Diagnostic yield and clinical impact of germline sequencing in children with CNS and extracranial solid tumors-a nationwide, prospective Swedish study

Abstract

Background: Childhood cancer predisposition (ChiCaP) syndromes are increasingly recognized as contributing factors to childhood cancer development. Yet, due to variable availability of germline testing, many children with ChiCaP might go undetected today. We report results from the nationwide and prospective ChiCaP study that investigated diagnostic yield and clinical impact of integrating germline whole-genome sequencing (gWGS) with tumor sequencing and systematic phenotyping in children with solid tumors.

Methods: gWGS was performed in 309 children at diagnosis of CNS (n = 123, 40%) or extracranial (n = 186, 60%) solid tumors and analyzed for disease-causing variants in 189 known cancer predisposing genes. Tumor sequencing data were available for 74% (227/309) of patients. In addition, a standardized clinical assessment for underlying predisposition was performed in 95% (293/309) of patients.

Findings: The prevalence of ChiCaP diagnoses was 11% (35/309), of which 69% (24/35) were unknown at inclusion (diagnostic yield 8%, 24/298). A second-hit and/or relevant mutational signature was observed in 19/21 (90%) tumors with informative data. ChiCaP diagnoses were more prevalent among patients with retinoblastomas (50%, 6/12) and high-grade astrocytomas (37%, 6/16), and in those with non-cancer related features (23%, 20/88), and ≥2 positive ChiCaP criteria (28%, 22/79). ChiCaP diagnoses were autosomal dominant in 80% (28/35) of patients, yet confirmed de novo in 64% (18/28). The 35 ChiCaP findings resulted in tailored surveillance (86%, 30/35) and treatment recommendations (31%, 11/35).

Interpretation: Overall, our results demonstrate that systematic phenotyping, combined with genomics-based diagnostics of ChiCaP in children with solid tumors is feasible in large-scale clinical practice and critically guides personalized care in a sizable proportion of patients.

Funding: The study was supported by the Swedish Childhood Cancer Fund and the Ministry of Health and Social Affairs.

Keywords: Childhood cancer predisposition; Germline variants; Somatic mutations; Whole-genome sequencing.

Fig. 1

Overview of study design and study cohort. a) Study design, figure created with BioRender.com; b) Nationwide inclusion. The Stockholm node includes both the Pediatric Oncology Department of Karolinska University Hospital and the Ocular Oncology Department of St. Erik Eye Hospital. Number of patients included by each center are presented in parenthesis (n). c) Treemap of the different tumors included. Diagnoses were classified according to International Classification of Childhood Cancer Third edition (ICCC-3). ICCC-3 groups are presented in parenthesis. CNS tumors emcompass both group III (n = 121) and group Xa (n = 2). Lymphoma (II) group includes also reticuloendothelial neoplasms. Nb = neuroblastoma; Rb = retinoblastoma; GCT = germ cell tumor. d) Comparison between study cohort (GMS-ChiCaP) and tumor diagnoses made in Sweden during the study period according to data from the Swedish Childhood Cancer Registry, grouped according to ICCC-3. Nb = neuroblastoma; Rb = retinoblastoma; GCT = germ cell tumor. CNS tumors emcompass both group III and group Xa.

Fig. 2

Germline findings. a) Tile plot where each row represents a unique patient with germline P/LP findings. The row names indicate the patient ID, the tumor type and the mutated gene. The columns present, from left to right, [column title, values], “Case ID”; “Diagnosis” WHO 2021 tumor type; “Gene” mutated in germline; “Tumor type”, CNS or extracranial solid tumor; “ChiCaP known at diagnosis”, if the ChiCaP syndrome was known at study inclusion (‘Yes’) or discovered within the study (‘No’); “Nr of positive ChiCaP criteria”, the number of fulfilled ChiCaP criteria (range 0–4); “Germline genotype”, the genotype of the germline finding with‘heterozygous_NA’ for patients where parental samples were not available; “Second hit”, presence and type of second hit in the same gene (‘inconclusive’ refers to tumor data were no somatic findings were made, possibly suggesting a non-representative sample); ‘CNLOH’ = copy number neutral loss of heterozygosity; ‘CNV’ = copy number variant); “TMB”, log10 tumor mutation burden, “Surveillance recommendation”, whether the ChiCaP finding resulted in potential or observed ChiCaP-informed follow-up; “Treatment recommendation”, whether the ChiCaP finding results in potential or observed ChiCaP-informed treatment choices. b) Number of patients diagnosed with ChiCaP in different tumor types according to main ICCC-3 groups. CNS tumors emcompass both group III (n = 121) and group Xa (n = 2). Nb = neuroblastoma; Rb = retinoblastoma; GCT = germ cell tumor. c) Number of patients with ChiCaP syndromes in categories of CNS tumors. HG = high-grade; LG = low-grade. d) Histogram of mutated genes in relation to main ICCC-3 groups. e) Proportion of somatic single base substitution (SBS) COSMIC mutational signatures detected by WGS in the tumor of the six patients with TMB > 10. BC14 with germline homozygous variants in MSH2 and MSH6 genes (CMMRD) and astrocytoma, IDH-mutant, CNS WHO grade 3; BC22 with germline heterozygous variant in MSH2 (Lynch syndrome, LS) and astrocytoma IDH-mutant CNS WHO grade 4; BC25 with germline heterozygous variant in MSH2 (LS) and astrocytoma IDH-mutant CNS WHO grade 4; BC275 with germline homozygous variants in PMS2 (CMMRD) and diffuse pediatric-type high-grade glioma, H3-wildtype and IDH-wildtype; BC47 with germline homozygous variant in ERCC5 (Xeroderma pigmentosum, XP) and BC86 with germline heterozygous variant in POLE and embryonal rhabdomyosarcoma. Signatures labeled with “∗” have unclear evidence for real signature according to COSMIC and are labeled according to their proposed etiology in the COSMIC database. SBS11 has been associated also with temozolomide chemotherapy, but BC275 was treatment naive at sampling. Different signatures with same etiology, either validated or proposed (∗) where assigned the same color. The calculated TMB for the specific tumor is displayed on top of each bar.

Fig. 3

ChiCaP indicators. a) Structure of ChiCaP criteria form. The ChiCaP criteria form is described in details in Supplementary methods. b) Number of patients fulfilling 0–3 ChiCaP criteria. No patient fulfilled 4 ChiCaP criteria. c) Diagnostic yield according to the number of fulfilled ChiCaP criteria. A and B include the 293 patients with ChiCaP criteria information available. “Other diagnosis” refers to patients with other genetic diagnoses without a well established linked to childhood cancer predisposition. d) Upset plot summarizing positive ChiCaP criteria in patients that fulfilled at least one criterion (n = 194). The bar charts on top display the number of patients who fulfilled a single criterion (single filled-in dot below the X-axis) or a combination of criteria (filled-in dots connected by lines below the X axis). “Other diagnosis” refers to patients with other genetic diagnoses without a well established linked to childhood cancer predisposition.