CCR Genomics Core

Division Of Basic Sciences - Nci

Investigators

Linked publications & trials

Abstract

CCR Genomics Core lists over 600 registered members in its iLab management and scheduling software. So far in FY23 there are 427 active users; 176 research groups of which 136 are from NCI and the remaining 40 from 11 other NIH institutes. These institutes include NCATS, NEI, NHGRI, NHLBI, NIA, NIAID, NIAMS, NICHD, NIDCR, NIDDK and NINDS. Of the 44 labs/branches/programs listed under the CCR, 26 utilized our services in FY23 (60%). These lab/branches include: Basic Research Laboratory, Cancer Innovation Laboratory, Cancer for Immuno-Oncology, Developmental Therapeutics Branch, Experimental Immunology Branch, Experimental Transplantation and Immunotherapy Branch, Genitourinary Malignancies Branch, HIV and AIDS Malignancy Branch, Laboratory of Biochemistry and Molecular Biology, Laboratory of Cancer Biology and Genetics, Laboratory of Cell Biology, Laboratory of Cellular and Molecular Biology, Laboratory of Cellular Oncology, Laboratory of Genitourinary Cancer Pathogenesis, Laboratory of Genome Integrity, Laboratory of Human Carcinogenesis, Laboratory of Immune Cell Biology, Laboratory of Integrative Cancer Immunology, Laboratory of Molecular Biology, Laboratory of Pathology, Laboratory of Receptor Biology and Gene Expression, Lymphoid Malignancies Branch, Thoracic and GI Malignancies Branch, Thoracic Surgery Branch, Urologic Oncology Branch, Vaccine Branch, and the Women's Malignancies Branch. So far in FY23, the Core has managed over 3,200 iLab requests processed over 15,000 samples for Sanger sequencing, 311 for Nanostring, 8816 for ddPCR and 9822 for tapestation. The Core has been involved in 364 different NGS projects featuring the iSeq, MiSeq, NextSeq 550 and 2000 platforms. Projects included 10X single cell sequencing, full plasmid sequencing, ChIP-Seq, RNA-Seq, amplicon sequencing, ATAC-seq, Cut&Tag, NS-Seq, END-SEQ, custom library and targeted panel sequencing amongst others. A total of 6 NanoString GeoMx DSP spatial profiling projects were performed using both human and mouse Whole Transcriptome Atlas and the Cancer Transcriptome Atlas assays for RNA as well as GeoMx protein assay for NGS and a pilot using spatial proteogenomics assay. The latter workflow enables co-detection of RNA and protein from the same tissue slide with NGS as the readout method. The two Cores are continuing to work on off-instrument data analysis and storage, which is an important area for further development. The Core undertook two long-read projects with the M1KC both with direct RNA sequencing and developed a workflow for library prep, sequencing and assembly of plasmid constructs. The portfolio for long-read technology will soon be expanded with the addition of the PromethION 2 Solo. This device will allow for higher data generation than the small ONT devices. A single P2 flow cell can generate nearly six times more data than the MinION. Other upgrades will include the addition of QX600 Droplet Reader to our ddPCR service. QX600 device will enable six-color multiplexing allowing discrimination of multiple targets with assays that are cross-compatible with our current QX200 Droplet Digital PCR (ddPCR) System. 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, Genetics Branch Annual Retreat as well as the annual meetings of the ABRF and the AGBT. The Core held its Annual Core Open House, in cooperation with CPTR, in December of more than 30 cores from both Bethesda and Frederick campuses. Numerous core-sponsored webinars were held in collaboration with Sequencing Facility and the Genomics Technology Lab in Frederick and the Single Cell Analysis Facility to include Illumina seminars on single cell multiomics and spatial analysis, uncovering the molecular drivers of cancer with single-cell multiomics, Avida Bio (Part of Agilent) on their highly sensitive cfDNA assays and Oxford Nanopore and 10X on single cell sequencing. In addition, the Core held Office hours with both Nanostring and Bio-Rad. The core also held a several month demo of Qiagen's QIAcuity Digital PCR System to allow NCI investigators to compare experimental results between the Bio-Rad and Qiagen digital dPCR systems. Presentations on core capabilities were also given to the Bldg. 41 seminar series and to the CCR Staff Scientist group. Other activities include monthly meetings with CPTR, Lab of Pathology, and NIAID's Rocky Mountain Lab to discuss issues with NIH procured NanoString GeoMx DSP instruments and with NCI CCR sequencing, genomics, and Single Cell Analysis Facility Core heads. Core members were awarded Federal Technology Transfer Awards and acknowledged in 4 papers reporting on work produced from the Core that have been published in high-impact journals, including Cancer Discovery, Cell, Endocrine and Nature Communications.