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

作者：Satomi Mitsuhashi, Sachiko Ohori, Kazutaka Katoh, Martin C. Frith, Naomichi Matsumoto · 发表于：Genome Medicine · 年份：2020 · DOI：10.1186/s13073-020-00762-1 · 被引用次数：40 · 研究领域：Genomic variations and chromosomal abnormalities、Genome Rearrangement Algorithms、Chromosomal and Genetic Variations

BACKGROUND: Many genetic/genomic disorders are caused by genomic rearrangements. Standard methods can often characterize these variations only partly, e.g., copy number changes or breakpoints. It is important to fully understand the order and orientation of rearranged fragments, with precise breakpoints, to know the pathogenicity of the rearrangements. METHODS: We performed whole-genome-coverage nanopore sequencing of long DNA reads from four patients with chromosomal translocations. We identified rearrangements relative to a reference human genome, subtracted rearrangements shared by any of 33 control individuals, and determined the order and orientation of rearranged fragments, with our newly developed analysis pipeline. RESULTS: We describe the full characterization of complex chromosomal rearrangements, by filtering out genomic rearrangements seen in controls without the same disease, reducing the number of loci per patient from a few thousand to a few dozen. Breakpoint detection was very accurate; we usually see ~ 0 ± 1 base difference from Sanger sequencing-confirmed breakpoints. 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. A rearrangement is more than the sum of its parts: some properties, such as sequence loss, can be inferred on...