The utility of circulating tumor DNA (ctDNA) analysis has not been well-established for disease detection and monitoring of childhood cancers, especially leukemias. We developed PeCan-Seq, a deep sequencing method targeting diverse somatic genomic variants in cell-free samples in childhood cancer. Plasma samples were collected at diagnosis from 233 children with hematologic, solid and brain tumors. All children with hematologic malignancy (n = 177) had detectable ctDNA at diagnosis. The median ctDNA fraction was 0.77, and 97% of 789 expected tumor variants were identified, including sequence mutations, copy number variations, and structural variations responsible for oncogenic fusions. In contrast, ctDNA was detected in 19 of 38 solid tumor patients and 1 of 18 brain tumor patients. Somatic variants from ctDNA were correlated with minimal residual disease levels as determined by flow cytometry in serial plasma samples from patients with B-cell acute lymphoblastic leukemia (B-ALL). We showcase multi-tumor detection by ctDNA analysis for a patient with concurrent B-ALL and neuroblastoma. In conclusion, PeCan-seq sensitively identified heterogeneous ctDNA alterations from 1 mL plasma for childhood hematologic malignancies and a subset of solid tumors. PeCan-seq provides a robust, non-invasive approach to augment comprehensive genomic profiling at diagnosis and mutation-specific detection during disease monitoring.

循环肿瘤 DNA （ctDNA） 分析在儿童癌症（尤其是白血病）的疾病检测和监测方面的效用尚未得到充分证实。我们开发了 PeCan-Seq，这是一种针对儿童癌症无细胞样本中不同体细胞基因组变异的深度测序方法。诊断时从 233 例血液肿瘤、实体瘤和脑肿瘤患儿中采集血浆样本。所有血液系统恶性肿瘤患儿 （n = 177） 在诊断时均可检测到 ctDNA。中位 ctDNA 分数为 0.77，鉴定出 97 个预期肿瘤变异中的 789%，包括序列突变、拷贝数变异和导致致癌融合的结构变异。相比之下，在 38 名实体瘤患者中有 19 名和 18 名脑瘤患者中有 1 名检测到 ctDNA。ctDNA 的体细胞变异与 B 细胞急性淋巴细胞白血病 （B-ALL） 患者系列血浆样本中通过流式细胞术测定的最小残留病灶水平相关。我们展示了通过 ctDNA 分析对并发 B-ALL 和神经母细胞瘤患者进行多肿瘤检测。总之，PeCan-seq 灵敏地识别了 1 mL 血浆中儿童血液系统恶性肿瘤和实体瘤亚群的异质性 ctDNA 改变。PeCan-seq 提供了一种稳健、无创的方法，可在诊断时增强全面的基因组分析，并在疾病监测期间增强突变特异性检测。