한빛사 논문
Se-Young Jo†, Eunyoung Kim† and Sangwoo Kim*
Department of Biomedical Systems Informatics and Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, South Korea
† Se-Young Jo and Eunyoung Kim contributed equally to this work.
*Correspondence : Sangwoo Kim
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 reference, including 467,232 (38.7%) alleles with high sensitivity to contamination, which are pervasive causes of false cancer mutations in public databases and are signatures for predicting global contamination. Next, we assess the performance of 8 filtering methods in terms of mouse read filtration and reduction of mouse-specific alleles. All filtering tools generally perform well, although differences in algorithm strictness and efficiency of mouse allele removal are observed. Therefore, we develop a best practice pipeline that contains the estimation of contamination level, mouse read filtration, and variant filtration.
Conclusions
The inclusion of mouse cells in patient-derived models hinders genomic analysis and should be addressed carefully. Our suggested guidelines improve the robustness and maximize the utility of genomic analysis of these models.
Keywords: Benchmark, Patient-derived model, Genomic analysis, Mouse contamination, Best practice, Read filtering
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