ZIC BC 011623 (ZIC) | |||
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Title | CCR Genomics Core | ||
Institution | NCI, Bethesda, MD | ||
Principal Investigator | Conner, Elizabeth | NCI Program Director | N/A |
Cancer Activity | N/A | Division | CCR |
Funded Amount | $665,279 | Project Dates | null - null |
Fiscal Year | 2018 | Project Type | Intramural |
Research Topics w/ Percent Relevance | Cancer Types w/ Percent Relevance | ||
Aging (2.0%) Cancer (100.0%) Digestive Diseases (20.0%) Childhood Cancers (10.0%) |
Breast (30.0%) Cervical Cancer (10.0%) Childhood Leukemia (10.0%) Hodgkins disease (10.0%) Leukemia (10.0%) Liver Cancer (10.0%) Lung (20.0%) |
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Research Type | |||
Resources & Infrastructure Related to Biology Resources and Infrastructure Related to Detection, Diagnosis, or Prognosis |
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Abstract | |||
CCR Genomics Core lists over 1000 registered members in its iLab management and scheduling software with 325 research groups of which 267 are from NCI and the remaining 58 from 13 other NIH institutes. These institutes include NIAID, NHGRI, NEI, NINDS, NHLBI, NIAMS, NIDDK, NIMH, NIA, NIAAA, NIDCD, NINCR, and NINR. Of the 52 labs/branches listed under CCR, 35 utilize our services. Those labs include: Basic Research Laboratory, Cancer Inflammation Program, 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 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 Protein Dynamics and Signaling, Laboratory of Receptor Biology and Gene Expression, Laboratory of Timor Immunology and Biology, Lymphoid Malignancies Branch, Neuro-Oncology Branch, Radiation Biology Branch, Radiation Oncology Branch, Surgery Branch, Thoracic and Gastrointestinal Oncology Branch, Thoracic and Oncologic-Surgery Branch, Vaccine Branch, Women's Malignancies Branch, Center of Advanced Preclinical Research, and NCI Rare Tumor Initiative 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 two different platforms, the MiSeq Desktop Sequencer, NextSeq 500 and NextSeq 550 which was recently added to the Core. 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 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. 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 $5/sample for NCI and non-NC |