Molecular Genomics Core
- Forbes D. Porter,
MD, PhD, Director, Molecular Genomics Core Facility - Vivek Mahadevan, PhD, Staff Scientist, Executive Director
- James R. Iben, PhD, Staff Scientist, Senior Bioinformatician
- Tianwei Li, PhD, Staff Scientist, Laboratory Supervisor
- Elizabeth J. Davis, BS, Postbaccalaureate 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.
Molecular Genomics Core Staff
Left to right: Vivek Mahadevan, Tianwei Li, James Iben, Elizabeth Davis
Molecular Genomics Core Staff
Left to right: Vivek Mahadevan, Tianwei Li, James Iben, Elizabeth Davis
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 (assay for transposase accessible chromatin) 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 68 Visium runs (that include 29 Visium HD runs) across diverse tissues (bone, ovary, brain). In preparation for embracing the spatial genomics revolution, we are geared to provide species-agnostic spatial genomics workflow, Curio Trekker (slide-Seq), Visium 3′ poly A-capture, and a complementary, imaging-based spatial genomics workflow, Xenium, in 2026.
Typically, the MGC's role begins with assistance in designing experiments and 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.
2025 performance metrics
During 2025, the MGC sequenced 3,427 samples across 128 sequencing runs for 42 different principal investigators (37 from NICHD and five non–NICHD collaborators). These runs were distributed across our three sequencers: 111 runs on the NovaSeq 6000, 13 runs on the MiSeq, and four runs on the Sequel IIe. These efforts generated 9,978.30 gigabases (approximately 10 terabases) of sequenced DNA and RNA samples across eight unique species (human, marmoset, mice, Drosophila, moth, zebrafish, Xenopus, and E. coli), utilizing 22 distinct sequencing technologies.
In addition to sequencing and providing our standard primary analysis of the resulting data, the MGC delivered enhanced bioinformatic support to investigators across seven Affinity Groups. MGC personnel contributed to the scientific community through six co-authorships on peer-reviewed publications, and the MGC's services were acknowledged in at least 10 publications (this is a conservative estimate, as actual numbers may be higher given non-overlapping sources between peer-reviewed and preprint articles).
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.
Additional Funding
- 2025 NICHD Career Development Awards
Publications
- The axillary lymphoid organ is an external, experimentally accessible immune organ in the zebrafish. J Exp Med 2025 222(6):e20241435
- Divergent opioid-mediated suppression of inhibition between hippocampus and neocortex across species and development. Neuron 2025 113(11):1805-1822
- Anatomical and molecular characterization of the zebrafish meninges. bioRxi 2025 10.1101/2025.04.09.646894;preprint
- Programmed meiotic errors facilitate dichotomous sperm production in the silkworm, Bombyx mori. bioRxiv 2025 10.1101/2025.08.03.667510;preprint
Collaborators
- Philip Adams, PhD, Group on Gene Regulation in Bacterial Pathogens, NICIHD, Bethesda, MD
- Hussam Alkaissi, MD, MS, Interinstitute Endocrinology Clinical Fellow, NIDDK, NICHD, 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
- James Bourne, PhD, Section on Cellular and Cognitive Neurodevelopment, NIMH, 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
- Thomas E. Dever, PhD, Section on Protein Biosynthesis, 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
- 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
- Senthil R. Muthuswamy, PhD, Laboratory of Cancer Biology and Genetics, NCI, 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, 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
- 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
- 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.