Ultra-rapid genomic profiling of brain tumors using whole-genome and targeted long-read sequencing

Abstract: The 2021 WHO classification of tumors of the central nervous system (CNS) made molecular testing and DNA methylation-based classification essential for diagnosing CNS tumors. However, traditional comprehensive genomic testing is fragmented and often requires weeks to months for results, delaying molecular diagnoses and treatment decisions. Long-read sequencing (LRS) could provide all necessary information faster using less sample material. In addition, real-time methylation analysis may enable tumor classification within minutes of sequencing initiation. The concordance of whole-genome (wgLRS) and targeted long-read sequencing (T-LRS) with clinical test results is not well-described in pediatric brain tumors. We performed wgLRS (n=9), T-LRS (n=20), or both (n=6) on 23 pediatric brain tumor samples to evaluate the concordance with the standard clinical testing. Using rapid DNA extraction and library preparation protocol reduced the average sample preparation time to approximately one hour. All samples underwent retrospective methylation analysis to evaluate the estimated amount of time and data required to properly classify each tumor by type using methylation alone. Evaluation by wgLRS and T-LRS identified most previously reported copy number variants, regions of loss of heterozygosity, gene amplifications, and non-mosaic single nucleotide or insertion/deletion variants. Methylation classification correctly classified the tumor by type for most samples within 10 minutes. Our results show that both wgLRS and T-LRS are highly concordant with clinical reports with some discrepancy due to tumor heterogeneity. They also show that LRS can rapidly classify tumors using methylation, which could facilitate intraoperative decision-making and accelerate personalized treatment strategies in pediatric neuro-oncology. Biography: Min Seon Park is a PhD student in the Institute of Public Health Genetics at the University of Washington, leveraging long-read sequencing to identify disease-causing variants and elucidate genotype-phenotype correlations. With a background as a certified genetic counselor, she is committed to translating genomic discoveries into patient-centered care.