Complex structural variation is prevalent and highly pathogenic in pediatric solid tumors

Abstract

In pediatric cancer, structural variants (SVs) and copy-number alterations contribute to cancer initiation as well as progression, thereby aiding diagnosis and treatment stratification. Although suggested to be of importance, the prevalence and biological relevance of complex genomic rearrangements (CGRs) across pediatric solid tumors is largely unexplored. In a cohort of 120 primary tumors, we systematically characterized patterns of extrachromosomal DNA, chromoplexy, and chromothripsis across five pediatric solid cancer types. CGRs were identified in 56 tumors (47%), and in 42 of these tumors, CGRs affect cancer driver genes or result in unfavorable chromosomal alterations. This demonstrates that CGRs are prevalent and pathogenic in pediatric solid tumors and suggests that selection likely contributes to the structural variation landscape. Moreover, carrying CGRs is associated with more adverse clinical events. Our study highlights the potential for CGRs to be incorporated in risk stratification or exploited for targeted treatments.

Keywords: CGRs; WGS; chromoplexy; chromothripsis; complex genomic rearrangements; complex structural variation; ecDNA; extrachromosomal DNA; pediatric solid tumors; whole-genome sequencing.

Graphical abstract

Figure 1

Occurrence of CGRs in pediatric solid tumors (A) Number of SVs per tumor colored by CGR type (top), number of nonsynonymous SNVs/indels (center), and FGA by CN gain or loss (bottom) across pediatric solid tumors. From left to right: Ewing sarcoma (EWS), neuroblastoma (NBL), fusion-positive rhabdomyosarcoma (FP-RMS), fusion-negative rhabdomyosarcoma (FN-RMS), Wilms tumor (WT), and hepatoblastoma (HBL). Symbols denote genomic instability mutations: TP53 disruption (triangle), MDM2 amplification (circle). ∗M002AAB has a germline TP53 alteration. (B) Characteristics of CGR types and circos plots of examples. From left to right: ecDNA/amplicon-type (patient M721AAC), chromoplexy (patient M135AAD), and chromothripsis (patient M050AAB). CGRs are categorized based on the following core characteristics: ecDNA/amplicon, SVs with breakpoints within 1 kbp of amplicons; chromoplexy, SVs form a closed cycle and connect multiple chromosomes via CN-balanced interchromosomal breakpoints; chromothripsis, footprints with oscillating CN segments and at least 10 overlapping SVs of mixed types, indicating randomly joined fragments. CGRs not complying with these criteria were categorized as complex other. See STAR Methods for more details. The circos plots contain SV breakpoints (links) involved in the CGR and depict gains (red) and losses (blue) of genomic material of the affected chromosomes.

Figure 2

Hotspots of CGRs overlap with cancer driver genes Genome-wide overview of recurrently altered genomic regions (Table S3) with SV breakpoints from three or more tumors (gray bars). CGR hotspots containing SV breakpoints that are part of a single CGR from three or more tumors are highlighted (circles, thick lines), colored according to their cancer type and annotated with overlapping cancer driver genes.

Figure 3

CGRs affect known cancer driver genes and chromosomal alterations Number of complex events (top) per tumor colored by CGR type and filled with patterns indicating their effect: cancer driver gene (cross) or unfavorable chromosomal alteration (lines). Patients are annotated by whether the tumors carry a clinically relevant driver alteration (circle) or an alteration in TP53 or MDM2 (triangle), as well as whether they experienced a clinical event (progression, relapse or death, red circle). ∗M002AAB has a germline TP53 alteration. Mutation status per tumor (bottom) across selected genes and genomic regions that are relevant in at least one of the included cancer types. Alterations are colored by type: complex (red), SV (green), SNV/indel (purple), or CN alteration (CNA, beige). Alterations of known relevance in that cancer type are highlighted by a black border. See also Figures S1–S10.

Figure 4

Focal chromothripsis in HBL Recurrent focal chromothripsis was identified in three HBLs (from left to right): tumors from patients M103AAA, M651AAB, and M333AAB. All three examples have breakpoints in the CGR hotspot on chromosome 1 (chr1:33517560-35493723) (Table S3) and a recurrently lost region on chr1p: chr1:1-34847815 (Table S5). The circos plots contain the SV breakpoints (links) of the CGR and the gains (red) and losses (blue) of genomic material of the affected chromosomes.