CCR Genomics Core

Division Of Basic Sciences - Nci

Investigators

Linked publications & trials

Abstract

CCR Genomics Core lists over 1800 registered members in its iLab management and scheduling software. So far in 2021 there are 450 active users; 172 research groups of which 142 are from NCI and the remaining 30 from 7 other NIH institutes. These institutes include NIAID, NEI, NINDS, NHLBI, NIDDK, NIA, and NIDCD. Of the 53 labs/branches/programs listed under CCR, 27 utilize our services. Those labs include: Cancer and Inflammation Program, Developmental Therapeutics Branch, Experimental Transplantation and Immunology Branch, Genetics Branch, HIV and AIDs Malignancy Branch, Laboratory of Biochemistry and Molecular Biology, Laboratory of Cancer Biology, Laboratory of Cancer Biology and Genetics, Laboratory of Cell and Developmental Signaling, Laboratory of Cell Biology and Genetics, 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 Metabolism, Laboratory of Molecular Biology, Laboratory of Pathology, Laboratory of Protein Dynamics and Signaling, Laboratory of Receptor Biology and Gene Expression, Laboratory of Tumor Immunology and Biology, Lymphoid Malignancies Branch, Neuro-Oncology Branch, Surgery Branch, Thoracic and GI Malignancies Branch, Thoracic Surgery Branch, Urologic Oncology Branch, Vaccine Branch, Center of Advanced Preclinical Research and NCI CCR Liver Cancer Program. Description of Core services: Sanger Sequencing is carried out using one 96 capillary 3730XL and two 3500xL Genetic Analyzers. The 3500xL instruments have increased read-length 800 base pairs, turn-around time with higher number of samples per run, improved data precision and maintain a 20% smaller footprint. Data are analyzed and made available within one business day. The current charges are $2.00 for electrophoresis only and $7.00 for the sequencing reactions, clean-up and electrophoresis. The Core also has a variety of bulk plate cost options including sets of 16 and full 96 well trays. Next-Generation Sequencing is performed with a variety of platforms: Illumina Desktop Sequencers iSeq and MiSeq, (3) NextSeq 550 sequencers and (1) NextSeq2000 and the Oxford Nanopore MinIon. Researchers can submit pre-made libraries or purified DNA/RNA for library construction and subsequent sequencing. The Core will also perform quality control (QC) on all libraries prior to sequencing. Individuals meet with Core members to discuss the best experimental designs and costs are offset by subsidies provided by the Office of Science and Technology Resources (OSTR). Digital Gene Expression Analysis is provided by the NanoString nCounter System. The nCounter system is capable of 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. The cost of the Codesets is subsidized by the OSTR for NCI, CCR investigators. Core charges range from $5/sample to $24/sample for NCI staff depending on what services and supplies are necessary. The cost for Non-NCI staff is $48/sample. Droplet Digital PCR is performed on a BioRad QX200 system absolute quantification of target DNA, including measurement of viral loads and microbial quantification; detection of copy number variations and rare mutations; absolute quantification of mRNA and miRNA and quantification of NGS libraries. Typically, after discussion with Core staff and if necessary BioRad for assay development, 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. Current costs $5/sample for NCI and non-NCI customers. Analytical and preparative electrophoresis is provided by Agilent TapeStation 4200 & 4150 and the Sage Science PippinHT. The Tapestation Systems allow for reproducible and user-independent quality control of DNA and RNA samples and libraries. QC services are provided to customers obtaining NGS services from our Core as well as the CCR Sequencing Facility at the Frederick National Laboratory. The Core charges range from $4/sample to $5/sample for NCI staff depending on number of samples and what supplies are necessary. The newer 4200 system allows for fully automated sample processing for up to 96 samples with results being obtained in as little as 1-2 minutes per sample, or less than 90 minutes for 96 samples while requiring only 1-2 uL of sample per run. The Sage Science PippinHT combines pre-cast agarose cassettes with a high-precision, automated solution for the accurate and targeted size-selection of DNA fragments for library construction in NGS workflows. Digital spatial profiling with the NanoString GeoMx Digital Spatial Profiling platform is offered in collaboration with the Collaborative Protein Technology Resource (CPTR). This newest platform provides high-plex and high-throughput spatial profiling of RNA or protein from a single FFPE section, enabling researchers to dissect the complexity of cellular interactions at a local level and facilitating novel discovery. Currently the cost is subsidized by the OSTR for NCI, CCR investigators. 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 FY21, the Core has managed over 3,300 iLab requests and processed 29,174 samples for Sanger sequencing, 348 for Nanostring, 7494 for ddPCR and 9606 for tapestation. The Core has been involved in over 250 different NGS projects featuring the MiSeq and NextSeq 500/550 platforms. The Big Dye Program where the Core purchases Big Dye in bulk discounted quantities and then aliquots it and sells it to Core users at cost continues to thrive and save the NCI money. Thus far in in FY21 we have had 20 requests totaling $11,364 in sales. The program is available for all investigators within CCR, even if they do not use the core for sequencing. 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 Principle 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. Two vendor Core-sponsored virtual seminars were held, one with Seqwell and the other NanoString on the GeoMx Digital Spatial Profiling technology applications. Other Core achievements have included acknowledgement in 6 manuscripts thus far in FY21 as well as Core members included as collaborators and authors on 3 manuscripts when extensive collaborative efforts have been involved. The Core Manager, Dr. Conner, continues to serve as the NCI Chair of the Occupational Safety and Health Committee. She is a member NCI Senior Lab Managers Group, a member of the NCI Reconstitution Committee and the cofounder of the NIH GeoMX DSP User Group.