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
With the goal of understanding genetic changes and mechanisms underlying human diseases, the Molecular Genomics Core Facility supports NICHD investigators by providing next-generation 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 three sequencing machines. Most of our work is conducted on our high-capacity, production-scale machine: an Illumina HiSeq 2500. The two other sequencers, an Illumina MiSeq and an Ion Torrent Personal Genomics Machine, are smaller, faster machines, which can generate longer sequence reads. Our recently acquired cBot liquid handler will allow even higher through-put on the Illumina HiSeq. 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 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 42 projects across the full spectrum of sequencing types; the projects involved 19 NICHD Principal Investigators from 10 Affinity Groups. In addition to sequencing and providing our standard primary analysis of the resulting data, the MGC delivered enhanced bioinformatic support for nine NICHD investigators across six 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, which promotes understanding of human health and development.
Publications
- Peng C, Yao G, Gao B-M, Fan C-X, Bian C, Wang J, Cao Y, Wen B, Zhu Y, Ruan Z, Zhao X, You X, Bai J, Li J, Lin Z, Zou S, Zhang X, Qiu Y, Chen J, Coon SL, Yang J, Chen J-S, Shi Q. High-throughput identification of novel conotoxins from the Chinese tubular cone snail (Conus betulinus) by multitranscriptome sequencing. GigaScience 2016;5:17.
- Gore AV, Athans B, Iben JR, Johnson K, Russanova V, Castranova D, Pham VN, Butler MG, Williams-Simons L, Nichols JT, Bresciani E, Feldman B, Kimmel CB, Liu PP, Weinstein BM. Epigenetic regulation of hematopoiesis by DNA methylation. Elife 2016;5:e11813.
- Gebert C, Rong Q, Jeong S, Iben J, Pfeifer K. H19ICR mediated transcriptional silencing does not require target promoter methylation. Biochem Biophys Res Commun 2016;476(3):121-126.
- Arimbasseri AG, Iben J, Wei FY, Rijal K, Tomizawa K, Hafner M, Maraia RJ. Evolving specificity of tRNA 3-methyl-cytidine-32 (m3C32) modification: a subset of tRNAsSer requires N6-isopentenylation of A37. RNA 2016;22(9):1400-1410.
- Hartley SW, Mullikin JC, Klein DC, Park M, NISC Comparative Sequencing Program, Coon SL. Alternative isoform analysis of Ttc8 expression in the rat pineal gland using a multi-platform sequencing approach reveals neural regulation. PLoS One 2016;11(9):e0163590.
Collaborators
- Paul Badenhorst, PhD, University of Birmingham, Birmingham, UK
- Tamás Balla, MD, PhD, Section on Molecular Signal Transduction, 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 Clark, PhD, Section on Chromatin and Gene Expression, NICHD, Bethesda, MD
- Robert Crouch, PhD, Section on Formation of RNA, NICHD, Bethesda, MD
- Angela Delaney, MD, Unit on Genetics of Puberty and Reproduction, NICHD, Bethesda, MD
- Benjamin Feldman, PhD, Zebrafish Core, NICHD, Bethesda, MD
- Kenneth Fischbeck, MD, Neurogenetics Branch, NINDS, Bethesda, MD
- Alan Hinnebusch, PhD, Section on Nutrient Control of Gene Expression, NICHD, Bethesda, MD
- Henry Levin, PhD, Section on Eukaryotic Transposable Elements, 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
- Richard Maraia, MD, Section on Molecular and Cellular Biology, NICHD, Bethesda, MD
- Joan Marini, MD, PhD, Bone and Extracellular Matrix Branch, NICHD, Bethesda, MD
- Anil Mukherjee, MD, PhD, Section on Developmental Genetics, NICHD, Bethesda, MD
- Karl Pfeifer, PhD, Section on Genomic Imprinting, NICHD, Bethesda, MD
- Tracy Rouault, MD, Section on Human Iron Metabolism, NICHD, Bethesda, MD
- Gisela Storz, PhD, Section on Environmental Gene Regulation, NICHD, Bethesda, MD
- Brant Weinstein, PhD, Section on Vertebrate Organogenesis, NICHD, Bethesda, MD
- Erin Wolff, MD, Unit on Reproductive and Regenerative Medicine, NICHD, Bethesda, MD
Contact
For more information, email fdporter@mail.nih.gov or visit http://mgl.nichd.nih.gov.
