Circulating Tumor DNA as a Biomarker in Patients With Stage III and IV Wilms Tumor: Analysis From a Children's Oncology Group Trial, AREN0533

Abstract

Purpose: The utility of circulating tumor DNA (ctDNA) analyses has not been established in the risk stratification of Wilms tumor (WT). We evaluated the detection of ctDNA and selected risk markers in the serum and urine of patients with WT and compared findings with those of matched diagnostic tumor samples.

Patients and methods: Fifty of 395 children with stage III or IV WT enrolled on Children's Oncology Group trial AREN0533 had banked pretreatment serum, urine, and tumor available. Next-generation sequencing was used to detect ctDNA. Copy-number changes in 1q, 16q, and 1p, and single-nucleotide variants in serum and urine were compared with tumor biopsy data. Event-free survival (EFS) was compared between patients with and without ctDNA detection.

Results: ctDNA was detected in the serum of 41/50 (82%) and in the urine in 13/50 (26%) patients. Agreement between serum ctDNA detection and tumor sequencing results was as follows: 77% for 1q gain, 88% for 16q deletions, and 70% for 1p deletions, with ĸ-coefficients of 0.56, 0.74, and 0.29, respectively. Sequencing also demonstrated that single-nucleotide variants detected in tumors could be identified in the ctDNA. There was a trend toward worse EFS in patients with ctDNA detected in the serum (4-year EFS 80% v 100%, P = .14).

Conclusion: ctDNA demonstrates promise as an easily accessible prognostic biomarker with potential to detect tumor heterogeneity. The observed trend toward more favorable outcome in patients with undetectable ctDNA requires validation. ctDNA profiling should be further explored as a noninvasive diagnostic and prognostic tool in the risk-adapted treatment of patients with WT.

Trial registration: ClinicalTrials.gov NCT00379340.

Figures

FIG 1.

Detection of ctDNA by identification of copy-number variants in serum and urine of patients with WT. (A) Violin plot of ctDNA levels in serum and urine samples restricted to cases with ctDNA above the limit of detection by ULP-WGS. Dashed vertical line within each violin plot indicates the median and the dotted lines indicate the boundaries between the first and second quartiles and the third and fourth quartiles. Probability densities are reflected by the upper and lower borders of the violin plot. Individual ctDNA data are indicated by black dots. (B) Summary of CNAs in chromosomes 1p, 1q, and 16q by case across sample types. Tissue is indicated at the top of the plot, data type indicated in the column label, and vertical black bars indicate the percent of total evaluable samples containing the variant (or with detectable ctDNA). Red blocks indicate copy gains, blue indicates copy losses, white indicates that a variant was not detected, dark gray indicates an unevaluable sample (no tissue or insufficient DNA for sequencing), and light gray indicates that no ctDNA was detectable in the sample. Percent ctDNA content indicated by number with higher ctDNA content shaded in dark teal and lower ctDNA by light teal. Cases plotted in (C-E) include “a” in the patient identifier. (C-E) Genome-wide plots represent the log2 ratio for each data point with blue data equivalent to two copies of the genomic location, teal equal to copy-number loss, and red equal to copy-number gains. Chromosomal segmental medians are also plotted as horizontal lines with light teal segments representing likely subclonal events. Arrows indicate CNAs that are not present in all matched samples from the patient. Case identifiers are present at the top of the panels. CNA, copy-number alteration; ctDNA, circulating tumor DNA; WT, Wilms tumor.

FIG 2.

SNVs identified in tumors and matched ctDNA samples. Plotted are somatic variants identified in genes frequently mutated in WTs. Open circles indicate variants identified in tumors, red circles indicate variants identified in serum, and open triangles identified from urine. The size of the symbols reflects the relative allelic fraction of the identified events. Vertical bar plots reflect the fraction of ctDNA identified in the serum (red bars) and urine (open bars with black outline). Horizontal blue bars summarize the number of variants identified in the indicated gene. aA case with two variants in the DICER1 gene identified in both the tumor and the serum. ctDNA, circulating tumor DNA; SNV, single-nucleotide variant; WT, Wilms tumor.

FIG 3.

EFS and OS in patients with and without detectable ctDNA in the serum: (A) EFS and (B) OS by ctDNA detection in the serum of patients with stage III and IV WT. ctDNA, circulating tumor DNA; EFS, event-free survival; OS, overall survival; WT, Wilms tumor.