National Institutes of Health

Eunice Kennedy Shriver National Institute of Child Health and Human Development

2015 Annual Report of the Division of Intramural Research

Molecular Genomics Core Facility

Ben Feldman
  • Forbes D. Porter, MD, PhD, Director, Molecular Genomics Core Facility
  • Steven L. Coon, PhD, Staff Scientist
  • James R. Iben, PhD, Senior Research Fellow
  • Tianwei Li, PhD, Staff Scientist

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

Next-Generation sequencing and bioinformatics support

The Molecular Genomics Core (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. Two are high-capacity, production-scale machines: an Illumina HiSeq 2500, and an Applied Biosystems SOLiD 5500xl. The two others, an Illumina MiSeq and an Ion Torrent Personal Genomics Machine, are smaller, faster machines, which can generate longer sequence reads. This array of sequencers provides a suite of scales and capabilities. Our sequencing services include 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 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 MGL provided sequencing for 14 projects across the full spectrum of sequencing types; the projects involved 12 NICHD Principal Investigators. In addition to sequencing and providing our standard primary analysis of the resulting data, the MGC delivered enhanced bioinformatic support for 15 NICHD investigators and one NICHD/NHGRI collaboration. Our mission is to offer accurate and innovative sequencing and bioinformatic tools to facilitate research into the diagnosis, counseling, and treatment of hereditary disorders.

Publications

  1. Wassif CA, Cross JL, Iben J, Sanchez-Pulido L, Cougnoux A, Platt FM, Ory DS, Ponting CP, Bailey-Wilson JE, Biesecker LG, Porter FD. High incidence of unrecognized visceral/neurological late-onset Niemann-Pick disease, type C1, predicted by analysis of massively parallel sequencing data sets. Genet Med 2015; 18(1):41-8.
  2. Hartley SW, Coon SL, Savastano LE, Mullikin JC, NISC Comparative Sequencing Program, Fu C, Klein DC. Neurotranscriptomics: The effects of neonatal stimulus deprivation on the rat pineal transcriptome. PLoS ONE 2015;10(9):e0137548.
  3. Hickey A, Esnault C, Majumdar A, Chatterjee AG, Iben JR, McQueen PG, Yang AX, Mizuguchi T, Grewal SI, Levin HL. Single nucleotide specific targeting of the Tf1 retrotransposon promoted by the DNA-binding protein Sap1 of Schizosaccharomyces pombe. Genetics 2015; 201(3):905-924.
  4. Zhang J, Hung GC, Lei H, Li T, Li B, Tsai S, Lo SC. Draft genome sequence of Pantoea sp. strain MBLJ3, isolated in a laboratory environmental control study. Genome Announc 2015;3(1):e01595-14.
  5. Singh P, Plumb M, Ferris A, Iben J, Wu X, Fadel H, Poeschla E, Hughes S, Kvaratskhelia M, Levin, HL. LEDGF/p75 interacts with mRNA splicing factors and targets HIV-1 integration to highly spliced genes. Genes Dev 2015; 29(21):2287-97.

Collaborators

  • Joan Bailey-Wilson, PhD, Computational and Statistical Genomics Branch, NHGRI, Baltimore, MD
  • Jeffrey Baron, MD, Program on Developmental Endocrinology and Genetics, NICHD, Bethesda, MD
  • David Clark, PhD, Program in Genomics of Differentiation, NICHD, Bethesda, MD
  • Angela Delaney, MD, Program on Developmental Endocrinology and Genetics, NICHD, Bethesda, MD
  • Thomas Dever, PhD, Program in Cellular Regulation and Metabolism, NICHD, Bethesda, MD
  • Douglas Fields, PhD, Section on Nervous System Development and Plasticity, OSD, NICHD, Bethesda, MD
  • Benjamin Feldman, PhD, Program on Genomics of Differentiation, NICHD, Bethesda, MD
  • Alan Hinnebusch, PhD, Program in Cellular Regulation and Metabolism, NICHD, Bethesda, MD
  • Henry Levin, PhD, Program in Cellular Regulation and Metabolism, NICHD, Bethesda, MD
  • Todd Macfarlan, PhD, Program in Genomics of Differentiation, NICHD, Bethesda, MD
  • Richard Maraia, MD, Program in Genomics of Differentiation, NICHD, Bethesda, MD
  • Constantine Stratakis, MD, D(med)Sci, Program on Developmental Endocrinology and Genetics, NICHD, Bethesda, MD
  • Brant Weinstein, PhD, Program in Genomics of Differentiation, NICHD, Bethesda, MD

Contact

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

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