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. 2024 May 31;15:4653. doi: 10.1038/s41467-024-47547-3

Fig. 3. An NSG-adapted mouse reference genome.

Fig. 3

A Detection of mouse DNA contamination in PDX model whole-exome sequencing (WES) data using FastQ Screen (n primary regions = 108, n PDX samples = 99). The box plot represents the upper and lower quartiles (box limits), the median (center line) and the whiskers span 1.5*IQR. Two-sided Wilcoxon rank sum test, p value as indicated. B Overview of PDX-unique non-driver mutations called in PDX models from two or more patients after using the mm10 reference genome (GRCm38; left) or a NOD scid gamma mouse-adapted (NSG-adapted) reference genome (right) for mouse WES read removal. C Percentage of genome-wide single nucleotide polymorphisms (total = 7,333,533) identified as non-concordant in whole-genome sequencing data from an NSG mouse, compared to the mm10 (GRCm38) reference genome.