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 ( 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.

Public Health Relevance

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.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Program Projects (P01)
Project #
Application #
Study Section
Special Emphasis Panel (ZRG1-GGG-G)
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
Brigham and Women's Hospital
United States
Zip Code
Wang, Jian; Yu, Tingting; Wang, Zhigang et al. (2016) A New Subtype of Multiple Synostoses Syndrome Is Caused by a Mutation in GDF6 That Decreases Its Sensitivity to Noggin and Enhances Its Potency as a BMP Signal. J Bone Miner Res 31:882-9
Chen, Xiaoli; An, Yu; Gao, Yonghui et al. (2016) Rare Deleterious PARD3 Variants in the aPKC-Binding Region are Implicated in the Pathogenesis of Human Cranial Neural Tube Defects via Disrupting Apical Tight Junction Formation. Hum Mutat :
Tai, Derek J C; Ragavendran, Ashok; Manavalan, Poornima et al. (2016) Engineering microdeletions and microduplications by targeting segmental duplications with CRISPR. Nat Neurosci 19:517-22
Ordulu, Zehra; Kammin, Tammy; Brand, Harrison et al. (2016) Structural Chromosomal Rearrangements Require Nucleotide-Level Resolution: Lessons from Next-Generation Sequencing in Prenatal Diagnosis. Am J Hum Genet 99:1015-1033
Mukherjee, Kusumika; Ishii, Kana; Pillalamarri, Vamsee et al. (2016) Actin capping protein CAPZB regulates cell morphology, differentiation, and neural crest migration in craniofacial morphogenesis†. Hum Mol Genet 25:1255-70
Brand, Harrison; Collins, Ryan L; Hanscom, Carrie et al. (2015) Paired-Duplication Signatures Mark Cryptic Inversions and Other Complex Structural Variation. Am J Hum Genet 97:170-6
Quintero-Rivera, Fabiola; Xi, Qiongchao J; Keppler-Noreuil, Kim M et al. (2015) MATR3 disruption in human and mouse associated with bicuspid aortic valve, aortic coarctation and patent ductus arteriosus. Hum Mol Genet 24:2375-89
Macera, M J; Sobrino, A; Levy, B et al. (2015) Prenatal diagnosis of chromothripsis, with nine breaks characterized by karyotyping, FISH, microarray and whole-genome sequencing. Prenat Diagn 35:299-301
Migliavacca, Eugenia; Golzio, Christelle; Männik, Katrin et al. (2015) A Potential Contributory Role for Ciliary Dysfunction in the 16p11.2 600 kb BP4-BP5 Pathology. Am J Hum Genet 96:784-96
Choi, Jin-Ho; Balasubramanian, Ravikumar; Lee, Phil H et al. (2015) Expanding the Spectrum of Founder Mutations Causing Isolated Gonadotropin-Releasing Hormone Deficiency. J Clin Endocrinol Metab 100:E1378-85

Showing the most recent 10 out of 65 publications