INNV-22. LIQUID BIOPSY DETECTION OF GENOMIC ALTERATIONS IN PEDIATRIC BRAIN TUMORS FROM CELL FREE DNA IN PERIPHERAL BLOOD, CSF, AND URINE. (5th November 2018)

• Record Type: Journal Article
• Authors: Pages, Mélanie; Rotem, Denisse; Gydush, Gregory; Reed, Sarah; Rhoades, Justin; Ha, Gavin; Lo, Chris; Tracy, Adam; Jones, Robert; Becker, Sarah; Haller, Michaela; Chi, Susan; Kieran, Mark; Goumnerova, Liliana; Love, J Christopher; Ligon, Keith; Bandopadhayay, Pratiti; Wright, Karen; Adalsteinsson, Viktor A; Beroukhim, Rameen
• Is Part Of: Neuro-oncology. Volume 20(2018)Supplement 6
• Page Start: vi142
• Page End: vi143
• Publication Date: 2018-11-05
• Subjects: Brain Neoplasms -- Periodicals; Brain -- Tumors -- Periodicals; Brain -- Cancer -- Periodicals; Nervous system -- Cancer -- Periodicals; 616.99481
• DOI: 10.1093/neuonc/noy148.595
• Languages: English
• ISSNs: 1522-8517

Abstract

Abstract: Brain tumors often require invasive neurosurgical procedures for diagnosis and tissue acquisition to guide precision medicine. Detection of tumor-derived cell-free DNA (cfDNA) would facilitate tumor profiling without risk of surgery-related morbidity and provide a means of tumor surveillance. Our aim is to validate a sample collection procedure and develop highly sensitive and specific methodologies to detect tumor-derived cfDNA in CSF, plasma and urine from pediatric patients with brain tumors to identify clinically relevant genomic alterations. Since July 2016, we have prospectively collected blood, urine and CSF samples from 235 patients across all histological subtypes at Dana-Farber Cancer Institute/Boston Childrens Hospital. In parallel, we sequenced the tumors to identify tumor-specific genomic alterations. We optimized a method to process cfDNA and perform ultra-low pass whole genome sequencing (ULP-WGS) using unique molecular identifiers, confirming we can reliably construct sequencing libraries from CSF-, plasma- and urine-derived cfDNA. ULP-WGS has also been used to assess sequencing library quality, copy number variations (CNVs) and tumor fraction. The vast majority of samples undergoing ULP-WGS exhibited no CNVs, consistent with either absence in the tumor or low levels of tumor-derived cfDNA. To distinguish between these, we developed a hybrid capture sequencing panel covering 46 genes, allowing identification of specific mutations and fusions more common in pediatric brain tumors. We are currently assessing the specificity and sensitivity of our assays for detection of tumor-derived cfDNA by sequencing samples with matched tumor NGS available. Furthermore, we are identifying cases with multiple time points of cfDNA, for which data from paired pre- and post-treatment tumors are available, to apply. Our results will provide insights regarding the feasibility of cfDNA assays to guide clinical care in children with brain tumors.