High Thoughput FISH Mapping

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To achieve our overall goal of identifying genes important in human development, Project 1 (High Throughput FISH Mapping) will map chromosomal breakpoints from individuals with apparently balanced rearrangements and congenital anomalies. We hypothesize that chromosomal rearrangements in these individuals are responsible for the abnormal phenotypes, either through haploinsufficiency or some other genetic mechanism(s). Study subjects will be identified and enrolled through our growing international network of clinical geneticists, genetic counselors, and clinical cytogeneticists, and from the NIGMS Human Genetic Cell Repository. Peripheral lymphocytes or fibroblast specimens will be obtained from consented research subjects, and lymphocytes will be immortalized to provide ongoing sources of cellular material for our studies. Participants have the option of granting permission for us to contribute aliquots of these samples to the NIGMS Human Genetic Cell Repository, through which they can be shared anonymously with the entire scientific community. Prior to intensive breakpoint mapping, we will use array comparative genomic hybridization (aCGH) technology to detect cryptic or submicroscopic changes that could potentially confound subsequent analyses, and further analysis of cases with significant deletions or evidence of complex rearrangements would be deferred. According to our existing prioritization criteria, 12 cases/year will be selected for high-resolution breakpoint mapping by FISH using fully or end-sequenced BAG and fosmid clones. The case selection criteria favor cases with a higher likelihood that a given chromosomal rearrangement is responsible for the abnormal phenotype and take advantage of the particular expertise of DGAP Investigators in diverse areas of developmental pathobiology. Breakpoint mapping will be enhanced by FISH performed on naked DMA fibers (i.e., fiber FISH) instead of metaphase chromosomes in selected cases, particularly those with segmental duplications. Such detailed mapping studies are the entry point for the identification and characterization of developmental^ important gene(s) (Project 2), as well as the generation of animal models (Project 3). Project 1 laboratories will lead the gene discovery, functional analysis, and validation of candidate genes in DGAP cases involving female genital tract disorders and hearing loss. Finally, Project 1 will continue to share DGAP results via the Internet (http://dqap.harvard.edu/) in keeping with our goal of being a karyotypephenotype resource for clinical geneticists, cytogeneticists, and developmental biologists worldwide. In summary, Project 1 will serve as the entry point for a functional genomics project generating a public resource of genes critical to human development. RELEVANCE (See instructions): The Developmental Genome Anatomy Project studies a group of patients underserved by the health care system: those with congenital abnormalities due to chromosome rearrangements. Our mission is to discover genes of importance in human development that are disrupted by these chromosomal rearrangements, genes that are difficult to identify by more traditional human genetic strategies, thereby opening investigation of the disorders that they cause.