tracks everything down to the level in the freezer: the rack, the box, the plate position," Dr. Stokes said.

It removes all information that could identify the CHOP Biobank study participant and replaces it with a unique code number. A key is made so there is a de-identified link in the system that connects the participant's code number to their identifiable information. This key is necessary since data may be updated in the future. 

Derived specimens are also tracked and automatically linked to their parent specimens. For instance, if a researcher makes plasma or serum from a blood sample, the system will link them to their original source. LIMS also tracks requests for usage and disposal.

In this Bench to Bedside podcast episode, listen in as Dr. Stokes shares how the BioRC has evolved over a decade to become one of CHOP's most unique and valuable research resources.

"Our LIM system tracks the specimens through their whole lifetime," Dr. Stokes said.

Next the BioRC team will take a portion of the blood, freeze it, and save it as a backup. The BioRC storage facility is in a 2,956-square-foot, temperature-controlled — including -20°C (-4°F) and -80°C (-112°F) robotic storage units — card-accessed facility in Colket Translational Research Building (CTRB). Its laboratory space, also located in the CTRB building, is outfitted for specimen accessioning, processing, and temporary storage.

They will also take a portion of the blood and extract DNA that may be sequenced, which will build up a sequence data bank of as many patients as the CHOP Biobank can consent.

The ultimate destination for a biospecimen is to reach the lab of a researcher who may use it in their studies, generate and analyze data, and potentially lead to improved diagnoses and treatment.

"The CHOP Biobank is poised to increase the scale of what we do over the next few years," Dr. Stokes said. "That ability is going to drive omics-based translational research, which I think will be transformative for pediatric healthcare."

Researchers Benefit From Aligned Biobanking Infrastructure

Biobanking at CHOP is not new, and many efforts already exist, such as the Birth Defects Biorepository, the Roberts Individualized Medical Genetics Center (RIMGC) Biorepository, and the Neuroscience Biorepository. The CHOP Biobank is not meant to replace or interfere with any of these existing efforts, but to integrate with them on an aligned infrastructure to combine the data and the specimens from multiple resources.

The biobanking common infrastructure will provide dashboards for CHOP researchers to visualize everything that's available across biobanks at CHOP. It will provide increased sample size, increased specimen types, and enhanced capability for sharing and future use.

"By doing this, we can start to decrease duplication of effort and be better stewards of the samples that CHOP patients generously donate," Dr. Driesbaugh said.

This infrastructure does not dictate what patients a researcher enrolls, what data they collect, or how an individual investigator would govern those samples. With support from CHOP's Translational Research Integration Group, it is meant to align processes behind the scenes so that this data can more easily be combined for investigators and archived in Arcus, a suite of search tools and services that seamlessly links biological, clinical, research, and environmental data.

By establishing a disease-agnostic, institution-wide biobank, all CHOP researchers will have access to a robust biorepository and data set.

Arcus enables the investigators to locate what data and specimens already exist and where they exist for the particular cohort they are interested in. It might be that everything they need is already available, or at least some of it.

"That saves time, saves money, and saves going back to these same patients and asking for more samples," Dr. Stokes said. "Arcus is a big part of the CHOP Biobank — it's the vehicle for people to know what's in there."

Researchers will be able to enhance and expand their cohorts by combining what's available across different biorepository efforts.

"What the CHOP Biobank allows us to begin to pivot toward is not only the deep dive into understanding disease, not only assisting us along the pathway of increasingly providing precision medicine, but the ultimate goal in pediatrics of providing predictive medicine," Dr. Guay-Woodford said.

Want to learn more? Biobank team members are happy to discuss Biobank participation. You can reach a study team member by calling 267-426-7755 or by emailing biobank [at] chop.edu (biobank[at]chop[dot]edu). Or interested participants can fill out this short form to receive more information.