Previous editions of the Research Resource Nexus introduced the Center for Advanced Genomics and the data production core labs represented there. This web hub will soon be reconfigured to include information on finding analytical support for genomic data, including the analytical services provided by the following facilities:
- Genomics Analysis Core
- Bioinformatics Core Facility at UPMC Children’s Hospital of Pittsburgh
- High Throughput Genomics
- Single Cell Core
These facilities collaborate and share information to ensure that each project receives the best analytical support tailored to its data types and aims. Analytical support available through the High Throughput Genomics and Single Cell Cores was described in previous editions of the nexus.
The Genomics Analysis Core (GAC) and Bioinformatics Core Facility at UPMC Children’s Hospital of Pittsburgh (CHP) provide comprehensive analytical support for a wide range of high-throughput sequencing and multiomics applications to advance cutting-edge biomedical research. Core services include analysis of Whole Genome Sequencing, Whole Exome Sequencing and epigenomic profiling methods, such as ChIP-seq, ATAC-seq and CUT&RUN. The facility also supports transcriptomic analyses across bulk RNA-seq, single-cell RNA sequencing (including multimodal platforms), spatial transcriptomics and T- and B-cell receptor sequencing. The cores are equipped to analyze proteomics, lipidomics, metabolomics and microbiomics datasets, enabling integrative systems-level insights.
A dedicated team of bioinformatics specialists provides end-to-end collaboration from study design and quality control through advanced computational analysis, data integration, visualization and interpretation. Investigators are actively engaged throughout the process to ensure that analytical strategies align with specific scientific goals, yielding high-quality, biologically meaningful results tailored to each research question.
In addition to analytical support, GAC works closely with the Center for Research Computing and is experienced in supporting multisite data-heavy Next-Generation Sequencing projects with data storage, development of bioinformatics pipelines, metadata annotation, data harmonization and FAIR (Findable, Accessible, Interoperable and Reusable) principles for data sharing.
Contact
- Genomics Analysis Core Director Uma Chandran
- Bioinformatics Core Facility Director Dhivyaa Rajasundaram
for a no cost consultation to discuss the project aims, study design, scope of analysis and estimated cost. Schedule your consultation early in the planning process, the most robust and meaningful analyses can be gained when analytical support is engaged during project design, rather than after data collection.
Selected Projects
- The naked mole rat (NMR) is a eusocial animal—a colony dweller reproducing through a single fertile queen. The queen has remarkable longevity, living as long as 25-30 years, maintaining fertility throughout and exhibiting exceptional resistance to cancers that normally proliferate in aging rodents, including ovarian cancer. In a recent longitudinal single-cell study of NMR ovaries from birth to 5 years, Miguel Brieno-Enriquez worked with analysts at GAC to identify an enzyme that maintains the fetal configuration of the ovarian extracellular matrix, protecting stem cells from differentiation and extending the reproductive life of the ovary. The enzyme is conserved in mice and humans, but in those species, it is only active in the fetus. Inhibiting this enzyme in NMRs leads to reduced reproductive lifespan and greater susceptibility to ovarian cancer. This analysis was particularly challenging due to the incomplete annotations available for NMR. “Uma and her team were fantastic,” said Brieno-Enriquez. “They didn’t just hand us numbers, they conferred on which changes made sense biologically and they taught us how to do the analysis, making it possible to be independent for simpler experiments in the future.”
- Itay Raphael and Gary Kohanbash, in collaboration with Dhivyaa Rajasundaram
from the CHP Bioinformatics Core, conducted a comprehensive retrospective analysis to identify tumor-associated antigens that are widely expressed in glioblastoma. Using bulk RNA-seq data from lower-grade glioma and glioblastoma patients available through The Cancer Genome Atlas, the team generated a library of glioma-specific, tumor-enriched isoform-junction antigens (TIAs). These TIAs were found to be broadly expressed across glioma samples. Through further refinement, they narrowed the list to 40 TIA peptides that were more commonly associated with high-grade, aggressive tumors. Additional analysis using single-cell RNA sequencing data highlighted POSTN-203 as a promising TIA candidate for future investigation.¹
1. Xiong Z, Sneiderman CT, Kuminkoski CR, Reinheimer J, Schwegman L, Sever RE, Habib A, Hu B, Agnihotri S, Rajasundaram D, Zinn PO, Forsthuber TG, Pollack IF, Li X, Raphael I, Kohanbash G. Transcript-targeted antigen mapping reveals the potential of POSTN splicing junction epitopes in glioblastoma immunotherapy. Genes Immun. 2025 Jun;26(3):190-199. doi: 10.1038/s41435-025-00326-6. Epub 2025 Apr 3. PMID: 40181162.