A method for complete characterization of complex germline rearrangements from long DNA reads

Many genetic/genomic disorders are caused by genomic rearrangements. Standard methods can often characterize these variations only partly, e.g. copy number changes. We describe full characterization of complex chromosomal rearrangements, based on whole-genome-coverage sequencing of long DNA reads from four patients with chromosomal translocations. We developed a new analysis pipeline, which filters out rearrangements seen in humans without the same disease, reducing the number of loci per patient from a few thousand to a few dozen. For one patient with two reciprocal chromosomal translocations, we find that the translocation points have complex rearrangements of multiple DNA fragments involving 5 chromosomes, which we could order and orient by an automatic algorithm, thereby fully reconstructing the rearrangement. Some important properties of these rearrangements, such as sequence loss, are holistic: they cannot be inferred from any part of the rearrangement, but only from the fully-reconstructed rearrangement. In this patient, the rearrangements were evidently caused by shattering of the chromosomes into multiple fragments, which rejoined in a different order and orientation with loss of some fragments. Our approach promises to fully characterize many congenital germline rearrangements, provided they do not involve poorly-understood loci such as centromeric repeats.