Genetics and Genomics | Core Facilities

Contents

1 Genotyping
- 1.1 Functional Genomics Core
- 1.2 Mammalian Genotyping Core
2 Expression Analysis
3 Sequencing
4 Genetic Screening
- 4.1 UNC CRISPR Core
5 Other Genomics
- 5.1 Bioinformatics and Analytics Research Collaborative (BARC)
- 5.2 Clinical Genomic Analysis (GENYSIS) Core

Genotyping

Functional Genomics Core

Functional Genomics Core performs expression profiling and SNP genotyping (Affymetrix) services. We currently have Beckman Coulter’s Biomek® FXP Target Prep Express robot and the GeneTitan Instrument from Affymetrix which allow the processing of hundreds of microarray samples in a week, and processing of high throughput expression peg arrays and Axiom genotyping high throughput peg arrays. Also, we have the Affymetrix GeneChip® Scanner 3000 7G Plus Targeted Genotyping System in the Core. It has the ability to scan all research arrays manufactured by Affymetrix including the high density expression arrays which place an entire genome on one GeneChip®. This equipment includes 2 Fluidics Station 450s and the GeneChip® Hybidization Oven 645.

Mammalian Genotyping Core

Mammalian Genotyping Core provides services using any of the Illumina microarrays (BeadChips) for genotyping, CNV analysis, or DNA methylation.

Expression Analysis

Center for Gastrointestinal Biology and Disease (CGIBD): Advanced Analytics Core

The CGIBD Advanced Analytics (AA) Core provides bulk and single-cell genomic and proteomic analysis, high-throughput qPCR, and cost-effective immunoassays. The AA Core offers turn-key research solutions – bring us samples, we send you processed data. Each project begins with an initial consultation to discuss experimental design and feasibility. Users receive their results electronically after work has been completed and can track the progress of their projects via cloud-based reports. The AA Core also offers assistance with end-user data analysis.

Functional Genomics Core

Vironomics Core

The Vironomics Core facilitates research at UNC by performing large-scale real time quantitative PCR reactions, amplicon generation, and ~200-600bp next generation sequencing. This is accomplished using Ion Torrent S5, companion Ion Torrent Chef, and robot-assisted PCR in 96 and 384 well format.
The Vironomics Core currently provides several real-time qPCR arrays for viruses and miRNAs profiling including: KSHV, EBV, HSV1 and HSV2, RRV, HCMV, NFkappaB, Pre-miRNA, and P53response12. The unique automated robotics also enables the Vironomics Core to offer custom and commercial real-time PCR assays to clients.
The Vironomics Core uses several automated robotics for the 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 Roche Lightcycler 480 II^©. This is a fast and effective way to amplify samples with RT-qPCR.

Immune Monitoring and Genomics Facility

The Immune Monitoring and Genomics Facility (IMGF) provides investigators with cellular immunology, molecular immunology, and immunogenomics services that can delineate interactions between the immune system and tumor tissues. The IMGF focuses on clinical trial correlative research studies but supports basic research studies as well. These studies include both FDA-approved government and industry-sponsored research.

Sequencing

High-Throughput Sequencing Facility

The High-Throughput Sequencing Facility applies the tools of high throughput sequencing technology to enrich cancer research of UNC scientists. High throughput sequencing is an extremely fast developing technology, used in many applications such as genome sequencing, genome re-sequencing, chip-seq, cDNA sequencing, digital expression, and microRNA abundance.
The HTSF is a full-service sequencing facility that offers multiple platforms and several different state-of-the-art techniques to assist with genetic and genomic research. These platforms available include: Illumina’s MiSeq, HiSeq2500 and HiSeq 4000, Ion Proton and PacBio RSII.
Genomic sequenced-based applications include: complete genome re-sequencing including for comprehensive polymorphism and mutation discovery in individual genomes; targeted genomic re-sequencing including for targeted polymorphism and mutation discovery; ChIP-seq (Chromatin immunoprecipitation-sequencing) for genome-wide mapping of protein-DNA interactions; small RNA sequencing; transcriptome sequencing for quantification of gene expression and alternative splicing, transcript annotation, and discovery of transcribed SNPs or somatic mutations; sequencing of bisulfite-treated DNA for the determination of the presence of methylated DNA; and metagenomic sequencing. The HTSF uses several automated robotic platforms for large-scale library preparation to ensure the reproducibility and quality of library preps. The new HTSF Research & Development group will work with investigators to develop new applications for high-throughput sequencing and providing opportunities for testing library prep kits in a beta stage of development and evaluating new sequencing or genome mapping technologies.

