NATIONAL CANCER INSTITUTE - CANCER.GOV

Contact Information

Primary Contact

Colm O'hUigin
Head

Location

Building 37, Room 4140 B
37 Convent Drive
Bethesda, MD 20892

Additional Contacts

Jane Yuan
Experimental lab
Richard Rodrigues
Bioinformatics

Overview

The Laboratory of Integrative Cancer Immunology, Microbiome and Genetics Core (LICI-MGC) grew out of the former Genetics Core to meet the increasing need for sequencing and analysis of commensal microbiota within NCI and NIH. The MGC team specializes in:

  • Sample handling, purification of nucleic acids,  amplicon (16S and ITS) as well as shotgun metagenomic and transcriptomic sequencing
  • Bioinformatic processing and computational analysis of sequenced reads, taxonomic and diversity characterization  (for amplicon)
  • Genomic assembly of contigs, diversity and analysis of differential representation of genes, species, and metabolomic pathways (shotgun metagenomic).
  • Trans-kingdom analysis of host and microbe genes and/or metabolomic profiles.
  • Support in genetics and statistical epidemiology 

Major Instrumentation

We use the Eppendorf epmotion 5073 and 5075 robots for handling, normalization of sample concentrations and sequencing library preparation.  For sequencing we use Illumina MiSeq, NextSeq, and NovaSeq platforms.  We also use a nanopore MinION long read system.

User Guidelines

Available to NIH.  Contact by email.

Publications

  • 1. E. Giampazolias, M. Pereira da Costa, K. C. Lam, K. H. J. Lim, A. Cardoso, C. Piot, P. Chakravarty, S. Blasche, S. Patel, A. Biram, T. Castro-Dopico, M. D. Buck, R. R. Rodrigues, G. J. Poulsen, S. A. Palma-Duran, N. C. Rogers, M. A. Koufaki, C. M. Minutti, P. Wang, A. Vdovin, B. Frederico, E. Childs, S. Lee, B. Simpson, A. Iseppon, S. Omenetti, G. Kelly, R. Goldstone, E. Nye, A. Suu00e1rez-Bonnet, S. L. Priestnall, J. I. MacRae, S. Zelenay, K. R. Patil, K. Litchfield, J. C. Lee, T. Jess, R. S. Goldszmid, C. Reis E Sousa, Vitamin D regulates microbiome-dependent cancer immunity. Science 384, 428u2013437 (2024).
  • N. K. Newman, M. S. Macovsky, R. R. Rodrigues, A. M. Bruce, J. W. Pederson, J. Padiadpu, J. Shan, J. Williams, S. S. Patil, A. K. Dzutsev, N. Shulzhenko, G. Trinchieri, K. Brown, A. Morgun, Transkingdom Network Analysis (TkNA): a systems framework for inferring causal factors underlying host-microbiota and other multi-omic interactions. Nat Protoc 19, 1750u20131778 (2024).
  • M. J. Bender, A. C. McPherson, C. M. Phelps, S. P. Pandey, C. R. Laughlin, J. H. Shapira, L. Medina Sanchez, M. Rana, T. G. Richie, T. S. Mims, A. M. Gocher-Demske, L. Cervantes-Barragan, S. J. Mullett, S. L. Gelhaus, T. C. Bruno, N. Cannon, J. A. McCulloch, D. A. A. Vignali, R. Hinterleitner, A. V. Joglekar, J. F. Pierre, S. T. M. Lee, D. Davar, H. M. Zarour, M. Meisel, Dietary tryptophan metabolite released by intratumoral Lactobacillus reuteri facilitates immune checkpoint inhibitor treatment. Cell 186, 1846-1862.e26 (2023).
  • J. Padiadpu, M. Garcia-Jaramillo, N. K. Newman, J. W. Pederson, R. Rodrigues, Z. Li, S. Singh, P. Monnier, G. Trinchieri, K. Brown, A. K. Dzutsev, N. Shulzhenko, D. B. Jump, A. Morgun, Multi-omic network analysis identified betacellulinu00a0as a novel target of omega-3 fatty acidu00a0attenuation of western diet-induced nonalcoholic steatohepatitis. EMBO Mol Med 15, e18367 (2023).

Keywords

16s sequencingbioinformaticscomputational analysisGenetics and Genomicsgeneticsgenomicsmicro biomemicrobiomemicrobiome servicesnci-corestatistical epidemiologyMetagenomic analysis