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Molecular Genomics Core

  • Forbes D. Porter, MD, PhD, Director, Molecular Genomics Core Facility
  • James R. Iben, PhD, Staff Scientist
  • Tianwei Li, PhD, Staff Scientist
  • Vivek Mahadevan, PhD, Staff Scientist
  • Elizabeth J. Davis, BS, Postbaccalaureate Intramural Research Training Award, Cancer Research Training Award Fellow
Forbes D. Porter

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

MGC Staff

Left to right: Ms. Elizabeth Davis, Dr. James Iben, Dr. Tianwei Li, Dr. Vivek Mahadevan
MGC Staff
Click image to enlarge.
MGC Staff
Click image to enlarge.

MGC Staff

Left to right: Ms. Elizabeth Davis, Dr. James Iben, Dr. Tianwei Li, Dr. Vivek Mahadevan

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 three sequencing machines: an Illumina NovaSeq 6000 that is a high-capacity, production-scale machine; an Illumina MiSeq that is a smaller, faster machine; and a third sequencer, a Pacific Biosciences Sequel single-molecule, third generation long-read sequencer (PacBio Sequel IIe). This 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 IIe permits mutation phasing, structural variant analysis, transposon location identification, nascent base modification reading, whole mRNA isoform sequencing, and other analyses that are not possible or practical with the other sequencers.

The MGC also operates a 10X Genomics Chromium Single Cell Controller for generating sequencing libraries from dissociated single cells/nuclei. The Chromium converts a suspension of single cells or nuclei into cDNA libraries that are barcoded by cell or nucleus of origin. The cDNAs can then be converted into sequenceable libraries and run on our Illumina NovaSeq 6000 machine to generate thousands of cell-specific transcriptomes. Similarly, a multi-ome analysis can be performed in which ATAC libraries reading chromatin accessibility are derived from the same cells. A more recent addition to the 10X Genomics suite includes the Cytassist for sequencing-based, unbiased spatial transcriptomics solutions in human and mouse tissue sections. While Visium was introduced in FY23, and an updated version, Visium HD was introduced in FY24. The MGC has successfully implemented these new workflows and completed 34 Visium runs across diverse tissues (bone, ovary, brain). In preparation to embrace the spatial genomics revolution, we are geared to provide species-agnostic spatial genomics workflow, Curio Trekker (slide-Seq), and a complementary, imaging-based spatial genomics workflow, Xenium, in 2025.

Typically, the MGC's role begins with assistance in designing experiments, identifying an appropriate sequencing strategy to address the scientific question brought by the NICHD investigator. Often, the MGC also refines existing sequencing strategies (for example, optimization of targeted exome design or tissue-specific single-cell sample preparation). In nearly all cases subsequent to receiving DNA/RNA samples, the MGC constructs the sequencing libraries, but the MGC also provides sequencing for libraries generated by investigators. Following a successful completion of sequencing, the MGC provides significant primary data-processing and downstream bioinformatic support. During FY24, the MGC sequenced 3,364 samples submitted as 193 projects for 42 different NICHD principle investigators. These efforts generated 16,893 giga-bases (about 16.9 tera-bases) of sequenced DNA and RNA samples. During the past year, the MGC sequenced 434 samples submitted as 29 projects for 13 different principle investigators. These efforts generated 2,413 giga-bases (about 2.4 tera-bases) of sequenced DNA and RNA samples. 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 diagnosis, counseling, and treatment of hereditary disorders, and to support basic research at NICHD that promotes understanding of human health and development.

Publications

  1. Poonia P, Valabhoju V, Li T, Iben JR, Niu X, Lin Z, Hinnebusch AG. Yeast poly(A)-binding protein (Pab1) controls translation initiation in vivo primarily by blocking mRNA decapping and decay. bioRxiv 2024 2024.04.19:PMC11188147 (preprint)
  2. Iben JR, Li T, Mattijssen S, Maraia RJ. Single-molecule poly(A) tail sequencing (SM-PATseq) using the PacBio Platform. Methods Mol Biol 2024 2723:285–301
  3. Kolli V, Frucci E, Werneck I, Iben JR, Kim SA, Mallappa A, Li T, Faucz FR, Kebebew E, Nilubol N, Quezado MM, Merke DP. Evidence of the role of inflammation and the hormonal environment in the pathogenesis of adrenal myelolipomas in congenital adrenal hyperplasia. Int J Mol Sci 2024 25(5):2543
  4. Boronat-Garcia A, Iben J, Dominguez-Martin E, Stopfer M. Identification and analysis of odorant receptors expressed in the two main olfactory organs, antennae and palps, of Schistocerca americana. Sci Rep 2022 12:22628

