Integration of Hi-C with short and long-read genome sequencing reveals the structure of germline rearranged genomes - Nature Communications

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Integration of Hi-C with short and long-read genome sequencing reveals the structure of germline rearranged genomes - Nature Communications
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The architecture of shattered genomes: Study demonstrates potential of new sequencing technologies NatureComms

, were computed as the fraction of the genomic feature with respect to the length of all chromosomes, excluding gaps of the reference genome in the computation.

Novel adjacencies with random connections: For the set of novel adjacencies from all cases, the connection between anchor points were permuted. Thus, the coordinates stayed the same, but the connection between breakpoints was altered. This permutation was used to evaluate A/B-compartment fusions and LAD/None-LAD fusions.

For case CT2, one chromosomal fragment was broken up manually in the reconstruction, because it led to the connection of chromosomal components, which were not compatible with the Hi-C grid . The position of the breakpoint was approximated from Hi-C alone.Manually curated large-scale novel adjacencies were used for the reconstruction of derivative chromosomes.

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