Shuffle cassettes and genome shuffle sequencing

Abstract

Provided herein are compositions and methods for multiplex generation, mapping, and characterization of structural variants in a host cell genome. A shuffle cassette includes a recombination site flanked by a pair of unique barcodes, a pair of primer binding sites, and a pair of promoters. Libraries of shuffle cassettes are integrated throughout a host cell genome, and their genomic positions are mapped by transcribing flanking genomic sequences via the promoters and associating barcode pairs with specific genomic coordinates. Upon introduction of a recombinase, recombination between integrated shuffle cassettes generates structural variants including deletions, inversions, translocations, and extrachromosomal circular DNAs. Novel barcode combinations arising from recombination events are detected to identify the class and breakpoints of each structural variant at base-pair resolution without whole-genome sequencing. The methods further enable co-capture of structural variant identity with single-cell transcriptomes, linking specific structural variants to gene expression phenotypes.

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