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 genome sequencing, RNA sequencing, metagenomics and amplicon 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 in support of both clinical and basic science projects.
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
  • CLIA certified genome sequencing with secondary findings test
  • 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 latest high-output sequencer from Illumina. The standard run type on this instrument is paired-end 2x150b reads, with additional flexibility to generate shorter read lengths as needed. Due to the high volume of sequence data output (1.5 to 25 billion read-pairs per run), this technology is primarily useful for projects requiring large numbers of reads, such as genome, single-cell or bulk RNA-sequencing.
  • Illumina MiSeq i100 - The latest low-output instrument from Illumina, the MiSeq i100 generates 5 to 100 million read-pairs per run. Read lengths vary from 2x50b to 2x500b making it a highly flexible instrument for short amplicon-based sequencing projects.
  • Illumina MiSeq - A small-scale benchtop sequencer primarily used for sequencing library QC prior to data runs on the NovaSeq X Plus.
  • Ultima Genomics UG 100 - The UG 100 is a cost-effective high-output short read sequencer. Single-end reads of ~100-400b can be used for a variety of data intensive sample types, like single-cell and genome sequencing. Illumina libraries can be converted to run on this instrument, or UG specific libraries can also be sequenced. Unique to this platform is ppmSeq, a method that generates reads with very low error rates, on the order of 1 in a million, and is therefore suitable for accurate detection of low frequency single-nucleotide substitutions.
  • Pacific Biosciences Revio - The PacBio Revio platform generates long read lengths while maintaining high consensus accuracy. 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 also detect base modifications. This platform can generate sequence reads that support (1) high-quality genome assemblies; (2) detection of variants and haplotype phasing; (3) characterization of full-length isoforms; (4) epigenomics and  (5) long-amplicon sequencing. For most applications, one SMRT cell/run generates 90-120 Gb of data and completes in ~30 hours.
  • Oxford Nanopore PromethION - The ONT platform can generate short to ultra-long reads (>100 kb) from DNA templates as well as sequencing data directly from RNA templates. Both DNA and RNA modifications can be detected with this platform. Typical projects that are run on this platform take advantage of the unique aspects of the technology, ie very long reads for genome assembly or structural variant detection, detection of base modifications, or the ability to directly sequence RNA. The amount of data generated per flowcell is dependent on the sample type, with ultra-long genome libraries typically yielding ~20 Gb of reads >100kb (~40 Gb total) while direct RNA libraries yield a few million reads averaging ~1 kb.

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

  • 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
  • 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
  • Leonardo Gomes de Lima, Andrea Guarracino, Sergey Koren, Tamara Potapova, Sean McKinney, Arang Rhie, Steven J Solar, Chris Seidel, Brandon L 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 Nature. 2025 Sep 24. doi: 10.1038/s41586-025-09540-8. Online ahead of print. 40993387
  • Diana M Proctor, Sarah E Sansom, Clay Deming, Sean Conlan, Ryan A Blaustein, Thomas K Atkins; NISC Comparative Sequencing Program; Thelma Dangana, Christine Fukuda, Lahari Thotapalli, Heidi H Kong, Michael Y Lin, Mary K Hayden, Julia A Segre Clonal Candida auris and ESKAPE pathogens on the skin of residents of nursing homes Nature. 2025 Feb 26. doi: 10.1038/s41586-025-08608-9. Online ahead of print. 40011766

Keywords

CLIAChIP seqDNA analysisDNA librariesDNA sequencingNGSNHGRINISCNational Human Genome Research InstituteRNA librariesRNA sequencingRNAseqbioinformaticsbisulfite sequencingcomparative vertebrate sequencingdeep amplicon sequencingepigeneticsGenetics and Genomicsgeneticgenomicshumanlibrary constructionlibrary preparationnext generation sequencingnextgen sequencingnih-corewhole exome sequencingwhole genome sequencing