OneD: increasing reproducibility of Hi-C samples with abnormal karyotypes.

ABSTRACT: The three-dimensional conformation of genomes is an essential component of their biological activity. The advent of the Hi-C technology enabled an unprecedented progress in our understanding of genome structures. However, Hi-C is subject to systematic biases that can compromise downstream analyses. Several strategies have been proposed to remove those biases, but the issue of abnormal karyotypes received little attention. Many experiments are performed in cancer cell lines, which typically harbor large-scale copy number variations that create visible defects on the raw Hi-C maps. The consequences of these widespread artifacts on the normalized maps are mostly unexplored. We observed that current normalization methods are not robust to the presence of large-scale copy number variations, pot

SUBMITTER: Vidal E 

PROVIDER: S-EPMC5934634 | biostudies-literature | 2018 May

REPOSITORIES: biostudies-literature