IDDRC: Genomics and Proteomics Core
The Genomics, Proteomics, and Bioinformatics (GPB) Core of the Intellectual and Developmental Disabilities Research Center (IDDRC) facilitates clinical and translational research through application of specialized expertise in high-throughput genetic/genomic and protein analysis methods, together with related bioinformatics analysis. The core is located in the Research Center for Genetic Medicine at Children’s National Medical Center. Associated faculty have joint appointments in the Department of Integrative Systems Biology (ISB) at The George Washington University School of Medicine and Health Sciences.
The GPB core has state-of-the-art equipment purchased through institutional funds, philanthropic donations, and research grants, totaling over $10 million.
Whereas core facilities in most institutions are stand-alone units staffed by personnel dedicated to the core services, the GPB core typically aligns IDDRC projects with an interested ISB faculty member who shares research interests and/or technologies. This provides investigators with more guidance for their projects, from experimental design and data generation all the way to data analysis and interpretation.
In addition to the GPB core, ISB/Genetic Medicine also supports two other NIH cores: the National Center for Medical Rehabilitation Research Core and the Clinical & Translational Science Institute at Children’s National Medical Center. Together, these considerable resources offer substantial opportunities for collaboration, subject recruitment, and implementation of cutting-edge technology to address research questions. Many core functions are provided at highly subsidized charge-back that covers reagent costs.
A list of current GPB services available to IDDRC investigators includes:
- DNA extraction
- DNA banking
- TaqMan Allele Discrimination Assays (two units)
- BioTrove/ABI Highly Parallel TaqMan Assays
- Illumina Bead Arrays for CGH/CNVs
- GWAS-Affymetrix SNP chips or Illumina Bead Arrays
- DMET chips
- Next generation sequencing:
- RainDance Emulsion PCR (Highly Parallel Re-Sequencing)
- Pacific BioSciences Single Molecular Sequencing
- Illumina 24k site Epigenomics Panel (human only)
- Pacific BioSciences Epigenomics by Sequencing
- RNA/miRNA extraction and quality check
- Expression Profiling (mRNA):
- Affymetrix Genechips
- Illumina Bead Array
- Illumina RNASeq
- Expression Profiling (miRNA):
- Affymetrix Genechips
- Illumina Bead Array
- Illumina miRNASeq
- Life Technologies (Taqman RT-PCR cards)
- Taqman RT-PCR
- Western Blotting
- Flow Cytometry-Based Bead ELISA
High-Content Project Design and Data Analysis
- Protein identification from gel bands/spots or from solutions
- Proteome profiling or quantitative proteomics using both stable isotope labeling strategy (SILAC, 15N labeling) and label free strategy
- Consultation for specialized studies including assistance with experimental design, data analysis and interpretation
- Basic training in proteomics including sample preparation and use of bioinformatics tools for protein identification and quantification
- High-throughput/genomic statistics
- Data visualization
- Data dissemination-public repositories
- Project Design and Interpretation Support
- Custom software tools
Rajagopal MU, Hathout Y, Macdonald TJ, Kieran MW, Gururangan S, Blaney SM, Phillips P, Packer R, Gordish-Dressman H, Rood BR. Proteomic profiling of cerebrospinal fluid identifies prostaglandin D2 synthase as a putative biomarker for pediatric medulloblastoma: A pediatric brain tumor consortium study. Proteomics. 2011 Mar;11(5):935-43. doi: 10.1002/pmic.201000198. Epub 2011 Jan 27. PubMed PMID: 21271676.
Aguirre A, Rubio ME, Gallo V. Notch and EGFR pathway interaction regulates neural stem cell number and self-renewal. Nature. 2010 Sep 16;467(7313):323-7. PubMed PMID: 20844536; PubMed Central PMCID: PMC2941915.
Singh RK, Stephens S, Berl MM, Chang T, Brown K, Vezina LG, Gaillard WD. Prospective study of new-onset seizures presenting as status epilepticus in childhood. Neurology. 2010 Feb 23;74(8):636-42. Epub 2010 Jan 20. PubMed PMID: 20089940; PubMed Central PMCID: PMC2830921.
Kesari A, Neel R, Wagoner L, Harmon B, Spurney C, Hoffman EP. Somatic mosaicism for Duchenne dystrophy: evidence for genetic normalization mitigating muscle symptoms. Am J Med Genet A. 2009 Jul;149A(7):1499-503. PubMed PMID: 19530190; PubMed Central PMCID: PMC2729699.
Kantor L, Pinchasi D, Mintz M, Hathout Y, Vanderver A, Elroy-Stein O. A point mutation in translation initiation factor 2B leads to a continuous hyper stress state in oligodendroglial-derived cells. PLoS One. 2008;3(11):e3783. Epub 2008 Nov 21. PubMed PMID: 19023445; PubMed Central PMCID: PMC2583043.