IDDRC Genomics and Data Integration Core

The Genomic Sequencing Service provides expert informatician-based analysis of genomic sequences obtained from either nuclear or mitochondrial DNA or RNA, including sequences taken from single cells and induced pluripotent stem cells (iPSCs). This service is directed by Dr. Hakon Hakonarson, an internationally recognized pioneer in the use of genome-wide mapping to understand the causes of IDD.

The Genomic Sequencing Service can advise and consult in the following areas:

• Educate on benefits and drawbacks of available options, cost analysis, and platform choices for data generation and analysis*
• Assist in design of experimental studies and platform selection to utilize the extensive array of validated genotyping and sequencing resources available and communicate availability of additional sequencing resources that may be appropriate for specific programs on a fee-for-service or collaborative basis*
• Review options and provision of cost-effective computational facilities*
• Discuss options for, and appropriate and efficient use of, genomic dataset analysis pipelines*
• On a per faculty/customer project, provide raw sequencing data across the nuclear and/or mitochondrial genomes, and annotated datasets by expert bioinformatics scientists
• Guide and assist with raw sequencing data submission to public databases, as required for NIH compliance and/or publication*
• Guide and assist with iPSC generation and differentiation with focus on DNA, RNA, and scSeq analysis work, in collaboration with the iPSC core of the IDDRC Preclinical Models Core.

*Indicates a free service for IDDRC-approved users. Additional services may be available for a fee, and/or opportunities may exist for collaborative research projects.

The Genomic Data Bioinformatics Resources and Variant Analysis Education Service provides users with access to MITOMAP/MITOMASTER and MSeqDR web toolkits, in order to enable self-analysis of genetic variants in both nuclear and mitochondrial genomes. These toolkits, developed by Drs. Douglas Wallace and Marni Falk, enjoy broad recognition as essential clinical and research instruments for understanding the genetics of mitochondrial disease. This service leverages CHOP resources that were used to support the Mitochondrial Medicine Frontier Program (MMFP) and the Center for Mitochondrial and Epigenomic Medicine.

The Genomic Data Bioinformatics Resources and Variant Analysis Education Service can advise and consult in the following areas:

• Educate genomic dataset, gene, variant, and phenotype data analysis tools in MSeqDR and MITOMAP/MITOMASTER*
• Assist with nuclear gene-disease and variant pathogenicity assertion interpretation*
• Assist with mitochondrial DNA sequencing and variant interpretation including identification of nucleotide variants relative to the rCRS, determination of haplogroup and species conservation information*
• Identify contamination of legitimate mtDNA sequence data with nuclear encoded mtDNA pseudogenes (NUMTs)*

*Indicates a free service for IDDRC-approved users. Additional services may be available for a fee, and/or opportunities may exist for collaborative research projects.

The Complex Data Integration and Visualization Service provides access to a custom "IDDRC-Tableau" data integration platform that accelerates research discovery by facilitating compilation, integration, visualization, and direct query by users of complex genetic and phenotypic data directly collated and modeled from diverse sources, including the electronic medical record. This service is particularly useful for review of cohort-level data, enabling outcome measure and subject selection for natural history studies and clinical trial development.

The Complex Data Integration and Visualization Service can advise and consult in the following areas:

• Educate on IDDRC-Tableau capabilities and use*
• Customize integration and modeling of visualizations of IDDRC user-specified data sources, to support queries and mining of individuals and cohorts on data directly extracted in real-time from the electronic medical record (EMR, EPIC), clinical trial databases (OnCore), REDCap and excel databases, etc.
• Create biological sample tracking interface with de-identified study IDs for laboratory personnel to access study samples’ description and location, along with appropriate clinical fields of information
• Assist with export of IDDRC-Tableau datasets via API or individual data outputs, as needed, for additional data modeling and machine learning*
• Create REDCap instruments for outcome measure tracking from clinician-entered or patient/family entered outcomes, in collaboration with IDDRC Clinical Translational Core and/or individual investigators.
• Provide tiered license options for IDDRC-Tableau use at variable levels as appropriate to meet different investigators’ capabilities and research needs.

*Indicates a free service for IDDRC-approved users. Additional services may be available for a fee, and/or opportunities may exist for collaborative research projects.