Chromatin conformation capture (Hi-C) sequencing of patient-derived xenografts: analysis guidelines.

ABSTRACT:

Background

Sequencing of patient-derived xenograft (PDX) mouse models allows investigation of the molecular mechanisms of human tumor samples engrafted in a mouse host. Thus, both human and mouse genetic material is sequenced. Several methods have been developed to remove mouse sequencing reads from RNA-seq or exome sequencing PDX data and improve the downstream signal. However, for more recent chromatin conformation capture technologies (Hi-C), the effect of mouse reads remains undefined.

Results

We evaluated the effect of mouse read removal on the quality of Hi-C data using in silico created PDX Hi-C data with 10% and 30% mouse reads. Additionally, we generated 2 experimental PDX Hi-C datasets using different library preparation strategies. We evaluated 3 alignment strateg

SUBMITTER: Dozmorov MG 

PROVIDER: S-EPMC8058593 | biostudies-literature | 2021 Apr

REPOSITORIES: biostudies-literature