Translational Genomics Lab

The UNC Lineberger Comprehensive Cancer Center Translational Genomics Lab (TGL) is a medium throughput facility providing comprehensive genomic services for investigators by employing Next Generation Sequencing (NGS) and NanoStringTM technologies. In addition, TGL can produce single-cell gene expression libraries using the 10X platform. The mission of TGL is to support translational human cancer genomics research at the University of North Carolina – Chapel Hill. The TGL facility performs sample processing and analyses for the molecular, pathologic, and genomic characterization of patient-derived specimens in preclinical research projects and clinical protocols. Our laboratory employs highly-automated, as well as manual, platforms for reproducible medium-throughput nucleic acid extraction, library preparation, and next-generation sequencing of tissue, cells, and blood samples. Our goal is to provide a resource that balances rigor and flexibility to meet the needs of academic and clinical research, and that can ultimately produce optimized and validated processes for adoption in clinical labs.

UNC Microbiome Core Facility

UNC Microbiome Core Facility provides the research community within the UNC School of Medicine and the state of North Carolina with the facilities and expertise to characterize complex microbial communities in a variety of environments. The Microbiome Core offers comprehensive services for microbiome analysis that include experimental design, isolation of nucleic acids (DNA/RNA), barcoding, library preparation and sequencing using the appropriate Illumina or Life Sciences platform, and bioinformatics analysis. Other services offered by the Core include: quantitative and digital PCR, creation of clone libraries, strain typing, optimization of bacterial culture conditions, and high-throughput liquid handling (PCR reaction set up, sample pooling, picogreen quantification of nucleic acids).

UNC NORC Genomics and Energy Metabolism: Nutrigenomics Core

The nutrigenomics component of the Genomics and Energy Metabolism (GEM) Core offers laboratory services as well as customized, cutting-edge research tools, including 1) whole genome, exome, and targeted gene sequencing; 2) RNA-sequencing; 3) targeted genotyping using PCR-based assays; 5) array-based gene expression profiling; 6) and bisulfide sequencing for methylation patterns in humans and mouse models. The Core provides investigators with the expertise and resources necessary to investigate the role of host genetic factors in biological responses to nutritional exposure. The mission of the Core is to provide a suite of precision nutrition services that enable investigators to integrate nutrigenomics into nutrition and obesity research to advance our understanding of how individual genetics influence individual variability related to nutritional exposures and adiposity.

Vironomics Core

The Vironomics Core performs next generation sequencing using Ion Torrent S5 and companion Ion Torrent Chef and by performing large-scale real time quantitative PCR reactions (please see expression analysis section).

Genetic Screening

UNC CRISPR Core

The CRISPR Screening Facility provides:

Arrayed Screens which includes: Consultation on screen design, benchmarks, and objectives, high quality CRISPR sgRNA arrayed into 96-well or 384-well format, automated assay with in-house robotics, individual acquisition and analysis for each target gene, and deliverable: high quality data sets for individual genes.

Pooled Screens which includes: Consultation on screen design, benchmarks, and objectives, high quality whole mammalian genome CRISPR sgRNA validated pools, assay run by our experienced team, or PI can choose to run assay in their lab, isolation of ‘hit’ genes, next generation sequencing and bioinformatics, and provides as a deliverable: rank list of genes identified in screen

Other Genomics

Bioinformatics and Analytics Research Collaborative (BARC)

The Bioinformatics and Analytics Research Collaborative (BARC) at the University of North Carolina at Chapel Hill is a multi disciplinary center that aims to provide bioinformatics expertise and analysis to researchers across the university and beyond for high throughput data. We analyze, visualize, interpret, and manage genomic data while also offering custom solutions to fit our researchers’ needs. Additionally, the center strives to educate researchers on current tools and techniques, foster a collaborative environment by hosting workshops, working groups, and seminars, and improve existing tools and/or invent new tools and algorithms.

We offer a free initial consultation during which we discuss the client’s project and how to ensure they are able to maximize the information that they learn. Afterwards, depending on the scale of the project we provide services by the hours or staff for grant for projects longer than six months. Each project is assigned to a project coordinator and bioinformaticist. The project coordinator is the point of contact for the client and is responsible for updating them on the status of their project.

Clinical Genomic Analysis (GENYSIS) Core

The Clinical Genomic Analysis (GENYSIS) Core collaborates with other core facilities on campus to provide clinical researchers support with analyzing genomic data. Specifically, the GENYSIS Core can provide bioinformatics support by performing human genome alignment of sequence data generated from the HTSF (or other sequencing center) and variant calling via a custom in-house pipeline and variant analysis by correlation with participant phenotypic data, and analysis of called variants by highly trained staff. Reportable variants are discussed at a weekly meeting attended by MDs, PhDs, and genetic counselors. Additionally, the core can generate clinical-grade test report for the variants clinically confirmed in the MGL that can also be uploaded to Epic if the participant is a UNC patient and provide post-test services such as assisting the study, clinician, participants, and their family, including reviewing results, providing educational resources, and identifying appropriate clinical follow-up.