CCR Genomics Core

The CCR Genomics Core is located in Building 37 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

MiSeq 100 plus, 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 GridION and PromethION 2 solo long-read sequencing of both DNA and RNA.

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 and QX600 ddPCR Systems

• Absolute quantification of target DNA, including viral load determination and microbial quantification
• Detection of copy number variations (CNVs) and rare mutations in wild-type backgrounds
• Absolute quantification of mRNA and miRNA, particularly for low-abundance targets
• Quantification of next-generation sequencing (NGS) libraries
• Advanced multiplex digital PCR using the Bio-Rad QX600 ddPCR System, which supports up to six-color detection for simultaneous quantification of multiple targets in a single reaction, increasing assay throughput and enabling more complex molecular analyses

The Core provides access to both the Bio-Rad QX200 AutoDG ddPCR System and the Bio-Rad QX600 ddPCR System for highly sensitive, absolute nucleic acid quantification without the need for standard curves. The QX200 system includes an Automated Droplet Generator (AutoDG) that partitions each ddPCR reaction into approximately 20,000 droplets containing target and background DNA or RNA. Hydrolysis probe (TaqMan®) and EvaGreen® chemistries are supported. Following PCR amplification, droplets are analyzed individually using the QX200 Droplet Reader to determine absolute target concentration.

The QX600 ddPCR System expands these capabilities by providing six-color multiplex detection, enabling simultaneous analysis of multiple DNA and RNA targets within a single reaction while maintaining the precision and sensitivity of droplet digital PCR. This platform is well suited for complex applications including multiplex gene expression analysis, rare variant detection, copy number analysis, pathogen detection, cell and gene therapy research, and biomarker studies.

Contact Core staff to schedule a project consultation, training, and access to the 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 Spatial Imagining Technology Resource (SpITR).

• 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.