我们设计了一种液体活检（LB）平台，采用低通全基因组测序（LP-WGS）和靶向测序细胞游离DNA（cfDNA），从血浆中检测儿童实体肿瘤的基因组范围复制数变异（CNAs）和基因融合。共分析了来自19个对照组和73名患者的143个血浆样本，包括44个骨骼或软组织肉瘤和12个肾、10个生殖细胞、5个肝和2个甲状腺肿瘤。cfDNA可从诊断时、治疗期间和/或复发时收集的血浆中分离。26/37（70%）未经放疗、手术或化疗而在诊断时入组的患者中，基于从LP-WGS中检测CNAs的循环肿瘤DNA（ctDNA）检测，有18/27（67%）患有局部疾病和8/10（80%）患有转移性疾病。对照组均未检测到体细胞CNAs的存在。LP-WGS检测到的CNAs与匹配肿瘤中的染色体微阵列分析检测到的CNAs高度一致。利用OncoKids®我们的下一代测序（NGS）平板在肿瘤样本中检测到的突变，在14个26个血浆样本的ctDNA中也可检测到。最后，我们开发了一种基于杂交捕获面板，用于靶向骨肉瘤或肺泡型横纹肌肉瘤（ARMS）患者的EWSR1和FOXO1融合。在12名骨肉瘤患者和2名ARMS患者的血浆中检测到融合。综上所述，这些数据表明我们的LB平台在评估不同实体肿瘤的儿童患者方面具有临床适用性。 ©2023。作者。

We designed a liquid biopsy (LB) platform employing low-pass whole genome sequencing (LP-WGS) and targeted sequencing of cell-free (cf) DNA from plasma to detect genome-wide copy number alterations (CNAs) and gene fusions in pediatric solid tumors. A total of 143 plasma samples were analyzed from 19 controls and 73 patients, including 44 bone or soft-tissue sarcomas and 12 renal, 10 germ cell, five hepatic, and two thyroid tumors. cfDNA was isolated from plasma collected at diagnosis, during and after therapy, and/or at relapse. Twenty-six of 37 (70%) patients enrolled at diagnosis without prior therapy (radiation, surgery, or chemotherapy) had circulating tumor DNA (ctDNA), based on the detection of CNAs from LP-WGS, including 18 of 27 (67%) patients with localized disease and eight of 10 (80%) patients with metastatic disease. None of the controls had detectable somatic CNAs. There was a high concordance of CNAs identified by LP-WGS to CNAs detected by chromosomal microarray analysis in the matching tumors. Mutations identified in tumor samples with our next-generation sequencing (NGS) panel, OncoKids®, were also detected by LP-WGS of ctDNA in 14 of 26 plasma samples. Finally, we developed a hybridization-based capture panel to target EWSR1 and FOXO1 fusions from patients with Ewing sarcoma or alveolar rhabdomyosarcoma (ARMS), respectively. Fusions were detected in the plasma from 10 of 12 patients with Ewing sarcoma and in two of two patients with ARMS. Combined, these data demonstrate the clinical applicability of our LB platform to evaluate pediatric patients with a variety of solid tumors.© 2023. The Author(s).