Spotlight

Rose F. Kennedy Intellectual and Developmental Disabilities Research Center

Neurogenomics (NGEN) Core

Director, NGEN Core – Dr. John Greally
Associate Director, NGEN Core – Dr. Bernice Morrow

The goal of the Neurogenomics Core is to provide the most advanced genomics and epigenomics assays and analyses to support the neurological and neuroscience research goals of the IDDRC community at the RFK IDDRC. Modern neuroscience and neurology research has an increasing need for sophisticated genome-wide genetic and epigenetic assays in the quest to understand not only disease states but also the normal functioning of the nervous system. With the goals for the IDDRC encompassing areas such as the study of the pathogenesis of autism; the links among nutrition, obesity and brain development; deafness and communication disorders; and the pathogenesis of neurogenetic disorders, both genetic and epigenetic influences are obvious potential factors that must be considered. A strong cutting-edge Neurogenomics Core that supplies access to the most up-to-date sophisticated genomic technologies in a cost-effective and efficient manner is therefore an essential resource within a center such as this.

Objectives

  1. To provide prioritized access to the most advanced epigenomic and genomic molecular assays
  2. To provide expert consultation with and training of IDDRC investigators performing these molecular assays
  3. To provide expert consultation on experimental approaches and design
  4. To maintain an advanced bioinformatic data analysis and management system
  5. To provide cost-reduced microgrants to promote pilot and feasibility studies

Resources/Services

The deliverable goal for the Neurogenomics Core Facility is to allow the investigator to take an interesting experimental question requiring genomic or epigenomic assays, get advice on how to approach the problem, have samples analyzed using powerful technologies and have analyses performed to generate a data set that can be integrated with phenotypic and imaging data.

Massively-parallel sequencing-based assays: 


a. Chromatin immunoprecipitation (ChIP) assays:

  • ChIP-seq

b. Cytosine methylation assays:

  • Restriction enzyme-based (HELP-tagging)
  • Bisulphite-based (MethylC-seq)

c. Transcription assays:

  • Directional transcriptome sequencing
  • RNA-seq
  • miRNA-seq

d. Genomic sequencing assays:

  • Whole genome sequencing
  • Targeted sequencing using capture techniques
  • De novo sequencing and assembly

Other genomics assays:

  • SEQUENCING, Traditional: Plasmid and PCR product sequencing
  • MICROARRAYS: Gene expression, Exon, SNP and CNV arrays (Affymetrix)
  • DNA PURIFICATION: Plasmid and PCR product purification
  • FRAGMENT ANALYSIS: High-resolution fluorescent electrophoresis
  • PYROSEQUENCING: SNP typing and CpG methylation
  • SEQUENOM: SNP typing, CpG methylation, Gene expression
  • REAL-TIME PCR: SYBR green and TaqMan assays
  • BIOANALYZER: RNA QC

Neurogenomics (NGEN) Core

For genomic and epigenomic analysis of IDDs involving both patient samples and animal models; Genomics ; Epigenomics 

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