CCR Genomics Core

The CCR Genomics Core is located in Building 41 on the NIH Bethesda campus. The primary goal of the Core is to provide investigators from CCR/NCI and other NIH Institutes access to genomic technologies and Next-Generation Sequencing (NGS) with rapid turnaround on smaller-scale projects or projects that are not ready for production. The Core is unique in granting user-accessible instrumentation. Additional resources include training, consultation services, bioinformatics support, and secure data delivery/management. We also provide DNA and RNA quality control (QC) services. The facility operates on a cost-recovery model for project-based expenses.

Established Technologies and Applications

Next-Generation Sequencing

Illumina iSeq, MiSeq, and NextSeq 2000

• Cancer panel sequencing
• Microbiome sequencing (16S rRNA)
• T-Cell and B-Cell receptor sequencing
• RNAseq
• Amplicon sequencing

Discuss your experimental design with the Core experts and a group of CCR bioinformaticians. Library preparation may be performed by the Core, or by individual users.

Nanopore Sequencing

Oxford Nanopore MinION (MinIT and MK1C instruments) and P2 Long-read sequencing of both DNA and RNA

Sanger Sequencing

2-3500xL Applied Genetic Analyzers

• Rapid and accurate sequencing of DNA samples
• Expertise in the use of software for sequencing data
• Troubleshooting sequencing reactions

Samples are accepted in which sequencing reactions are completed by the user, as well as samples in which the sequencing reactions and clean-up are performed by the core.

Whole Plasmid Sequencing 

Performed using long-read technology from Oxford Nanopore Technologies

Obtain full length consensus plasmid sequence without the use of primers

Analytical & Preparative Electrophoresis

Sage Science PippinHT- high-throughput sizing

Agilent 4200 & 4150 Tapestation – QC platform

RIN values

Droplet Digital PCR

Bio-Rad QX 200 AutoDG ddPCR System

• Absolute quantification of target DNA, including measurements of viral loads and microbial quantification
• Detection of copy number variations and rare mutations in wild type backgrounds
• Absolute quantification of mRNA and miRNA, especially in low species
• Quantification of NSG libraries

The system includes an Automated Droplet Generator (ADG) that generates 20,000 droplets from one ddPCR reaction containing your target or background DNA. Hydrolysis probes (Taqman) or EvaGreen chemistry can be used on the system. After PCR the samples are transferred to a QX 200 Droplet Reader where individual droplet intensities are read. Contact Core staff to schedule project consultation, training, and access to instrumentation.

• Pathway expression profiling
• miRNA profiling
• Validation of complex gene expression signatures
• Validation of RNA-Seq and array data CNV analysis
• Performed directly on total RNA (no RT, IVT, and PCR) or lysates from a wide variety of sample types including (cells, tissues, FFPE, and blood).

The assays are designed to measure up to 800 targets in a single reaction. The platform processes 12 samples simultaneously.

Digital Spatial Profiling of RNA and Proteins

NanoString GeoMx Digital Spatial Profiling (GeoMx DSP) offered in collaboration with the Collaborative Protein Technologies Resource (CPTR)

• FFPE or fresh frozen tissue Profiling data for 100s of validated proteins
• Cancer Transcriptome Atlas (CTA) > 1,800 genes
• Whole Transcriptome Atlas (WTA) > 18,000 genes

The Core has a dedicated bioinformatic consultant who advises customers on experimental design, interpretation of QC data and directs users to existing bioinformatic tools and other available bioinformatic entities.