The introduction of DNA sequencing instruments capable of producing millions of DNA sequence reads in a single run has profoundly altered the landscape of genetics and cancer biology. Complex questions can now be answered at previously unthinkable speeds and a fraction of their former cost. At the Sequencing Facility, researchers are provided access to the latest technologies, with consultation and Q&A services available throughout the design and execution of sequencing projects. SF is a CCR-dedicated facility open to all CCR Investigators. Dedicated capacity has also been established for NAID Investigators. This core is operated by Leidos Biomedial Research Inc. on behalf of NCI as part of the Frederick National Laboratory.
Established Technologies
We have two NovaSeq 6000, three NextSeq 500, two MiSeq, one 10X Genomics and PacBio Sequel technologies for our sequencing.
De Novo Sequencing
- Paired-end reads – Generate long scaffolds and contigs using multiple insert lengths
- Read length – Use paired-end reads in excess of 75 base pairs for mammalian-scale de novo assembly
Resequencing
- SNP discovery and confirmation
- Insertions and deletions (indels) and copy number variations (CNVs)
- Structural variant discovery
Transcript Profiling and Discovery
- Characterize splice variants, coding SNPs, and relative expression of transcripts
- mRNA-Seq, tag profiling, and small RNA analysis
- Measurement of alternative isoforms, discovery of novel structures and coding SNPs
Bisulfite Sequencing and DNA-Protein Interactions
- Detection of variations in methylation signatures at single-base resolution
- Sequencing of repetitive bisulfite-converted genomes using proprietary reversible-terminator chemistry
- CpG methylation, histone modifications, chromatin structure, or DNA-protein interactions
- Chromatin immunoprecipitation-paired sequencing approach (ChIP-Seq)
PacBio Sequel Sequencing
- Sequencing via single molecule, real-time (SMRT) technology allows rapid identification of long nucleotide chains.
- Read lengths averaging greater than 6,000 bases per molecule, with maximum read lengths > 30,000 bases, facilitate genome assembly and mapping of repetitive regions.
- Amplification-free direct sequencing of individual molecules precludes PCR bias and artifacts.
- Low-input Protocol developed by the Sequencing Facility enables sequencing of as little as 500 picograms of starting material for many applications.
- Minimal machine turnaround time provides flexibility in experimental and run design.
Developing Technologies
Single Cell Genomics
The Facility is actively working with CCR investigators to provide single-cell RNA Sequencing support following cell isolation and processing using either the 10X Genomics, Fluidigm C1 or Cellular Research’s WTA Precise Assay.
User Guidelines
SF services are available to all CCR and NIAID Investigators. Excess capacity can be made available to other NCI and NIH Investigators on a case-by-case basis. To request services from this CCR core facility, you must submit your requisition through NAS. Prior to filling out the proposal, you are advised to consult with Bao Tran (SF Director) and Maggie Cam to discuss your project design and bioinformatics approach to data analysis.