CCR Genomics Core

Division Of Basic Sciences - Nci

Investigators

Linked publications, trials & patents

Abstract

In FY25 the CCR Genomics Core lists 375 active users from 172 research groups from its iLab management and scheduling software. Of these, 123 groups are from NCI and the remaining 34 from 13 other NIH institutes. These institutes include: NIH Clinical Center, NCATS, NEI, NHGRI, NHLBI, NIA, NIAID, NIAMS, NICHD, NIDCR, NIDDK, NIMH and NINDS. Of the 40 labs/branches/programs listed under the CCR, 32 (80%) utilized our services in FY25. These lab/branches include: Basic Research Laboratory, Cancer Innovation Laboratory, Center for Immuno-Oncology, Developmental Therapeutics Branch, Experimental Immunology Branch, Genetics Branch, Genitourinary Malignancies Branch, HIV and AIDS Malignancy Branch, Immune Deficiency Cellular Therapy Program, Laboratory of Biochemistry and Molecular Biology, Laboratory of Cancer Biology and Genetics, Laboratory of Cell and Developmental Signaling, Laboratory of Cell Biology, Laboratory of Cellular and Molecular Biology, Laboratory of Cellular Oncology, Laboratory of Genome Integrity, Laboratory of Human Carcinogenesis, Laboratory of Integrative Cancer Immunology, Laboratory of Molecular Biology, Laboratory of Pathology, Laboratory of Receptor Biology and Gene Expression, Lymphoid Malignancies Branch, Mouse Genetic Program, Neuro-Oncology Branch, Pediatric Oncology Branch, Radiation Oncology Branch, Surgical Oncology Program, Thoracic and GI Malignancies Branch, Thoracic Surgery Branch, Urologic Oncology Branch, and the Women's Malignancies Branch. In FY25, the Core has managed over 2,500 iLab requests and processed more than 50,000 samples to include 13,530 samples for Sanger sequencing, 180 for NanoString, 8,989 for ddPCR, 6,502 for TapeStation and 406 for Qubit. The Core has been involved in 242 different NGS projects featuring the iSeq, MiSeq, and NextSeq 2000 platforms. Projects include 10X single cell sequencing, Takara Shasta Single Cell System, bulkRNA-Seq, small RNASeq, amplicon sequencing, ChIP seq, HiChIP, ATAC-seq (bulk and single cell), CutandTag, NS-Seq, END-SEQ, CRISPR screens, Hi-C and custom library sequencing. 6 NanoString GeoMx DSP spatial profiling projects were also performed using both human and mouse Whole Transcriptome Atlas and GeoMx protein assay for NGS. The Core continued to further develop applications on the ONT long read platforms processing more than 20,000 samples. Long-read projects included bacterial whole genome sequencing, amplicon sequencing, single-cell RNAseq, and whole plasmid sequencing. This year the Core provided sequencing support for the FiberSeq assay, in which the long read capabilities and direct base modifications of the ONT platform were used to examine the chromatin architecture and regulatory elements at the single molecule level. Outreach efforts of the core facility have included active membership in the NIH Single Cell Interest Group, participation in CCR-FYI Colloquium, Staff Scientist and Principal Investigator Retreats, as well as the annual meetings of the ABRF and the AGBT. In April, the Core held its Annual Core Open House in cooperation with the CCR Mass Spectrometry Resource, which highlighted the cutting-edge technologies and expertise available from over 30 cores from both Bethesda and Frederick campuses. Core staff contributed to professional development by presenting at the SSC/SC Professional Development Day, CCR Collaborative Bioinformatics Resource Project and Technology Development meetings, providing support for the NCI Bioinformatics Training and Education Program (BTEP) initiatives, and co-leading workshops on Long-Read Technologies in partnership with ONT. Multiple Core sponsored seminars were held including ONT on updates to its technology and expanding applications, and NanoString nCounter Building on RNA Content with protein confirmation. Core staff also organize the long-read analysis community discussion group, a group of over 40 NCI bioinformaticians interested in the analysis of long-read technologies. Other activities include regularly scheduled meetings with Spatial Imaging Technology Resource (SpITR), NCI CCR Sequencing, Genomics, and Single Cell Analysis Facility Core heads. Staff attended and participated in presentations from Element Biosciences on next generation multiomics, Ellis Bio on Ultra-fast bisulfite conversation kit, BioQule NGS System for low-throughput library preparation, Roche SBX (Sequencing by Expansion) on its novel single-molecule sequencing technology, Illumina's Innovation Roadmap and Discovery Day, and Quantum-Si: Single-Molecule Protein Sequencing Solutions. The Core has been in discussion with Element on the AVITI system to learn more about the capabilities of these bench-top sequencers and continues to explore Pixelgen Technologies' approach to examine cell surface proteins at the single cell level. This fiscal year, Core members co-authored three peer-reviewed publications and were acknowledged in 29 others featuring work and data produced at the facility. Core members were also recognized with Federal Technology Transfer awards for their efforts to deliver cutting-edge long read and other advanced genomics technologies to the CCR. The Core received a Gold-Level NIH Green Labs Program (GLP) Certificate, reflecting commitment to sustainable lab practices, and was featured in the June 2025 "Core Corner" in the CCR Staff Scientist and Staff Clinician newsletter The Dossier, highlighting our services offered, innovative efforts and institutional contributions.