The Genomics Technology Laboratory is an integrated, high-throughput molecular biology laboratory focusing on the development of genetics and genomics technologies, data analysis, and information management tools, in support of CCR Investigators. The laboratory develops integrated strategies using multiple technology platforms that maximize the value of research or clinical samples and lead to the identification of pathways, genes, or gene products involved in the development of disease, as well as the assembly of genetic or expression profiles for the identification of prognostic and diagnostic indicators. The laboratory also specializes in the development of custom genomics assays for quantitation and identification of specific molecules in complex clinical samples. GTL is operated by Leidos Biomedial Research Inc. on behalf of NCI as part of the Frederick National Laboratory.
Next Generation Sequencing
- Illumina NextSeq, MiSeq
- Whole exome capture using Agilent’s SureSelect or Illumina Truseq reagents
- Targeted sequencing for smaller custom gene panels or regions using capture or amplicon approach on Illumina such as NCI OncoVar panel
- ImmunoSEQ T-cell receptor sequencing using Adaptive Biotechnologies kit for TCR repertoire profiling for DNA samples, or SMARTer TCR a/b kit from Takara for RNA samples.
- CRISPR-Cas9 high-throughput screening pipeline or validation using NGS and ddPCR
- Retroviral integration site analysis for target genes or clonality analysis
- HTG EdgeSeq for extraction-free gene expression analysis for miRNA or targeted gene panels
- 16S Microbiome Pipeline: Automated fecal sample extraction, library preparation, normalization, and sequencing of MiSeq for bacterial 16S RNA gene.
DNA Assay/Mutation Detection/Methylation/Copy Number Analysis
- Global DNA methylation using Illumina 850K Epic array
- Targeted DNA methylation analysis using Qiagen Pyromark platform with bisulfite conversion, CpG methylation quantification
- Genome-wide copy number and LOH analysis for fresh and FFPE samples using Affymetrix OncoScan array
- SNP or mutation detection using Sanger or NextGen sequencing or ddPCR, or Illumina SNP array
- Droplet Digital PCR copy number variation assays for specific genes
- DNA extraction and QC
RNA Assay/Gene Expression
- NanoString nCounter platform for gene expression analysis on focused gene panels, such as miRNA, PanCancer Immune panels
- HTG EdgeSeq platform for gene expression analysis on focused gene panels, such as miRNA, PanCancer Immune panels, no RNA extraction needed.
- Digital Droplet PCR (ddPCR) for highly accurate absolute quantification of single gene(s)
- Low-cost global gene expression analysis on Affymetrix single cartridge arrays and high throughput formats arrays (96 sample/plate), including most common model system. Many options to choose from including 3’ array, Gene array, and Exon arrays.