Molecular Genomics Core Facility
- Forbes D. Porter, MD, PhD, Director, Molecular Genomics Core Facility
- Fabio Rueda Faucz, PhD, Staff Scientist
- James R. Iben, PhD, Staff Scientist
- Tianwei Li, PhD, Staff Scientist
- Cameron Padilla, BS, Postbaccalaureate Intramural Research Training Award Fellow
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.
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 NovaSeq 6000. 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. The fourth sequencer is a Pacific Biosciences (PacBio) Sequel IIe (recently upgraded), which can sequence long single molecules of more than 100,000 base pairs. 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 and some related 10X instruments. 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 multiome analysis can be performed in which ATAC libraries reading chromatin accessibility are derived from the same cells. The Visum platform and Cytassist controller allow for spatial resolution of transcriptomes in tissue slices.
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 FY23, MGC sequenced 2,749 samples submitted as 187 projects across the full spectrum of sequencing types, generating 14.695 terabytes of sequencing data; the projects involved 40 NICHD Principal Investigators and collaborators from other Institutes. 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
- 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.
- Piña JO, Raju R, Roth DM, Winchester EW, Chattaraj P, Kidwai F, Faucz FR, Iben J, Mitra A, Campbell K, Fridell G, Esnault C, Cotney JL, Dale RK, D'Souza RN. Multimodal spatiotemporal transcriptomic resolution of embryonic palate osteogenesis. Nat Commun 2023 14:5687.
- Trivellin G, Daly AF, Hernández-Ramírez LC, Araldi E, Tatsi C, Dale RK, Fridell G, Mittal A, Faucz FR, Iben JR, Li T, Vitali E, Stojilkovic SS, Kamenicky P, Villa C, Baussart B, Chittiboina P, Toro C, Gahl WA, Eugster EA, Naves LA, Jaffrain-Rea ML, de Herder WW, Neggers SJ, Petrossians P, Beckers A, Lania AG, Mains RE, Eipper BA, Stratakis CA. Germline loss-of-function PAM variants are enriched in subjects with pituitary hypersecretion. Front Endocrinol (Lausanne) 2023 14:1166076.
- Piña JO, Roth DM, Raju R, Winchester EW, Chattaraj P, Kidwai F, Faucz FR, Iben J, Padilla C, Cotney JL, D'Souza RN. Dkk2 interacts with Pax9 in palate mesenchyme to pattern and tune osteogenesis. bioRxiv 2023 doi:10.1101/2023.05.16.541037.
- 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
- Jeffrey Baron, MD, Section on Growth and Development, 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
- Jeff 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
- Deborah Merke, MD, Section on Congenital Disorders, NICHD, 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
- 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
- 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 https://www.nichd.nih.gov/about/org/dir/osd/cf/mgl.
