NATIONAL CANCER INSTITUTE - CANCER.GOV

Contact Information

Primary Contact

Jim Thomas
Group Director

Location

5625 Fishers Lane
Room 5S-16
Rockville, MD 20852

Overview

NISC’s role within NHGRI, and more broadly across NIH, aims to advance genome sequencing and its many applications, with a goal not simply to produce sequence data, but to produce the infrastructure required to bring genomic sequence to biology and medicine. We accomplish this by meeting with each NIH investigator to discuss the details of their project to determine which method(s) would work best. The most common types of sequencing projects include whole exome sequencing, RNA sequencing, custom capture sequencing, CHiP-seq, and whole genome sequencing. However, we are always interested in exploring new methods and expanding our repertoire in this rapidly changing field. We also work closely with other investigators across the NHGRI Intramural Research Program to develop novel methods to analyze genomics data with applicability to clinical and basic science questions that were thought to be intractable only a few years ago.
List of Services
  • Whole genome sequencing (Eukaryotic and microbial) – FAQ
  • Bulk RNA-Seq – FAQ
  • Whole Exome sequencing analysis – FAQ
  • Single-Cell RNA-Seq – FAQ
  • ChIP-Seq – FAQ
  • Amplicon sequencing
  • Custom capture projects – FAQ
  • Library Construction – NISC has a highly skilled library construction group able to make a wide range of libraries compatible with all of our sequencing platforms. You deliver high-quality DNA or RNA, and we construct the library. We prefer to start a sequencing project at this point, which allows our experienced hands to control each step for optimal performance and ensure the highest rate of success at the end.
  • Data Return – The raw data from the sequencers is extensively processed, and data is evaluated for quality. For Illumina data, the general deliverable is fastq files which contain the base calls as well as sequence quality scores.

Major Instrumentation

  • Illumina NovaSeq X Plus - The NovaSeq X Plus offers scalable sequencing through multiple flow cell modules. The most cost-effective module is the 25B which produces ~8 Tb per flow cell or ~1 Tb per lane. Due to the extremely high quantity of sequence output, this technology is primarily useful for projects requiring a very large number of reads, such as whole genome, and multiplexed transcriptome experiments.
  • Illumina MiSeq - MiSeq is a small-scale benchtop sequencer. This instrument is compatible with any of the Illumina libraries described above. MiSeq produces reads up to 300 bases in length from a paired-end read run (2×300 b) with a yield of ~10 Gb. This capability is primarily useful for sequencing microbial genomes and amplicons.
  • PacBio Revio - The PacBio Revio platform generates long read lengths while maintaining high consensus accuracy and unbiased coverage. Multi-pass sequencing of both strands of the template is used to generate circular consensus (CCS) reads up to ~15-20 kb that can achieve accuracy > 99.9% (termed High Fidelity/HiFi reads) and detect base modifications. This platform can generate sequence reads that support:
    • High-quality assemblies from small bacterial genomes to diploid human genomes
    • Detection of variants and phasing haplotypes
    • Characterization of RNA including full-length isoforms, whole transcriptome analysis and annotation, full-length 16S, and single-cell transcript
    • Amplicons
    • Epigenomics
    • Metagenomics
For most applications, one SMRTcell generates 60-90 Gb of data and completes in ~30 hours.
  • Oxford Nanopore PromethION - The Oxford Nanopore platform is the newest and most rapidly evolving platform in our portfolio of sequencing technologies. Monitoring current fluctuations as native DNA or RNA molecules pass through nanopores, this approach has key advantages of being able to read ultra-long fragments (some > 1 Mb) and detecting modified bases without special library construction. Base calling is done in real time, making sequence data available right from the start of the run. DNA read accuracy, including modified base detection, is currently >99%. The primary uses of this technology to date at NISC have taken advantage of the ultra-long reads to detect large structural variants and create de novo genome assemblies. The amount of data generated per flowcell is dependent on the sample type, with ultra-long genome libraries typically yielding ~20 Gb of reads >100 kb (~40 Gb total). Other capabilities beyond whole-genome sequencing and detection of base modifications include direct RNA and full-length cDNA sequencing.

User Guidelines

The NIH Intramural Sequencing Center provides cost-recovery sequencing services to the NIH Intramural Community. 

