Mélanie Pagès1,2,3, Denisse Rotem4, Gregory Gydush4, Sarah Reed4, Justin Rhoades4, Gavin Ha4, Christopher Lo4, Mark Fleharty4, Madeleine Duran4, Robert Jones5, Sarah Becker5, Michaela Haller5, Claire E Sinai5, Liliana Goumnerova6, Todd R Golub1,4, J Christopher Love7, Keith L Ligon1,4,6, Karen D Wright1, Viktor A Adalsteinsson4,7, Rameen Beroukhim4,8,9,10, Pratiti Bandopadhayay1,4. 1. Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts, USA. 2. GHU-Paris-Sainte-Anne Hospital, Department of Neuropathology, Paris University, Paris, France. 3. Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA. 4. Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA. 5. Department of Oncologic Pathology, Dana Farber/Brigham and Women's Cancer Center, Boston, Massachusetts, USA. 6. Department of Neurosurgery, Boston Children's Hospital, Boston, Massachusetts, USA. 7. Massachusetts Institute of Technology, Cambridge, Massachusetts, USA. 8. Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA. 9. Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA. 10. Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.
Abstract
BACKGROUND: The ability to identify genetic alterations in cancers is essential for precision medicine; however, surgical approaches to obtain brain tumor tissue are invasive. Profiling circulating tumor DNA (ctDNA) in liquid biopsies has emerged as a promising approach to avoid invasive procedures. Here, we systematically evaluated the feasibility of profiling pediatric brain tumors using ctDNA obtained from plasma, cerebrospinal fluid (CSF), and urine. METHODS: We prospectively collected 564 specimens (257 blood, 240 urine, and 67 CSF samples) from 258 patients across all histopathologies. We performed ultra-low-pass whole-genome sequencing (ULP-WGS) to assess copy number variations and estimate tumor fraction and developed a pediatric CNS tumor hybrid capture panel for deep sequencing of specific mutations and fusions. RESULTS: ULP-WGS detected copy number alterations in 9/46 (20%) CSF, 3/230 (1.3%) plasma, and 0/153 urine samples. Sequencing detected alterations in 3/10 (30%) CSF, 2/74 (2.7%) plasma, and 0/2 urine samples. The only positive results were in high-grade tumors. However, most samples had insufficient somatic mutations (median 1, range 0-39) discoverable by the sequencing panel to provide sufficient power to detect tumor fractions of greater than 0.1%. CONCLUSIONS: Children with brain tumors harbor very low levels of ctDNA in blood, CSF, and urine, with CSF having the most DNA detectable. Molecular profiling is feasible in a small subset of high-grade tumors. The level of clonal aberrations per genome is low in most of the tumors, posing a challenge for detection using whole-genome or even targeted sequencing methods. Substantial challenges therefore remain to genetically characterize pediatric brain tumors from liquid biopsies.
BACKGROUND: The ability to identify genetic alterations in cancers is essential for precision medicine; however, surgical approaches to obtain brain tumor tissue are invasive. Profiling circulating tumor DNA (ctDNA) in liquid biopsies has emerged as a promising approach to avoid invasive procedures. Here, we systematically evaluated the feasibility of profiling pediatric brain tumors using ctDNA obtained from plasma, cerebrospinal fluid (CSF), and urine. METHODS: We prospectively collected 564 specimens (257 blood, 240 urine, and 67 CSF samples) from 258 patients across all histopathologies. We performed ultra-low-pass whole-genome sequencing (ULP-WGS) to assess copy number variations and estimate tumor fraction and developed a pediatric CNS tumor hybrid capture panel for deep sequencing of specific mutations and fusions. RESULTS: ULP-WGS detected copy number alterations in 9/46 (20%) CSF, 3/230 (1.3%) plasma, and 0/153 urine samples. Sequencing detected alterations in 3/10 (30%) CSF, 2/74 (2.7%) plasma, and 0/2 urine samples. The only positive results were in high-grade tumors. However, most samples had insufficient somatic mutations (median 1, range 0-39) discoverable by the sequencing panel to provide sufficient power to detect tumor fractions of greater than 0.1%. CONCLUSIONS: Children with brain tumors harbor very low levels of ctDNA in blood, CSF, and urine, with CSF having the most DNA detectable. Molecular profiling is feasible in a small subset of high-grade tumors. The level of clonal aberrations per genome is low in most of the tumors, posing a challenge for detection using whole-genome or even targeted sequencing methods. Substantial challenges therefore remain to genetically characterize pediatric brain tumors from liquid biopsies.
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