ArticleNPJ precision oncology2023
Combined low-pass whole genome and targeted sequencing in liquid biopsies for pediatric solid tumors.
Article in NPJ precision oncology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers, 1 of them a synthesis that pooled it.
What it found
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
44 citing papers in PubMed, 1 synthesis or guideline pooled it, 55 citations in OpenAlex.
- Prognostic value of circulating tumor DNA in different cancer types detected by ultra-low-pass whole-genome sequencing: a systematic review and patient-level survival data meta-analysis.Carcinogenesis · 2025Pooled it
- Cerebrospinal Fluid in Pediatric Neuro-Oncology: Molecular Diagnosis, Disease Monitoring, and Clinical Translation.International journal of molecular sciences · 2026Review
- Clinical Liquid Biopsy Testing for Detection of Actionable Genomic Alterations in Children and Young Adults With Advanced Solid Tumors on the GAIN Study.JCO precision oncology · 2026Article
- Liquid biopsy in malignant primary bone tumors: Clinical applications of circulating tumor DNA and circulating tumor cells for diagnosis, prognosis and treatment monitoring (Review).Oncology reports · 2026Review
- Safety Assessment of Aqueous Humor Liquid Biopsy in Retinoblastoma: A Multicenter Study of 1203 Procedures.Ophthalmology · 2026Article
- Cell-free DNA from cerebrospinal fluid cytology specimens as a novel liquid biopsy approach for pediatric patients with primary central nervous system tumors.Acta neuropathologica communications · 2026Article
- Prospective implementation of an aqueous humor liquid biopsy platform informs clinical diagnosis and management of retinoblastoma and other intraocular lesions.NPJ precision oncology · 2026Article
- Circulating Tumor DNA and microRNA-Based Liquid Biopsy for Longitudinal Treatment Monitoring and Recurrence Prediction in Pediatric Sarcomas: A Prospective Cohort Study.Oncology research · 2026Article
- Fusion of Generative AI Techniques and Machine Learning Models to Generate and Investigate Biosignals for Glucose Sensors.ACS omega · 2025Article
- Aqueous humor biomarkers in ocular oncology: Insights and advances.Cell reports. Medicine · 2025Review
- Patient-specific sequencing panels enable sensitive circulating tumor DNA analysis in rhabdomyosarcoma independent of genetic profile.NPJ precision oncology · 2025Article
- Reply to the Letter to the Editor: Can a Liquid Biopsy Detect Circulating Tumor DNA With Low-passage Whole-genome Sequencing in Patients With a Sarcoma? A Pilot Evaluation.Clinical orthopaedics and related research · 2025Article
- Genome-wide cfDNA fragmentation patterns in cerebrospinal fluid reflect medulloblastoma groups.NPJ precision oncology · 2025Article
- Global Health and Genomics.The Nursing clinics of North America · 2025Review
- Review
- A perspective review on the systematic implementation of ctDNA in phase I clinical trial drug development.Journal of experimental & clinical cancer research : CR · 2025Review
- Multicentre analysis of nucleic acid quantification using aqueous humour liquid biopsy in uveal melanoma: implications for clinical testing.Canadian journal of ophthalmology. Journal canadien d'ophtalmologie · 2025Article
- Article
- Whole genome sequencing completes the molecular genetic testing workflow of patients with Lynch syndrome.NPJ genomic medicine · 2025Article
- The use of aqueous humor cfDNA for low-pass whole genome sequencing as a clinical test to identify intraocular retinoblastoma recurrence.ScienceBank · 2025Article
Corrections and comments
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Authors and funding
14 authors at 2 institutions in 1 country.
Funding
Abstract
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.
Identifiers
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.