Collaborators

  • Philip Adams, PhD, Group on Gene Regulation in Bacterial Pathogens, NICIHD, Bethesda, MD
  • Anirban Banerjee, PhD, Section on Structural and Chemical Biology, NICHD, Bethesda, MD
  • Jeffrey Baron, MD, Section on Growth and Development, NICHD, Bethesda, MD
  • Juan S. Bonifacino, PhD, Section on Intracellular Protein Trafficking, NICHD, Bethesda, MD
  • Harold Burgess, PhD, Section on Behavioral Neurogenetics, NICHD, Bethesda, MD
  • Michael Cashel, MD, PhD, Section on Molecular Regulation, NICHD, Bethesda, MD
  • Rachel Caspi, PhD, Immunoregulation Section, NEI, Bethesda, MD
  • Daniel Chertow, MD, PhD, Critical Care Medicine, NIH Clinical Center, Bethesda, MD
  • Prashant Chittiboina, PhD, Surgical Neurology Branch, NINDS, 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
  • An Ngoc Dang Do, PhD, Office of the Clinical Director, NICHD, Bethesda, MD
  • Mary Dasso, PhD, Section on Cell Cycle Regulation, NICHD, Bethesda, MD
  • Rena N. D'Souza, PhD, Section on Therapies for Craniofacial Disorders, NICHD, Bethesda, MD
  • Jeffrey Farrell, PhD, Division of Developmental Biology, NICHD, Bethesda, MD
  • Benjamin Feldman, PhD, Zebrafish Core, NICHD, Bethesda, MD
  • Veronica Gomez-Lobo, MD, Pediatric & Adolescent Gynecology Program, NICHD, Bethesda, MD
  • Alan Hinnebusch, PhD, Section on Nutrient Control of Gene Expression, NICHD, Bethesda, MD
  • Judith Kassis, PhD, Section on Gene Expression, NICHD, Bethesda, MD
  • Sergey Leikin, PhD, Section on Physical Biochemistry, 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
  • Y. Peng Loh, PhD, Section of Cellular Neurobiology, 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 J. McBain, PhD, Section on Cellular and Synaptic Physiology, NICHD, Bethesda, MD
  • Deborah Merke, MD, Section on Congenital Disorders, NICHD, Bethesda, MD
  • Susan L. Moir, PhD, B-Cell Immunology Section, NIAID, Bethesda, MD
  • Luigi Notarangelo, MD, Immune Deficiency Genetics Diseases Section, NIAID, 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
  • Manu Platt, PhD, Center for Biomedical Imaging & Technology, NIBIB, Bethesda, MD
  • Pedro Rocha, PhD, Unit on Genome Structure and Regulation, NICHD, Bethesda, MD
  • Katherine W. Rogers, PhD, Unit on Developmental Signaling, NICHD
  • Mihaela Serpe, PhD, Section on Cellular Communication, NICHD, Bethesda, MD
  • Sarah Sheppard, PhD, Unit on Vascular Malformations, NICHD, Bethesda, MD
  • Yun-Bo Shi, PhD, Section on Molecular Morphogenesis, NICHD, Bethesda, MD
  • Mark A. Stopfer, PhD, Section on Sensory Coding and Neural Ensembles, NICHD, Bethesda, MD
  • Gisela Storz, PhD, Section on Environmental Gene Regulation, NICHD, Bethesda, MD
  • Christina Tatsi, MD, MHSc, PhD, Unit on Hypothalamic and Pituitary Disorders, NICHD, Bethesda, MD
  • Brant Weinstein, PhD, Section on Vertebrate Organogenesis, NICHD, Bethesda, MD
  • Benjamin White, PhD, Section on Neural Function, NIMH, Bethesda, MD
  • Jack A. Yanovski, MD, PhD, Section on Growth and Obesity, NICHD, Bethesda, MD

Contact

For more information, email fdporter@mail.nih.gov or visit https://www.nichd.nih.gov/about/org/dir/osd/cf/mgl.