PROJECT 1 ABSTRACT. Gene discovery has been the backbone of DGAP since its inception. Using classical positional cloning techniques, complemented by deep mechanistic studies, DGAP has represented one of the few and most productive studies in human genetics to investigate balanced chromosomal abnormalities (BCAs). The advent of genome-wide surveys of dosage imbalance and now point mutations in the coding portion of the genome by whole-exome sequencing has enabled the rapid growth of large cohort studies to evaluate the genetic architecture of complex disorders, including congenital anomalies, yet these studies still fail to access BCAs. In the previous funding cycle, the P.I. of this newly created Project 1 and the former Project 2 (Gusella) developed novel methods of whole-genome sequencing to delineate rapidly the precise breakpoints of chromosomal abnormalities to nucleotide resolution. We applied these techniques to karyotypically detected BCAs and revealed the informative power of these events as a uniquely efficient route to strong effect mutations that are not routinely accessed by any other approaches, and illuminated the potentially transformative implementation of the technology in clinical diagnostic testing. We also highlighted the impact of cryptic BCAs, a class of genomic variation that remains a glaring blind spot in human genetics and clinical diagnostics. These variants are particularly significant to the study of congenital anomalies as an astounding 80-85% of all clinical genetic dosage array testing fails to find a clinically significant result. In this renewal of DGAP, Project 1 is a newly formed Project, which has been transformed into the high-throughput genomics and computational biology hub of DGAP. It will facilitate integrative interpretation of BCA breakpoints for gene discovery and prioritization of functional studies in the newly focused Projects 2 and 3. We will apply cutting edge technology and algorithm development to rapidly discover genes disrupted by BCAs. We will sequence at least 1,000 genomes, including individuals harboring a BCA with or without a congenital anomaly, and individuals with congenital anomalies for which conventional genetic testing failed to detect a clinically meaningful result. We hypothesize that this latter cohort will be significantly enriched for pathogenic cryptic BCAs, as is suggested by our preliminary studies. This approach will be, to our knowledge, the first large-scale effort to characterize and evaluate the impact of cryptic BCAs in human disease. We will provide a convergent genomic interpretation of BCA disruptions using genomic data from over 100,000 independent subjects. Project 1 of DGAP will thus bring this unique approach to delineating chromosomal abnormalities into the era of large cohort genomic studies. As a final product, Project 1 will leverage these incredibly high yield genetic lesions into new insights about the genetic etiology of congenital anomalies, provide a bolus of novel loci for further study, and establish an integrative annotation of the morbid human genome for the benefit of future mechanistic studies, as DGAP has always done.