Impact of mouse contamination in genomic profiling of patient-derived models and best practice for robust analysis.

ABSTRACT:

Background

Patient-derived xenograft and cell line models are popular models for clinical cancer research. However, the inevitable inclusion of a mouse genome in a patient-derived model is a remaining concern in the analysis. Although multiple tools and filtering strategies have been developed to account for this, research has yet to demonstrate the exact impact of the mouse genome and the optimal use of these tools and filtering strategies in an analysis pipeline.

Results

We construct a benchmark dataset of 5 liver tissues from 3 mouse strains using human whole-exome sequencing kit. Next-generation sequencing reads from mouse tissues are mappable to 49% of the human genome and 409 cancer genes. In total, 1,207,556 mouse-specific alleles are aligned to the human genome refer

SUBMITTER: Jo SY 

PROVIDER: S-EPMC6844030 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature