Project Summary/Abstract Numerous human diseases result from recurrent DNA rearrangements involving unstable genomic regions. They are facilitated by the presence of region-specific low-copy repeats (LCRs) and are the result of nonallelic homologous recombination (NAHR) between such paralogous genomic segments. The 22q11.2 region undergoes a significant number of germline rearrangements. As such, it has been classified as one of the more unstable regions of the human genome. The 22q11.2 deletion syndrome (22q11DS) is the most common microdeletion disorder. It is associated with phenotypic and neuropsychiatric pathology, both of which are widely variable. In most affected individuals, the deletion is de novo and is the result of NAHR mediated by four chromosome22-specific low copy repeats (LCRA, -B, -C and -D) in 22q11. Their size and the presence of numerous segments with near-identical sequence render these chromosome specific LCRs as substrates for NAHR. Numerous genomic disorders, including the 22q11DS are the result of NAHR. LCR22s are extremely difficult to reliably map and sequence because of their structural characteristics. Currently, an accurate reference sequence for the region does not exist. Also, they are recalcitrant to short read sequencing such that the level of their polymorphism and variability in the general population is unknown. However, optical mapping of the region with Bionano Genomics' Saphyr technology overcomes this difficulty. Thus, 22q11.2 becomes a test case for LCR delineation by optical mapping. Our preliminary optical mapping data suggests a complex organization of duplicated 160kb modules within LCRA and LCRD, including copy number and orientation differences. Further, a common inversion polymorphism within LCRD has been identified. Our preliminary data suggests that this polymorphic inversion is less prevalent in African Americans (AAs), which may finally explain the relative deficit of AAs in our CHOP-based 22q11DS cohort. We propose to employ innovative Bionano optical mapping technology to determine the frequency of 22q11 LCR polymorphisms in the general population and explore the role they play in facilitating rearrangements. The prevalence of the LCRD inversion in several different populations (CEU, African, and African American subjects from the 1000 Genomes Project; local white and AA 22q11DS trios) will be determined. The LCR22-containing regions associated with 22q11DS will be examined in these same populations to determine their structure and variation. Finally, we propose to analyze the breakpoints of some typical and atypical 22q11.2 deletions and duplications guided by Bionano optical maps derived from probands in the 22q11DS and duplication trios. By leveraging the increased sensitivity afforded by long single molecule optical mapping on nanochannel arrays, this proposal will elucidate the previously unmapped structure and variation of LCR22s and surrounding regions in greater detail. The data and ...