Initiating A Project – If you are thinking about initiating a new sequencing project, please visit https://www.nisc.nih.gov/contact.cgi. After this form is submitted, we will set up a meeting with you to plan the best approach for your needs. Please note that our sequencing service is restricted to intramural investigators at the NIH. Human DNA samples will need to be properly consented and de-identified.

Publications

  • Leonardo Gomes de Lima, Andrea Guarracino, Sergey Koren, Tamara Potapova, Sean McKinney, Arang Rhie, Steven J Solar, Chris Seidel, Brandon Fagen, Brian P Walenz, Gerard G Bouffard, Shelise Y Brooks, Michael Peterson, Kate Hall, Juyun Crawford, Alice C Young, Brandon D Pickett, Erik Garrison, Adam M Phillippy, Jennifer L Gerton The formation and propagation of human Robertsonian chromosomes [Preprint]. 2024 Sep 26:2024.09.24.614821. doi: 10.1101/2024.09.24.614821. 39386535
  • Joseph W Palmer, Kyrene M Villavicencio, Misgana Idris, Ian J Baranyk, Nunaya Polycarp, Alex D Dawson, Dominique Weddle; NISC Comparative Sequencing Program; William J Pavan, Fabian V Filipp, Melissa L Harris Quiescence and aging of melanocyte stem cells and a novel association with programmed death-ligand 1 iScience. 2024 Sep 12;27(10):110908. doi: 10.1016/j.isci.2024.110908. eCollection 2024 Oct 18. 39351197
  • Pulak R Nath, Mary Maclean, Vijay Nagarajan, Jung Wha Lee, Mehmet Yakin, Aman Kumar, Hadi Nadali, Brian Schmidt, Koray D Kaya, Shilpa Kodati, Alice Young, Rachel R Caspi, Jonas J W Kuiper, H Nida Sen Single-cell profiling identifies a CD8bright CD244bright Natural Killer cell subset that reflects disease activity in HLA-A29-positive birdshot chorioretinopathy Nat Commun. 2024 Jul 31;15(1):6443. doi: 10.1038/s41467-024-50472-0. 39085199
  • Sean Conlan, Poorani Subramanian, Beatriz Plata Barril, Jung-Ho Youn, Pamela J Thomas, Sergey Koren, Gabrielle A Dotson, Morgan Park, Arang Rhie, Julie A Segre, John P Dekker, Adrian M Zelazny Whole-genome sequence of Mucor velutinosus NIH1002, a strain associated with disseminated disease Microbiol Resour Announc. 2024 Jun 20:e0006224. doi: 10.1128/mra.00062-24. Online ahead of print. 38899875
  • Pilar Alvarez Jerez, Kensuke Daida, Francis P Grenn, Laksh Malik, Abigail Miano-Burkhardt, Mary B Makarious, Jinhui Ding, J Raphael Gibbs, Anni Moore, Xylena Reed, Mike A Nalls, Syed Shah, Medhat Mahmoud, Fritz J Sedlazeck, Egor Dolzhenko, Morgan Park, Hirotaka Iwaki, Bradford Casey, Mina Ryten, Cornelis Blauwendraat, Andrew B Singleton, Kimberley J Billingsley Characterizing a complex CT-rich haplotype in intron 4 of SNCA using large-scale targeted amplicon long-read sequencing NPJ Parkinsons Dis. 2024 Jul 26;10(1):136. doi: 10.1038/s41531-024-00749-4. 39060285

Keywords

AcinetobacterAeromonasBACBacteriaCLIACaenorhabditis elegansChIP seqCitrobacterClostridiumCorynebacteriumDNA analysisDNA librariesDNA sequencingE.coliESTEnterobacterEnterococcusHelicobacterHydractiniaKlebsiellaMnemiopsisMoraxellaNGSNHGRINISCNational Human Genome Research InstituteNon-human primatesPantoaePlasmodiumRNA librariesRNA sequencingRNAseqRhesus macaqueSAGESchizosaccharomyces pombeStaphylococcusbacterial artificial chromosomesbatbioinformaticsbisulfite sequencingblack bearbutterflychickenchimpanzeecomparative vertebrate sequencingdeep amplicon sequencingdogepigeneticsexpressed sequence tagsGenetics and Genomicsflyfungusgeneticgenomicsgibbonhoneycreeperhorseflyhumanjellyfishlibrary constructionlibrary preparationmosquitomousenext generation sequencingnextgen sequencingnih-coreratserial analysis of gene expressionsquidtickwhole exome sequencingwhole genome sequencingzebrafinchzebrafish