HolistIC: leveraging Hi-C and whole genome shotgun sequencing for double minute chromosome discovery.

ABSTRACT:

Motivation

Double minute (DM) chromosomes are acentric extrachromosomal DNA artifacts that are frequently observed in the cells of numerous cancers. They are highly amplified and contain oncogenes and drug-resistance genes, making their presence a challenge for effective cancer treatment. Algorithmic discovery of DM can potentially improve bench-derived therapies for cancer treatment. A hindrance to this task is that DMs evolve, yielding circular chromatin that shares segments from progenitor DMs. This creates DMs with overlapping amplicon coordinates. Existing DM discovery algorithms use whole genome shotgun sequencing (WGS) in isolation, which can potentially incorrectly classify DMs that share overlapping coordinates.

Results

In this study, we describe an algorithm called

SUBMITTER: Hayes M 

PROVIDER: S-EPMC9991898 | biostudies-literature | 2022 Feb

REPOSITORIES: biostudies-literature