The Children’s Research Institute is home to a variety of resources available to assist researchers at all levels, both at Children’s Mercy and at collaborating institutions. These resources include everything from laboratory services, such as world-class genomic sequencing, to informatics programs and large scale data repositories.
The Children’s Research Institute Biorepository (CRIB) is a biological specimen repository that collects, processes, stores and distributes biospecimens to support scientific investigation. The CRIB is a state-of-the-art, secure, badge-access 770-square foot dedicated laboratory facility equipped with containment hoods, conditioned emergency power and environmental controls.
The CRIB offers specimen storage in continuously monitored, ultra-low environments, as well as room-temperature storage. Specimens are uniquely barcoded for tracking and monitoring within FreezerWorks, the fully-featured sample tracking, biorepository management and freezer inventory program. This database allows the CRIB to not only keep track of specimens, but also to electronically attach pertinent clinical and research data to each individual specimen.
The CRIB offers nucleic acid extraction, utilizing both manual and robotic magnetic bead procedures. Further available resources include blood component separations, live cell preservation and flash freezing. The CRIB staff members are available for consultation and assistance on specimen preservation and study design. This core resource is available to serve and assist researchers in standardizing specimen preservation in accordance with best practices.
Center for Pediatric Genomic Medicine
Additional Lab Resources
The Center for Pediatric Genomic Medicine (CPGM) is well equipped with state-of-the-art instrumentation to handle both large and small sequencing projects. Conducting intramural research, clinical diagnostics and collaborative projects, it harnesses expertise in all areas of genomic medicine. Currently, the center has two Illumina MiSeqs, one HiSeq 2500 with v4 chemistry, one HiSeq 4000, and the very high-throughput NovaSeq 6000 system. The CPGM routinely prepares and sequences samples for exome (IDT exome enrichment), genome and whole genome bisulfite sequencing. Both shotgun, as well as targeted (Roche EpiCap enrichment), are supported for the latter. The center also supports sample processing and sequencing for RNAseq; including both total stranded RNA and mRNA protocols. Providing unprecedented insight into cellular heterogeneity for both RNA and DNA, single-cell sequencing is supported using the 10x Genomics Chromium and Fluidigm C1 platforms.
- Exome, Genome
- Software Design – The Children’s Research Institute can provide design and development information technology services for research-funded projects including databases, applications and interfaces.
- Human Factors Analysis – Human Factors is the scientific discipline that uses a systems approach to understand how people think, behave and react in a multitude of environments. The Human Factors consulting service can include ethnography, workflow analysis, hierarchical task analysis, contextual inquiry, heuristic analysis and usability testing.
Informatics and Data Resources
- i2b2 (DORA) – DORA is a de-identified data repository of Children’s Mercy electronic medical records based on Cerner's implementation of standard i2b2 framework. It allows Children’s Research Institute researchers to conduct feasibility analysis, analyze retrospective data without PHI, inform quality initiatives and generate hypotheses.
- PHIS – Children’s Mercy is a member of the Children’s Hospital Association and has access to the Pediatric Health Information System® (PHIS), a comparative pediatric database. This database includes clinical and resource utilization data for inpatient, ambulatory surgery, emergency department and observation unit patient encounters for more than 45 children's hospitals.
- Cerner Health Facts® – Cerner Health Facts® is a data warehouse of HIPAA-compliant de-identified electronic health record level detailed data from participating hospitals and clinics. Pharmacy orders, laboratory results, discrete clinical findings, demographic and billing information are available for a wide variety of research projects and analysis.
- REDCap – REDCap is a secure HIPAA-compliant web application for building and managing online surveys and databases.
- Supercomputing Cluster – The Children’s Mercy supercomputer is located within a secure dedicated data center. The computing cluster consists of nearly 2,600 cores and over 15TB of total RAM. Also available are an Edico Dragen Genomics Bio-IT processor and a 10-node test cluster. Children’s Mercy has more than 3PB of high-performance storage.
- Bioinformatics Applications – Deployed on Children’s Mercy clusters are the latest versions of Apache HADOOP, Partek Flow & Genetics Suite, GATK, Bowtie, TopHat, Cufflinks, R, Python, BreakDancer, et al., and many locally developed software suites to aid in next-gen sequencing analysis.
- Statistics Applications – Statistical analysis applications such as SAS, SPSS and R are available for use by researchers.
- Cerner’s PowerTrials® – Cerner’s PowerTrials® integrates research processes into the workflow of Cerner’s electronic health record, ensuring that clinical research and clinical care share relevant data. It is used to screen potential participants by coding inclusion/exclusion criteria into a set of rules, then tracks enrollment status.
Translational Research Seminar Series: Children’s Mercy and the Stowers Institute for Medical Research are collaborating on a new seminar series. In this one-hour seminar, two presenters, one from Children’s Mercy representing the clinical perspective and one from the Stowers Institute representing basic science, will address their mutual interests as they relate to a translational research topic. Example topics include: Metabolism & Diabetes, Turner Syndrome, Rare Genetic Disorders and more. For speakers, dates/times and location, contact us at CRI-Inquiry@cmh.edu.
Connect with Us
For more information about these resources, email us at CRI-Inquiry@cmh.edu.