Sequence resolution of complex human genome structural variation

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ABSTRACT Understanding the genetic basis of human disease requires a comprehensive assessment of the full spectrum of human genetic variation. While the majority of structural variation can now be routinely discovered by application of long reads and phased genome assembly, inversions have proven more difficult to characterize due to their association with repetitive DNA and their location/structure in the genome. These represent some of the largest forms of naturally occurring human genetic variation but are the least understood. That is because these loci are preferentially associated with gaps and are frequently subject to the highest frequency of recurrent mutation making them difficult to genotype using standard approaches. In this competing renewal, we focus on the complete sequence resolution of inversion hotspots of structural variation flanked by multi- copy segmental duplications. We apply long-read high-fidelity sequencing, ultra-long-read sequencing, and Strand-seq data to fully phase and assemble all inversion polymorphisms and flanking sequence for 120 human genomes (Aim 1). We use the associated haplotype data to develop methods to identify inversions associated with recurrent mutation and then test whether recurrent mutations are preferentially associated with altered structural configurations of flanking segmental duplications by genotyping these variants in a diversity panel of 3,200 human genomes where short-read whole-genome sequence data are available (Aim 2). Finally, we use the sequence-resolved haplotype structures coupled to long-read sequencing of patients to delineate breakpoints of rearrangements identified in 125 individuals harboring de novo large-scale deletions or duplications (Aim 3). This aim will test whether certain structural configurations are predisposed to recurrent rearrangement and improve breakpoint mapping associated with de novo rearrangement events. New sequence-based methods will also be developed to characterize more complex forms of human genetic variation and provide fundamental insight into their diversity, mechanism of origin, and mutational properties. This research has the additional benefit that it will improve genome assembly, characterize a large class of missing genetic variation, and provide us with the ability to more systematically explore this form of human genetic variation as part of future disease-association studies.