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Molecular Genomics Core Facility

• Forbes D. Porter, MD, PhD, Director, Molecular Genomics Core Facility
• Steven L. Coon, PhD, Staff Scientist
• James R. Iben, PhD, Staff Scientist
• Tianwei Li, PhD, Staff Scientist
• Joseph Zoeller, BS, Postbaccalaureate Intramural Research Training Award Fellow

With the goal of understanding genetic changes and mechanisms underlying human diseases, the Molecular Genomics Core (MGC) Facility supports NICHD investigators by providing next-generation deep sequencing and project data analysis.

Next-Generation sequencing and bioinformatics support

The MGC provides DNA and RNA sequencing services for genomic and genetic research to investigators within the NICHD. The MGC is currently operating with four sequencing machines. Most of our work is conducted on our high-capacity, production-scale machine: an Illumina HiSeq 2500. Two of the other sequencers, an Illumina MiSeq and an Ion Torrent Personal Genomics Machine, are smaller, faster machines, which can generate longer sequence reads of up to 400 base pairs. Our most-recent acquisition is a Pacific Biosciences (PacBio) Sequel, which can sequence long single molecules of more the 50,000 base pairs. To increase the throughput of the HiSeq 2500 even further, we have a cBot liquid handler for automated high-precision loading of sequencing chips. Our array of sequencers provides a suite of scales and capabilities. Our sequencing services include whole-genome, whole-exome, targeted exome, and gene-specific DNA sequencing, as well as whole-transcriptome sequencing (RNA-Seq), microRNA sequencing, microbiome sequencing, bisulfite sequencing (DNA methylome), ChIP-Seq, and ribosomal profiling. The PacBio Sequel enables mutation phasing, structural variant analysis, transposon location identification, and other analyses that are not possible or practical with the other sequencers.

Recently, the MGC acquired a 10X Genomics Chromium Single Cell Controller. The Chromium converts a suspension of single cells into cDNA libraries that are barcoded by cell of origin. The cDNAs can then be converted into sequenceable libraries and run on our Illumina HiSeq 2500 to generate cell-specific transcriptomes.

The MGC provides significant primary data-processing and downstream bioinformatic support and can assist in designing experiments or sequencing strategies (for example, optimization of targeted exome design). During the past year, the MGC provided sequencing for 97 projects (1,266 samples) across the full spectrum of sequencing types, generating 8,490 gigabases of sequence; the projects involved 32 NICHD Principal Investigators from 10 Affinity Groups. In addition to sequencing and providing our standard primary analysis of the resulting data, the MGC delivered enhanced bioinformatic support to 15 NICHD investigators across seven Affinity Groups. Our mission is to offer accurate and innovative sequencing and bioinformatic tools to facilitate research into the diagnosis, counseling, and treatment of hereditary disorders, and to support basic research that promotes understanding of human health and development.

Publications

1. Cougnoux A, Drummond RA, Collar AL, Iben JR, Salman A, Westgarth H, Wassif CA, Cawley NX, Farhat NY, Ozato K, Lionakis MS, Porter FD. Microglia activation in Niemann-Pick disease, type C1 is amendable to therapeutic intervention. Hum Mol Genet 2018;27(12):2076-2089.
2. Cougnoux A, Movassaghi M, Picache JA, Iben JR, Navid F, Salman A, Martin K, Farhat NY, Cluzeau C, Tseng WC, Burkert K, Sojka C, Wassif CA, Cawley NX, Bonnet R, Porter FD. Gastrointestinal tract pathology in a BALB/c Niemann-Pick disease type C1 null mouse model. Dig Dis Sci 2018;63(4):870-880.
3. Brown JL, Sun M, Kassis JA. Global changes of H3K27me3 domains and Polycomb group protein distribution in the absence of recruiters Spps or Pho. Proc Natl Acad Sci USA 2018;115(8):E1839-E1848.
4. Jee YH, Wang J, Yue S, Jennings M, Clokie SJH, Nilsson O, Lui J, Baron J. Mir-374-5p, mir-379-5p, and mir-503-5p regulate proliferation and hypertrophic differentiation of growth plate chondrocytes in male rats. Endocrinology 2018;159(3):1469-1478.
5. Lui JC, Jee YH, Garrison P, Iben JR, Yue S, Ad M, Nguyen Q, Kikani B, Wakabayashi Y, Baron J. Differential aging of growth plate cartilage underlies differences in bone length and thus helps determine skeletal proportions. PLoS Biol 2018;16(7):e2005263.
6. Patterson-West J, James TD, Fernández-Coll L, Iben JR, Moon K, Knipling L, Cashel M, Hinton DM. The E. coli global regulator DksA reduces transcription during T4 infection. Viruses 2018;10(6):E308.

