Abstract 967: Clinical applicability of targeted panel sequencing in liquid biopsies for disease diagnosis and monitoring of patients with pediatric solid tumors
Authors: Eirini Christodoulou, Venkata Yellapantula, Katrina O'Halloran, Liya Xu, Jesse L. Berry, Fariba Navid, Dejerianne Ostrow, Jaclyn A. Biegel
Journal: Cancer Research (2024)

Abstract Liquid biopsy assays based on sequence analysis of cell-free DNA (cfDNA) have the potential to transform patient care. We recently validated a liquid biopsy platform, LBSeq4Kids, for patients with retinoblastoma, brain tumors and solid tumors using low pass whole genome sequencing (LP-WGS) of cfDNA from aqueous humor (AH), cerebrospinal fluid (CSF), and plasma (PL) to detect Copy Number Alterations (CNAs) in circulating tumor DNA (ctDNA). Herein, we present phase 2, a high-depth comprehensive Next-Generation Sequencing (NGS) panel using cfDNA that allows us to detect SNV’s, indels and gene fusions in clinically relevant genes for pediatric solid and brain tumors. Seventy-four cfDNA specimens have been analyzed to date, using plasma from 43 patients with solid tumors, CSF from 25 patients with brain tumors and AH from six patients with ocular tumors including retinoblastoma. cfDNA was extracted at diagnosis, during therapy, at remission and/or relapse. Sequencing libraries were constructed with the xGen Prism DNA Library Prep Kit using 5ng of cfDNA. For the detection of recurrent mutations and fusions we designed a custom panel using a hybridization-based capture method (Twist Bioscience) that included full coverage of the exons of 136 genes harboring recurrent mutations and selected introns for five genes with recurrent rearrangement breakpoints including BRAF, EWSR1, SYT, FOXO1 and NTRK1. Hybridized libraries were paired-end sequenced (Illumina NextSeq 500) at an average 1000x collapsed coverage. Mutations identified in cfDNA were compared with those in the primary or metastatic tumors profiled with our OncoKids® NGS panel. A total of 35/43 (81%) plasma specimens were positive for either an SNV, deletion or fusion with the most common events being a somatic missense variant in TP53 (13/35, 37%) or translocation involving EWSR1 (9/35, 26%). A total of 16/25 (64%) CSF specimens were positive for SNVs and fusions, most often involving KIAA1549::BRAF (7/25, 28%) in low grade gliomas. A germline variant in RB1 was detectable in two AH specimens from the left and right eye of a patient with bilateral retinoblastoma while plasma from a patient with metastatic retinoblastoma demonstrated clinically relevant variants in RB1 and DICER1. Serial cfDNA profiling revealed a clinically reported TP53 c.746G&amp;gt;C missense variant in the plasma of a patient with osteosarcoma at multiple timepoints through the disease course, with evidence for relapse prior to standard imaging. These data suggest that clinical implementation of a second version of LBSeq4Kids that combines CNA and mutation analysis allows for diagnosis, residual disease detection and risk stratification for pediatric patients with diverse tumor types, regardless of histologic grade, with a variety of pediatric solid and brain tumors. Citation Format: Eirini Christodoulou, Venkata Yellapantula, Katrina O'Halloran, Liya Xu, Jesse L. Berry, Fariba Navid, Dejerianne Ostrow, Jaclyn A. Biegel. Clinical applicability of targeted panel sequencing in liquid biopsies for disease diagnosis and monitoring of patients with pediatric solid tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 967.