Identification and utilization of copy number information for correcting Hi-C contact map of cancer cell lines.

ABSTRACT:

Background

Hi-C and its variant techniques have been developed to capture the spatial organization of chromatin. Normalization of Hi-C contact map is essential for accurate modeling and interpretation of high-throughput chromatin conformation capture (3C) experiments. Hi-C correction tools were originally developed to normalize systematic biases of karyotypically normal cell lines. However, a vast majority of available Hi-C datasets are derived from cancer cell lines that carry multi-level DNA copy number variations (CNVs). CNV regions display over- or under-representation of interaction frequencies compared to CN-neutral regions. Therefore, it is necessary to remove CNV-driven bias from chromatin interaction data of cancer cell lines to generate a euploid-equivalent contact map.

SUBMITTER: Khalil AIS 

PROVIDER: S-EPMC7648276 | biostudies-literature | 2020 Nov

REPOSITORIES: biostudies-literature