Project Summary The proposed project serves as a platform to obtain the key training and research experiences in achieving the long-term career goal of becoming a leading academic principal investigator with a primary focus of developing and applying genomic methods to understand the complex genetic components and biological mechanisms of neuropsychiatric disorders. Chromosomal aberrations in the form of large deletions or duplications (copy number variants, CNVs), such as those on 1q21.1, 16p11.2, and 22q11.2, are the strongest known risk factors for neuropsychiatric disorders. For this reason, these large CNVs serve as key points of entry for investigating the molecular etiology. However, it is unknown why each of these CNVs is associated with diverse clinical outcomes. For example, deletions and duplications at 16p11.2 are strong risk factors for schizophrenia (SZ) and autism spectrum disorder (ASD). Duplications produce a greater than 10-fold increase in risk for SZ, but ASD is frequent in carriers of deletions as well as duplications. The large stretches of human-specific segmental duplications (HSDs) that both constitute and mediate the formation of these large “neuropsychiatric” CNVs are inaccessible to current genome sequencing analysis due to their high degree of repetitiveness and complexity. CNV studies to date have not been able to consider the genetic variations inside these hundreds of kilobases to megabases of HSDs. Thus, we do not know the exact “genomic scar” of each CNV in individual carriers including additional smaller-scale rearrangements, gene fusions, and copy number changes of paralogs, the diversity HSD rearrangements across different CNV carriers, and the concomitant functional effects. The major aims here are to (1) develop generalizable genome analysis methods to solve this important problem in psychiatric genetics in established cell lines carrying the 16p11.2 deletions and duplications as the first targets of this new approach, (2) to develop high-throughput genotyping assays so that studying the diversity of HSD rearrangements can be applied to expanded groups of affected individuals where only DNA sample (no cell lines) is available and to future cohort association studies, and (3) to investigate the functional effects of HSD rearrangement diversity on CNV biology using cortical organoid models. To facilitate career development and transition to an independent investigator, the following five training goals will be achieved under the support and guidance of the mentorship team: (1) developing expertise in targeted genome assembly analysis and optical DNA mapping; (2) expanding knowledge in developmental neuroscience and pathophysiology of psychiatric disorders; (3) gaining hands-on expertise in neuronal organoid modelling (4) acquiring expertise in chromatin interaction analysis and single-cell RNA expression analysis of neural organoids; (5) gaining experience in grant writing. The hands-on training will prima...