Abstract LB016: Sensitive detection of MYCN amplified neuroblastoma in blood samples with structural variants using standard whole genome sequencing

Abstract Background: MYCN amplification (MNA) is a defining biomarker of highrisk neuroblastoma with a poor clinical outcome. While tumorbased wholegenome sequencing (WGS) coupled with copynumber analysis (CNA) reliably identifies MNA, its detection in blood has remained uncertain due to low circulating tumor cell (CTC) burden. There is increasing interest in exploiting structural variants (SVs), which exhibit extremely low sequencing error rates, to enable ultra-sensitive tumor detection in liquid biopsies. Methods: We analyzed MNA neuroblastoma cases across three institutional cohorts with available paired tumor and peripheral blood (PB) WGS data. Mathematical modeling was performed to model limit of detection in using CNA versus SVbased approaches under varying tumor purities and sequencing depths. CNA detection was performed using CNVkit, ichorCNA, and DELLY, whereas tumorspecific SVs were genotyped in matching PB with our recently published error suppression method SVInDelGenotyper, and their error profiles are investigated using gnomAD and a healthy control cohort SJLIFE. Buccal samples and blood samples at remission were evaluated as alternative germline references. Results: CNAbased detection identified MNA in 32% of PB samples (9/28), with methodspecific sensitivities ranging from 4-25%. Integration of tumorinformed SV genotyping uncovered additional MYCN-linked breakpoints in CNAnegative PB samples, increasing overall detection sensitivity to 64% (18/28). SVs remained detectable even when PB samples exhibited no visible copynumber elevation (diploidlevel coverage), revealing tumor fractions as low as ∼0. 01%. Deeper WGS coverage and SV burden correlated with improved SV detection across cohorts. Our findings highlight the risk of missing detection of key mutations for childhood neuroblastoma by standard tumor vs normal comparison when diagnostic PB is used as normal control. Buccal samples and remissionstage blood showed no tumorspecific SVs, supporting their role as reliable germline controls. Conclusions: Standarddepth WGS (30-100×), when combined with SVbased liquidbiopsy analysis, enables sensitive detection of MNA neuroblastoma from blood, outperforming CNAonly approaches especially in lowpurity samples. These findings establish tumorspecific SV genotyping as a powerful noninvasive strategy for identifying highrisk MNA neuroblastoma. Our data further suggests the future study design of childhood neuroblastoma liquid biopsy to employ buccal samples as normal controls. Citation Format: Pandurang Kolekar, Rebecca S. Kaufman, Hanxia Li, Yanling Liu, Yuan Feng, Bo Wang, Xi Wang, Li Fan, Lu Wang, Jinghui Zhang, John M. Maris, Sharon J. Diskin, Xiaotu Ma. Sensitive detection of MYCN amplified neuroblastoma in blood samples with structural variants using standard whole genome sequencing abstract. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts) ; 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86 (8Suppl): Abstract nr LB016.