You are here: Home > Molecular Genomics Core

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 than 100,000 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 permits 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 166 projects (2,798 samples) across the full spectrum of sequencing types, generating 12,395 gigabases of sequence; the projects involved 35 NICHD Principal Investigators from 11 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. Mays JC, Kelly MC, Coon SL, Holtzclaw L, Rath MF, Kelley MW, Klein DC. Single-cell RNA sequencing of the mammalian pineal gland identifies two pinealocyte subtypes and cell type-specific daily patterns of gene expression. PLoS One 2018;13(10):e0205883.
2. Coon SL, Fu C, Hartley SW, Holtzclaw L, Mays JC, Kelly MC, Kelley MW, Mullikin JC, Rath MF, Savastano LE, Klein DC. Single cell sequencing of the pineal gland: the next chapter. ront Endocrinol (Lausanne) 2019;10:590.
3. Fletcher PA, Smiljanic K, Previde RM, Iben J, Li T, Rokic MB, Sherman A, Coon SL, Stojilkovic SS. Cell type- and sex-dependent transcriptome profiles of rat anterior pituitary cells. Front Endocrinol (Lausanne) 2019;10:623.
4. Wester JC, Mahadevan V, Rhodes CT, Calvigioni D, Vankatesh S, Maric D, Hunt S, Yuan X, Zhang Y, Petros TJ, McBain CJ. Neocortical projection neurons instruct inhibitory interneuron circuit development in a lineage dependent manner. Neuron 2019;102(5):960-975.
5. Tabor KM, Marquart GD, Hurt C, Smith TS, Geoca AK, Bhandiwad AA, Subedi A, Sinclair JL, Rose HM, Polys NF, Burgess HA. Brain-wide cellular resolution imaging of Cre transgenic zebrafish lines for functional circuit-mapping. eLife 2019;8:e42687.

Collaborators

• Jeffrey Baron, MD, Section on Growth and Development, NICHD, Bethesda, MD
• Juan Bonifacino, PhD, Section on Intracellular Protein Trafficking, NICHD, Bethesda, MD
• Andres Buonanno, PhD, Section on Molecular Neurobiology, NICHD, Bethesda, MD
• Harold Burgess, PhD, Section on Behavioral Neurogenetics, NICHD, Bethesda, MD
• Michael Cashel, MD, PhD, Section on Molecular Regulation, 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
• Melvin Depamphilis, PhD, Section on Eukaryotic DNA Replication, NICHD, Bethesda, MD
• Thomas Dever, PhD, Section on Protein Biosynthesis, NICHD, Bethesda, MD
• Katie Drerup, PhD, Unit on Neuronal Cell Biology, NICHD, Bethesda, MD
• Benjamin Feldman, PhD, Zebrafish Core, 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
• Mary Lilly, PhD, Section on Gamete Development, 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
• Keiko Ozato, PhD, Section on Molecular Genetics of Immunity, 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
• Pedro Rocha, PhD, Unit on Genome Structure and Regulation, NICHD, Bethesda, MD
• Dan Sackett, PhD, Division of Basic and Translational Biophysics, NICHD, Bethesda, MD
• Mihaela Serpe, PhD, Section on Cellular Communication, NICHD, Bethesda, MD
• Yun-Bo Shi, PhD, Section on Molecular Morphogenesis, 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
• Constantine Stratakis, MD, D(med)Sci, Section on Endocrinology and Genetics, 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.

Top of Page