SEQUENCING AND GENOMICS SHARED RESOURCE Sequencing and Genomics (SEQ) provides an integrated platform of technology, expertise, education, and infrastructure to create an accessible environment for LCCC researchers to undertake cutting-edge genomics projects. The Core specializes in six major technologies: Next Generation short-read sequencing (Illumina), long-read sequencing and genomic mapping (Oxford Nanopore Technologies, BioNano Inc.), NanoString digital RNA quantification, Affymetrix microarrays, Illumina bead array genotyping, and RNAi screening for functional validation. Through reciprocity with North Carolina State University, the SR also has access to the Pacific Biosciences Sequel system. These are complemented by LCCC investments in computational infrastructure and analysis. Over the past five years, LCCC has integrated two new units in partnership with TPF and CPDM to compliment SEQ, specifically to facilitate translational cancer genomics to seamlessly support the coordination, project management, and tracking necessary to perform genomics studies on patient samples from protocol-driven trials. In addition the Translational Genomics Laboratory (TGL) focuses solely on cancer sample preparation for downstream sequencing, NanoString analysis, or other molecular testing. This laboratory uses automated instrumentation and stable protocols optimized for limited input and degraded cancer specimens collected from clinical trials and translational studies. TGL initiates a pathway for clinical genomics projects through SEQ and subsequent analysis by the bioinformatics SR (BIOIN). SEQ SR requests $195,591, 3% of the total fiscal year 2019 budget. LCCC faculty were 43% of fiscal year 2020 users. During the past five years SEQ supported the LCCC investigators involved in TCGA. This project oversaw the molecular characterization of over 20,000 primary tumor and matched normal samples across 33 cancer types. Within the next year, SEQ will acquire an ONT PromethION 24 system, which uses a high- capacity, long-read sequencing technology capable of high production whole genome sequencing and transcriptomics. This technology allows for efficient resequencing of whole genomes including repetitive elements, structural variation, and other problematic regions of the genome. ONT sequencing provides reproducible detection of small, medium, and large size structural variations, and in the near future the detection of 5mC.

National Institute of Health (NIH)
National Cancer Institute (NCI)
Center Core Grants (P30)
Project #
Application #
Study Section
Subcommittee I - Transistion to Independence (NCI)
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
University of North Carolina Chapel Hill
Chapel Hill
United States
Zip Code
Curtis 2nd, Alan D; Jensen, Kara; Van Rompay, Koen K A et al. (2018) A simultaneous oral and intramuscular prime/sublingual boost with a DNA/Modified Vaccinia Ankara viral vector-based vaccine induces simian immunodeficiency virus-specific systemic and mucosal immune responses in juvenile rhesus macaques. J Med Primatol 47:288-297
Williams, Lindsay A; Nichols, Hazel B; Hoadley, Katherine A et al. (2018) Reproductive risk factor associations with lobular and ductal carcinoma in the Carolina Breast Cancer Study. Cancer Causes Control 29:25-32
Amunugama, Ravindra; Willcox, Smaranda; Wu, R Alex et al. (2018) Replication Fork Reversal during DNA Interstrand Crosslink Repair Requires CMG Unloading. Cell Rep 23:3419-3428
Little, Michael S; Pellock, Samuel J; Walton, William G et al. (2018) Structural basis for the regulation of ?-glucuronidase expression by human gut Enterobacteriaceae. Proc Natl Acad Sci U S A 115:E152-E161
Knott, Simon R V; Wagenblast, Elvin; Khan, Showkhin et al. (2018) Erratum: Asparagine bioavailability governs metastasis in a model of breast cancer. Nature 556:135
Anderson, Chelsea; Smitherman, Andrew B; Nichols, Hazel B (2018) Conditional relative survival among long-term survivors of adolescent and young adult cancers. Cancer 124:3037-3043
Liu, Meng-Xi; Jin, Lei; Sun, Si-Jia et al. (2018) Metabolic reprogramming by PCK1 promotes TCA cataplerosis, oxidative stress and apoptosis in liver cancer cells and suppresses hepatocellular carcinoma. Oncogene 37:1637-1653
Chai, Zheng; Zhang, Xintao; Rigsbee, Kelly Michelle et al. (2018) Cryoprecipitate augments the global transduction of the adeno-associated virus serotype 9 after a systemic administration. J Control Release 286:415-424
Butler, Kyle V; Chiarella, Anna M; Jin, Jian et al. (2018) Targeted Gene Repression Using Novel Bifunctional Molecules to Harness Endogenous Histone Deacetylation Activity. ACS Synth Biol 7:38-45
Zhang, Yang; Hwang, Bin-Jin; Liu, Zhen et al. (2018) BP180 dysfunction triggers spontaneous skin inflammation in mice. Proc Natl Acad Sci U S A 115:6434-6439

Showing the most recent 10 out of 1525 publications