CCR Genomics Core

Division Of Basic Sciences - Nci

Investigators

Linked publications & trials

Abstract

CCR Genomics Core lists over 700 registered members in its iLab management and scheduling software. So far in FY22 there are 410 active users; 166 research groups of which 134 are from NCI and the remaining 32 from 9 other NIH institutes. These institutes include NEI, NHGRI, NHLBI, NIA, NIAID, NIA, NIAID, NIAMS, NICHD, NIDDK and NINDS. Of the 45 labs/branches/programs listed under CCR 38 utilize our services (84%). Those labs include: Basic Research Laboratory, Cancer Data Science Laboratory, Cancer Innovation Laboratory, Developmental Therapeutics Branch, Experimental Immunology Branch, Experimental Transplantation and Immunotherapy 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 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, Mouse Cancer Genetics Program, Neuro-Oncology Branch, Pediatric Oncology Branch, Radiation Biology Branch, Radiation Oncology Branch, Surgery Branch, Surgical Oncology Program, Thoracic and GI Malignancies Branch, Thoracic Surgery Branch, Urologic Oncology Branch, Vaccine Branch, Women's Malignancies Branch and the Office of Science Technology Resource. Core instrumentation and services include: Sanger Sequencing (2 ABI 3500xL and 1-3730 xL DNA sequencers). The Core prepares the sequencing reaction or the user can provide their own sequencing reaction. Data are typically analyzed and made available within one business day. Illumina Next-Generation Sequencing (1-iSeq, 1-MiSeq, 2- NextSeq550, 2- NextSeq2000)- Researchers meet with the core prior to discuss the best experimental designs, costs, turn-around time and data analysis needs and submit pre-made libraries or purified DNA/RNA for library construction and subsequent sequencing. Samples we had sequenced includes 10X single cell sequencing, full plasmid sequencing, ChIP-Seq, RNA-Seq, amplicon sequencing, ATAC-Seq, END-Seq, and targeted panel sequencing. Nanopore Sequencing (Oxford Nanopore MinION, MinIT, MinION Mk1C). A sequencing technology that generates ultra-long reads, some of them more than 100kb. Here, single DNA (or RNA) molecules are sequenced without the need for PCR amplification. Digital Gene Expression (Nanostring nCounter Analysis System). Direct quantification of individual mRNAs in a biological sample without the use of enzymes or amplification. NanoString designs each CodeSet and then investigators bring their samples to the core to be processed. Digital Droplet PCR (Bio-Rad QX200 Droplet Digital PCR System). This technology is the absolute quantification of a PCR reaction. Customers bring prepared samples in a sealed plate ready to be applied to Automatic Droplet Generator. Results are usually available within 24 h. Data analysis software is available for use on customers' own computer. DNA/RNA & Library QC (Agilent TapeStation 4150 & 4200, Fragment Analyzer, QuantStudio RT-PCR system, Pippen HT Pippin HT (spelling)). Every sample submitted to the Genomics Core for sequencing undergoes a variety of quality control (QC) procedures to verify the integrity of samples, and to ensure that every sequencing run produces the best quality data possible. QC is also performed for customers submitting samples to the Sequencing Facility in Frederick or outside vendors. Digital Spatial Profiling (NanoString GeoMx DSP). This platform combines spatial and molecular profiling technologies by generating digital whole transcriptomes and profiling data. This technology is offered in collaboration with the Collaborative Protein Technology Resource (CPTR). In addition, the CCR Genomics Core functions as a support lab, containing instruments for various applications for use by CCR investigators. The Core has several robotic liquid handlers to include the Agilent Bravo and the Formulatrix. Analytical software for the various technologies is also made available. So far in FY22, the Core has managed over 3,500 iLab requests and processed over 17,000 samples for Sanger sequencing, 516 for Nanostring, 8985 for ddPCR and 11,703 for tapestation. The Core has been involved in over 368 different NGS projects featuring the MiSeq, NextSeq 550 and 2000 platforms. Projects included 10X single cell sequencing, full plasmid sequencing, ChIP-Seq, RNA-Seq, amplicon sequencing, ATAC-seq, END-SEQ, and targeted panel sequencing amongst others. The NanoString GeoMx DSP is our newest platform that continues to advance. This new spatial profiling technology is being offered through a cooperation with the CPTR under Dr. Noemi Kedei and relies heavily on each Core's expertise. Workflows are now being offered for NGS utilizing NanoString's newest releases of the Cancer Genomics Atlas (CTA, 1800 genes) and the Whole Transcriptome Atlas (WTA, 18,000 genes). The CPTR and the GC are presently working with 7 investigators on DSP projects. Thus far, 9 nCounter and 26 NGS (23 CTA and 3 WTA) runs have been performed on the DSP. Our work with Dr. Chen Zhao, M.D. in the Thoracic and GI Malignancies Branch has resulted in a recent manuscript currently in accepted in Journal for ImmunoTherapy of Cancer. The two Cores are continuing to work on off-instrument data analysis and storage, which is an important area for further development. Toward this end, the Cores are in discussion with both the CCR Collaborative Bioinformatics Resource and NCI Center for Biomedical Informatics & Information Technology (CBIIT) to establish standardized data workflows to ease the burden on individual PI laboratories. In addition, the Core collaborates with NCI investigators on the long-read technology utilizing the Oxford NanoPore MinION. Outreach efforts of the core facility have included active membership in the NIH Single Cell Interest Group, virtual 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. In in lieu of Annual Core Open House, the Core in cooperation with CPTR put together a NCI Core Resource Guide which was posted to CCR Central of more than 20 Cores from Buildings 37, 41 and Frederick. Three vendor Core-sponsored virtual seminars were held, one with Fisher Scientific on online tools for CRISPR-CAS9 gene editing, Illumina on Liquid biopsy using RNA, and Nanostring on exploring spatial biology. The Core also held demos on the I.DOT liquid dispenser and the Absolute Q digital PCR system from Thermo Fisher. As we are open-access Core it is not a requirement that we be collaborators for investigators to use our facility nor do we ask that our names be included as authors on publications. We do ask that users acknowledge the facility if they use data generated from the Core in a publication, but we do not require it. Overall, the CCR Genomics Core was acknowledged in 5 peer reviewed publications with co-authorship of Core members in 6 manuscripts in this review period.