Fig. 6: ctDNA CNV detection in FP- and FN-RMS.

a Clinical timeline with different timepoints throughout treatment course in a FN-RMS showing BCOR and CDKN2A copy number changes (log₂ ratio) in plasma using shallow (4X) WGS correlated with disease burden. Baseline WES from the same patient tumor showed 2Kb Xp11 deletions and 650Kb 9p21 involving BCOR and CDKN2A loci, respectively. b Same patient whole chromosome X and whole chromosome 9 visualization confirming the ctDNA CNV changes in BCOR and CDKN2A loci. c Comparative whole-genome visualization of copy number changes (log₂ ratio) by shallow WGS in a FP-RMS using two different sample types at the time of diagnosis (blood and bone marrow) confirming the MYCN gene-level amplification (green arrow) detected in the tumor profile at baseline (chr2p24.3 1.4 Mb MYCN amplification). d Comparative whole-genome visualization of copy number changes (log₂ ratio) derived from shallow WGS from the same FN-RMS illustrated in (a), (b), on matched tumor sample and blood at diagnosis showing a similar arm-level CNV profile. WES of primary tumor showed whole chromosomal copy number gain (green) of chromosomes 8, 11, and 20. Chemo, chemotherapy; XRT, radiotherapy.