CCR Genomics Core currently lists over 640 registered members through its iLab Management and scheduling software with 248 Principal Investigators of which 211 are from NCI. Of the 47 labs/branches listed under CCR, 32 utilize our services on a routine basis. Those labs include: Basic Research Laboratory, Cancer Inflammation Program, Dermatology Branch, Developmental Therapeutics Branch, Endocrine Oncology Branch, Experimental Immunology Branch, Experimental Transplantation and Immunology Branch, Genetics Branch, HIV and AIDs Malignancy Branch, HIV Dynamics and Replication, 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 Immune Cell Biology, Laboratory of Metabolism, Laboratory of Molecular Biology, Laboratory of Pathology, Laboratory of Protein Dynamics and Gene Expression, Laboratory of Receptor Biology and Gene Expression, Lymphoid Malignancies Branch, Neuro-Oncology, Radiation Biology Branch, Surgery Branch, Thoracic and Gastrointestinal Oncology Branch, Urologic Oncology Branch, Vaccine Branch, and Women's Malignancies Branch. The Core also provides services to investigators in the Clinical Center as well as 10 other NIH institutes including NIAID, NHLBI, NIDDK, NEI, NIAMS, NIMH, NINDS, NIAAA, NIA and NICHD. Available Core services include: Sanger Sequencing carried out using two ABI 16-capillary 3130XLs, one 96 capillary 3730XL. These instruments are capable of reading up to 800 base pairs with 95% accuracy. 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. Illumina Next Generation Sequencing is performed with two different platforms, the MiSeq Desktop Sequencer featured in the Core since 2012 and NextSeq 500 which was recently added. 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). NanoString Digital Gene Expression Analysis 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. Core charges range from $5/sample to $24/sample for NCI staff depending on what services and supplies are necessary. Non-NCI staff pays $24 to $48/sample. Bio-Rad QX200 Droplet Digital PCR System provides 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 $4/sample and $6/sample for NCI and non-NCI customers, respectively. Fluidigm C1 Single Cell Autoprep System for genomic analysis of single cells is an automated single-cell isolation and preparation system that provides an easy and reproducible workflow to process 96 single cells for genomic analysis including RNA-Seq, Whole Genome Amplification and sequencing and Gene Expression Profiling on Biomark HD qPCR. Customers contact the Core manager to schedule training and access to the instrument. The core also provides access to the Nexcelom Vision CBA image cytometry system to determine cell size, number and viability prior to C1single cell isolation. Subsidies for this new technology are provided by the OSTR. Agilent TapeStation 2200 allows 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 $3/sample to $4/sample for NCI staff depending on number of samples and what supplies are necessary. BioNano Genomics Irys System enables visualization of single-molecules of DNA for the direct observation and measurement of genome complexities. This system permits optical imaging of genomes for measuring insertions, deletions, inversions, and complex rearrangements in extremely long strands of DNA. Individuals meet with the Core and OSTR to discuss the best experimental designs and costs are offset by subsidies provided by OSTR. In addition, the CCR Genomics Core has Agilent BioAnalyzer and Qubit Fluorometric Quantitation available for use by any investigator that wants to use them. Bench space is furnished by the Core and the staff maintains a sign-up calendar on a first-come, first-served basis. So far in FY16, the Core has managed over 3525 iLab requests and processed 31, 235 samples for Sanger sequencing, 1712 for Nanostring, 4491 for ddPCR and 1426 for tapestation. The Core has been involved in 31 different NGS projects featuring the MiSeq. Partnerships with members in BRL, SB and GB continue with single cell isolation using the Fluidigm C1 with both the 96 well IFC and the new single-cell mRNA Seq HT workflow allowing isolation and processing up to 800 individual cells per run. The Core has also been working closely with Genomics Core at the Frederick National Lab to further develop the BNG Irys System into a true core service. Users thus far have used the Irys sytem to identify double strand break containing regions and DNA Repair. 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. In FY16 we had 36 requests totaling $47,495 in sales saving the NCI more than $17,000 in true cost. Without the program the amount of Big dye purchased would have cost over $68,000. The program is available for all investigators within CCR, even if they do not use the core for sequencing. Our users were asked to select the area of research for each submission to the core. There were over 92 different areas selected. The top 20 areas of research based on the number of total submissions for all platforms are: molecular biology, immunology, leukemia, genomics, biotechnology research, breast cancer - basic, microbial genetics, chemotherapy, infectious diseases, kidney disease - research, DNA repair, genetic diseases, sarcomas - soft tissue, liver cancer, ALS, hematology, aging, oncogenes, colon/rectum and gene mapping - human.
