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Principal Investigator: Elizabeth Conner
Organization: DIVISION OF BASIC SCIENCES - NCI
Fiscal Year: 2020
Award: $1,642,585
Funding agency: National Cancer Institute
CCR Genomics Core lists over 1040 registered members in its iLab management and scheduling software with 270 research groups of which 192 are from NCI and the remaining 77 from 13 other NIH institutes. These institutes include NIAID, NHGRI, NEI, NINDS, NHLBI, NIAMS, NIDDK, NIMH, NIA, NIAAA, NIDCD, NINCR, and NINR. Of the 54 labs/branches/programs listed under CCR , 33 utilize our services. Those labs include: Basic Research Laboratory, Cancer and Inflammation Program, Developmental Therapeutics Branch, Experimental Immunology Branch, Experimental Transplantation and Immunology Branch, Genetics Branch, HIV and AIDs Malignancy Branch, 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 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, Radiation Biology Branch, Radiation Oncology Branch, Surgery Branch, Thoracic and GI Malignancies Branch, Thoracic Surgery Branch, Urologic Oncology Branch, Vaccine Branch, Women's Malignancies Branch, Center of Advanced Preclinical Research, Comparative Oncology Program, NCI Rare tumor Initiative, NCI CCR Liver Cancer Program. Available Core services include: Sanger Sequencing is carried out using one 96 capillary 3730XL and two newly acquired 3500xL Genetic Analyzers, replacing two obsolete ABI 16-capillary 3130XLs. These upgraded instruments have increased read-length 800 base pairs, turn-around time with higher number of samples per run, improved data precision and maintains 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. Illumina Next-Generation Sequencing is performed with different platforms, the MiSeq Desktop Sequencer and 3 NextSeq 500/550 sequencers. 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. Under development in collaboration with the Collaborative Protein Technology Resource (CPTR) and soon to be a Core service is the NanoString GeoMx Digital Spatial Profiling platform. This new technology 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. 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 FY20, the Core has managed over 2600 iLab requests and processed 14,470 samples for Sanger sequencing, 264 for Nanostring, 3220 for ddPCR and 6802 for tapestation. The Core has been involved in nearly 200 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 FY20 we have had 23 requests totaling $31464 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 participation in CCR-FYI Colloquium, participation in Staff Scientist and Principle Investigator Retreats, as well as the annual meetings of the ABRF and AGBT. Staff also attended Nanopore Day and NHLBI/NICHD Genomics Symposium Long Read Sequencing Workshop held at the NIH. In addition, the Core annually organizes NCI Core Open House of more than 20 cores from Bldgs. 37 & 41 and Frederick in the Atrium of Bldg 35. The 4th Annual Core Open House was held in early October. The core continues to hold Vendor Office hours with Bio-Rad and NanoString on a quarterly basis. Two vendor Core-sponsored seminars were held, one with Tecan and the other Swift Biosciences on new applications. Other Core achievements have included acknowledgement in 4 manuscripts thus far in 2020 as well as Core members included as collaborators and authors on manuscripts when extensive collaborative efforts have been involved (Therapeutics and Prevention, 11(1): e02530-19, 2020) The Core Manager, Dr. Conner, also serves as the NCI Chair of the Occupational Safety and Health Committee. She completed the NIH Senior Leadership Program and was nominated for Technology Transfer Award for her many areas to introduce and develop new technologies to the entire CCR research community.
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