UNC’s home of long-read sequencing
SUBMISSION/DROP-OFF DEADLINES:
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The Vironomics core is a core facility tailoring our resources to fit your individual project. We feature NGS instruments with unique capabilities, such as long-read sequencing, Sanger sequencing and ThermoFisher Oncomine an targeted assays
The Vironomics Core is led by our Principal Investigator, Dr. Dirk Dittmer, and includes several research staff. Our facilities are located on the 1st floor of the Lineberger Cancer Center (wing parallel with West Dr). The main research focus of the Dittmer lab is understanding viral tumorigenesis, especially that associated with Kaposi’s Sarcoma Herpesvirus (KSHV).
The Vironomics core operates all assays under good clinical laboratory practices (GCLP), which means we can generate information to support clinical trials and to support FDA approval, but cannot generate information that is reported back to the patient, or be used in treatment decisions.
Assays & Services
Long-Read NGS Sequencing
The Vironomics Core facilitates research using long-read sequencing. The sequencers in the core are ideal for longer DNA fragment sequencing. Many clients use the longer reads for large genomes, de novo sequencing, 16S sequencing, long amplicons, etc. Customization is available, or take advantage of the current expertise in whole genome sequencing (WGS), de novo assembly, STR cell line verification, targeted amplicon sequencing, plasmid verification, strand-specific RNAseq, and exome sequencing.
The PacBio SeqIIe instrument is capable of long, long reads up to 100,000 bp, although the average is between 5,000 to 20,000 depending in DNA quality. We offer the complete range of PacBio assays.
The PacBio Sequel IIe long-read sequencer at UNC provides a unique and essential capability for genomic research. Its ability to generate reads between 6,000 and 20,000 base pairs fills a critical gap in the university’s sequencing infrastructure, enabling the generation of complete genomes rather than limited exome sequences. This is particularly beneficial for the detection of DNA translocations and repeat contractions across diverse organisms, including human, murine, viral, and bacterial genomes. Furthermore, the instrument’s capacity to sequence complete mRNA transcripts using new chemistry allows for the direct identification of spliced isoforms and splice junctions, a significant improvement over inferences drawn from short-read data. Crucially, PacBio’s HiFi sequencing technology delivers high base call accuracy (≥Q30) and consensus quality, surpassing that of Oxford Nanopore. This elevated accuracy is paramount for the analysis of clinical samples and addresses the NIH’s stringent requirements for rigor, robustness, and reproducibility in scientific investigations. Therefore, the PacBio Sequel IIe is indispensable for advanced genomics research at UNC.
The Applied Biosystems genetic analyzers is capable ideal for orthogonal validation. This Sanger sequencing instrument is easy to use across a broad range of applications, including de novo, targeted, and plasmid Sanger sequencing, CRISPR-Cas9 genome editing confirmation, cell line authentication, and detection of single nucleotide polymorphisms (SNPs). Setup is simple and you will be ready to go in minutes. The SeqStudio Genetic Analyzer offers data quality, usability, service, and support at an affordable price.
The Ion GeneStudio S5 is capable of up to 400bp read lengths and has a maximal output of 130 million 200 bp reads in 12 hours or 4 human exomes per day.
qPCR and Digital PCR
The Vironomics Core currently provides real-time qPCR assays for viruses and miRNAs profiling, such as KSHV, EBV, HSV-1, RRV, HCMV, and miRNAs. The unique automated robotics also enables them to offer custom and commercial real-time PCR assays to clients. The Vironomics Core uses several automated robotic systems for large-scale real-time PCR. A Tecan Freedom Evo© is used to set up reactions in a 384-well plate, which is then run by the QuantStudio Q7 with 4 color multiplexing. This is a fast and effective way to amplify samples with RT-qPCR and qPCR.
We offer digital PCR on the Applied Biosystems QuantStudio Absolute Q Digital PCR System