Molecular Cytogenetics and Microarray
The Cytogenetics and Microarray facilities are highly complex laboratories providing tests to identify constitutional and acquired genomic abnormalities. Individuals receiving these tests include those with neurodevelopmental disabilities in which genetics either plays a role or is suspected of playing a role (e.g., epilepsy, autism, congenital malformations and dysmorphic features). Tests offered include tissue culture and processing, high-resolution karyotype, and special staining techniques such as C- and Q-banding. Chromosome breakage analysis is offered for patients with suspected increased genomic instability. We perform fluorescence in situ hybridization with commercial and custom BAC and fosmid probes especially designed to address hypotheses from each project. Analysis of sub-microscopic copy number changes and detection of regions of genomic homozygosity is offered utilizing a high-density single nucleotide polymorphism (SNP) microarray assay, and our laboratory keeps current with platforms as they evolve.
Tissue Culture Services and Cell Repository
We offer cell line establishment of fibroblasts from skin biopsies and long-term transformed lymphoblast cell lines from peripheral blood samples. These cell lines can be utilized for ongoing projects and are also stored for future research. In our searchable tissue culture database, we maintain basic information including date and reason for storage, submitting investigator, specific genetic-related information, phenotypic data, and basic demographics.
Bioinformatics and Software Development
The Bioinformatics service of the core provides support on experimental design, data acquisition, and data analysis for single nucleotide polymorphism (SNP) arrays. Bioinformatics offers comprehensive analysis of whole genome and whole exome sequence data, as well as targeted resequencing data through next-generation sequencing. Gene expression microarray analysis for the assessment of RNA transcript levels in various samples is routinely performed at other local core facilities, including the Microarray Core Facility at the McKusick-Nathans Institute of Genetic Medicine.
The IDDRC Genetics Core offers services in experimental design and data analysis. Data analysis occurs in three areas:
- Preprocessing, including normalization using the GC-RMA and related approaches
- Exploratory analyses, including hierarchical clustering, principal components analysis, and multidimensional scaling
- Inferential statistics including ANOVA to determine sets of significantly regulated RNA transcripts at various false discovery rates
Interface with Hopkins Genetic Resources Core Facility (GRCF)
The IDDRC Genetics Core assists supported investigators with accessing the resources of the GRCF. Dr. Valle, co-director, is also the director of the broad range of services needed to support cutting-edge studies of the human genome.