Collaborators

• Tamás Balla, MD, PhD, Section on Molecular Signal Transduction, NICHD, Bethesda, MD
• Jeffrey Baron, MD, Section on Growth and Development, NICHD, Bethesda, MD
• Juan Bonifacino, PhD, Section on Intracellular Protein Trafficking, NICHD, Bethesda, MD
• Harold Burgess, PhD, Section on Behavioral Neurogenetics, NICHD, Bethesda, MD
• Janice Chou, PhD, Section on Cellular Differentiation, NICHD, Bethesda, MD
• David J. Clark, PhD, Section on Chromatin & Gene Expression, NICHD, Bethesda, MD
• Robert J. Crouch, PhD, Section on the Formation of RNA, NICHD, Bethesda, MD
• Mary Dasso, PhD, Section on Cell Cycle Regulation, NICHD, Bethesda, MD
• Angela Delaney Freedman, MD, Office of the Clinical Director, NICHD, Bethesda, MD
• Benjamin Feldman, PhD, Zebrafish Core, NICHD, Bethesda, MD
• Richard D. Fields, PhD, Section on Nervous System Development & Plasticity, NICHD, Bethesda, MD
• Kenneth H. Fischbeck, MD, Hereditary Neurological Disease Section, NINDS, Bethesda, MD
• Dax A. Hoffman, PhD, Section on Molecular Neurophysiology & Biophysics, NICHD, Bethesda, MD
• Michael J. Iadarola, PhD, Anesthesia Section, Clinical Center, Bethesda, MD
• Judith Kassis, PhD, Section on Gene Expression, NICHD, Bethesda, MD
• David Klein, PhD, Scientist Emeritus, NICHD, Bethesda, MD
• Claire E. Le Pichon, PhD, Unit on the Development of Neurodegeneration, NICHD, Bethesda, MD
• Henry L. Levin, PhD, Section on Eukaryotic Transposable Elements, NICHD, Bethesda, MD
• Paul Love, MD, PhD, Section on Cellular and Developmental Biology, NICHD, Bethesda, MD
• Todd Macfarlan, PhD, Unit on Mammalian Epigenome Reprogramming, NICHD, Bethesda, MD
• Matthias Machner, PhD, Section on Microbial Pathogenesis, NICHD, Bethesda, MD
• Richard Maraia, MD, Section on Molecular and Cellular Biology, NICHD, Bethesda, MD
• Joan C. Marini, MD, PhD, Section on Heritable Disorders of Bone & Extracellular Matrix, NICHD, Bethesda, MD
• Chris McBain, PhD, Section on Cellular and Synaptic Physiology, NICHD, Bethesda, MD
• Timothy J. Petros, PhD, Unit on Cellular and Molecular Neurodevelopment, NICHD, Bethesda, MD
• Karl Pfeifer, PhD, Section on Epigenetics, NICHD, Bethesda, MD
• Stanko S. Stojilkovic, PhD, Section on Cellular Signaling, NICHD, Bethesda, MD
• Gisela Storz, PhD, Section on Environmental Gene Regulation, NICHD, Bethesda, MD
• Brant Weinstein, PhD, Section on Vertebrate Organogenesis, NICHD, Bethesda, MD

Contact

For more information, email fdporter@mail.nih.gov or visit http://mgl.nichd.nih.gov.

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