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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
• Rachel Lazris, 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) 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 five sequencing machines. Most of our work is conducted on our two high-capacity, production-scale machines: an Illumina HiSeq 2500 and an Illumina NovaSeq 6000. To increase the throughput of the HiSeq 2500 even further, we have a cBot liquid handler for automated high-precision loading of sequencing chips. 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 fifth sequencer, is a Pacific Biosciences (PacBio) Sequel, 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 permits mutation phasing, structural variant analysis, transposon location identification, and other analyses that are not possible or practical with the other sequencers.

The MGC also operates a 10X Genomics Chromium Single Cell Controller. 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 HiSeq 2500 or NovaSeq 6000 machines to generate thousands of 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 245 projects (2,902 samples) across the full spectrum of sequencing types, generating 20,177 gigabases of sequence; the projects involved 37 NICHD Principal Investigators from 13 Affinity Groups. In addition to sequencing and providing our standard primary analysis of the resulting data, the MGC delivered enhanced bioinformatic support to 18 NICHD investigators across eight 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. Bloyd M, Settas N, Faucz FR, Sinaii N, Bathon K, Iben J, Coon S, Caprio S, Stratakis CA, London E. The PRKAR1B p.R115K variant is associated with lipoprotein profile in African American youth with metabolic challenges. J Endocr Soc 2021;5(8):bvab071.
2. Cherkasova V, Iben JR, Pridham KJ, Kessler AC, Maraia RJ. The leucine-NH4+ uptake regulator Any1 limits growth as part of a general amino acid control response to loss of La protein by fission yeast. PLoS One 2021;16(6):e0253494.
3. Coon SL, Li T, Iben JR, Mattijssen S, Maraia RJ. Single-molecule polyadenylated tail sequencing (SM-PAT-Seq) to measure polyA tail lengths transcriptome-wide. Methods Enzymol 2021;655:119-137.
4. Nguyen TH, Vicidomini R, Choudhury SD, Coon SL, Iben J, Brody T, Serpe M. Single-cell RNA sequencing analysis of the Drosophila larval ventral cord. Curr Protoc 2021;1(2):e38.
5. Patterson-West J, Tai CH, Son B, Hsieh ML, Iben JR, Hinton DM. Overexpression of the bacteriophage T4 motB gene alters H-NS dependent repression of specific host DNA. Viruses 2021;13(1):84.

Collaborators

• Jeffrey Baron, MD, Section on Growth and Development, NICHD, Bethesda, MD
• Diana Bianchi, MD, Prenatal Genomics & Therapy Section, NHGRI, Bethesda, MD
• Juan 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
• Ajay Chitnis, MBBS, PhD, Section on Neural Developmental Dynamics, 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
• Katie Drerup, PhD, Unit on Neuronal Cell Biology, NICHD, Bethesda, MD
• Maria L. Dufau, PhD, Section on Molecular Endocrinology, NICHD, Bethesda, MD
• Benjamin Feldman, PhD, Zebrafish Core, NICHD, Bethesda, MD
• Marc Ferrer, MD, 3-D Tissue Bioprinting Laboratory, NCATS, Rockville, MD
• Judith Kassis, PhD, Section on Gene Expression, NICHD, Bethesda, MD
• David Klein, PhD, Scientist Emeritus, 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
• 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
• Deborah Merke, MD, Section on Congenital Disorders, 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
• Forbes D. Porter, MD, PhD, Section on Molecular Dysmorphology, 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
• Michael E. Ward, MD, PhD, 3-D Tissue Bioprinting Laboratory, NINDS, Bethesda, MD
• Brant Weinstein, PhD, Section on Vertebrate Organogenesis, NICHD, Bethesda, MD
• Jack 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.

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