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. 2020 Sep 15;11:4629. doi: 10.1038/s41467-020-18388-7

Fig. 3. Genomic and proteomic characterization of paired PDX and PPC samples.

Fig. 3

a Copy-number variant (CNV) analysis of PDXs and corresponding PPCs (passage <11). Red arrows indicate detected copy number changes between PDX and PPC for samples where both DMEM- and NB-derived cultures were available. b Comparison of the mutational landscape of PDXs and corresponding PPCs. The table depicts all confirmed somatic SNVs in cases with available matched germline sequencing data. For samples without available germline data, comparison to dbSNP and 1000 g databases was used to identify potential non-synonymous SNVs in the same genes. Focal amplifications refer to genes with more than 10 gene copies. c Principal component analysis comparing DNA methylation profiles of RMS PDXs, PPCs and cell lines. DNA methylation data for 15 RMS PDX and PPC pairs, 9 additional PDXs and 10 cell lines were analyzed using the top 5000 most varied DNA methylation probes across all samples. Samples were indicated as color coded dots. Red and pink denote FP PDXs and corresponding PPCs respectively; blue and brown, FN PDX and corresponding PPCs; yellow and green, additional FP and FN PDXs; orange and purple, FP and FN cell lines. d Number of exonic SNVs in PDX and PPC model. P, PDX, C, PPC.