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Updated: Nov 8, 2025
An Integrated Platform for Genome-wide Mapping of Chromatin States Using High-throughput ChIP-sequencing in Tumor Tissues
Published on: April 5, 2018
Chromatin conformation capture (Hi-C) sequencing of patient-derived xenografts: analysis guidelines
Mikhail G Dozmorov1,2, Katarzyna M Tyc1,3, Nathan C Sheffield4
1Department of Biostatistics, Virginia Commonwealth University, Richmond, VA 23298, USA.
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 strategies (Direct, Xenome, Combined) and 3 pipelines (Juicer, HiC-Pro, HiCExplorer) on Hi-C data quality.
Conclusions:
Removal of mouse reads had little-to-no effect on data quality as compared with the results obtained with the Direct alignment strategy. Juicer extracted more valid chromatin interactions for Hi-C matrices, regardless of the mouse read removal strategy. However, the pipeline effect was minimal, while the library preparation strategy had the largest effect on all quality metrics. Together, our study presents comprehensive guidelines on PDX Hi-C data processing.
Insights
Removing mouse DNA sequences from patient-derived xenograft (PDX) chromatin conformation capture (Hi-C) data has minimal impact. Library preparation strategy significantly affects Hi-C data quality more than mouse read removal.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Patient-derived xenograft (PDX) models enable studying human tumor mechanisms in mice.
- PDX sequencing involves both human and mouse genetic material.
- Mouse read removal methods exist for RNA-seq and exome data, but their impact on Hi-C data is unclear.
Purpose of the Study:
- To evaluate the effect of mouse read removal on the quality of Hi-C data from PDX models.
- To compare different alignment strategies and bioinformatics pipelines for PDX Hi-C data processing.
Main Methods:
- In silico generated PDX Hi-C data with 10% and 30% mouse reads were used.
- Two experimental PDX Hi-C datasets were generated using distinct library preparation methods.
- Three alignment strategies (Direct, Xenome, Combined) and three pipelines (Juicer, HiC-Pro, HiCExplorer) were assessed.
Main Results:
- Mouse read removal showed minimal effect on Hi-C data quality compared to the Direct alignment strategy.
- The Juicer pipeline identified more valid chromatin interactions in Hi-C matrices, irrespective of mouse read removal.
- Library preparation strategy had the most substantial impact on all evaluated quality metrics.
Conclusions:
- Mouse read removal is not critical for PDX Hi-C data quality when using the Direct alignment strategy.
- The choice of library preparation method is paramount for optimal PDX Hi-C data quality.
- This study provides essential guidelines for processing PDX Hi-C data effectively.
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