Clinical Validation of the Belay Ascent™ Test to Report on Chromosomal Arm-Level Aneuploidy and Gene-Level Copy Number Variants in Cerebrospinal Fluid Using Low-Pass Whole-Genome Sequencing
Authors:
Qian Nie, Kala F. Schilter, Alexandra Larson, Vindhya Udhane, Viriya Keo, Sakshi Khurana, Jennifer N. Adams, Anthony Acevedo, Daniel Sanchez, Tarin Peltier, Kathleen Mitchell, DeElegant Robinson, Kyle M. Hernandez, Christopher Douville, Chetan Bettegowda and Honey V. Reddi
Chromosomal and gene alterations are crucial for cancer diagnosis, classification, and treatment selection, which are potentially identified through tumor tissue testing when feasible. For brain and spinal cord cancers, surgery poses significant patient risks, and plasma-based liquid biopsy tests often fail due to the blood–brain barrier, which restricts tumor-derived DNA from entering the bloodstream. This study evaluates the Belay Ascent™ liquid biopsy test, which analyzes tumor-derived DNA in cerebrospinal fluid. This test detects chromosome arm-level changes and gene-level alterations through low-pass whole-genome sequencing. The results indicate that the test effectively identifies genomic changes, demonstrating that Belay Ascent provides a minimally invasive alternative to biopsy or surgery and helps inform diagnosis, prognosis, and therapeutic decision-making in primary and metastatic central nervous system cancers.
Abstract:
Background:
Evaluation of chromosome aneuploidy and gene-level copy number alterations for diagnosis, prognosis, and therapeutic decision-making in solid tumors is the standard of care. Chromosomal microarray (CMA), next-generation sequencing (NGS), immunohistochemistry (IHC), and fluorescence in situ hybridization (FISH) are the gold standard for detecting these variants in tumor tissue. In contrast to most solid tumors, cancers of the central nervous system (CNS) pose a unique challenge for effective detection via plasma due to the blood–brain barrier (BBB), with the additional challenges of brain biopsy or surgery being highly invasive and posing a significant risk to the patient. The Belay Ascent liquid biopsy test uses low-pass whole-genome sequencing (LP-WGS) to report on chromosome arm-level aneuploidy and gene-level copy number variants (CNVs) in cerebrospinal fluid (CSF) to inform diagnosis, prognosis, and therapeutic decision-making in CNS tumors.
Methods:
This study presents the equivalence of Belay Ascent in detecting chromosome arm-level aneuploidy and gene-level CNVs using 48 tissue specimens followed by a clinical validation using a cohort of 32 CSF specimens with matched tissue-based tumor profiling information.
Results:
Equivalence of Belay Ascent in detecting chromosome arm-level aneuploidy and gene-level CNVs using 48 tissue specimens was shown to have 100% and 97% positive percent agreement (PPA), respectively, compared to the gold standard of CMA/NGS. The validation cohort of 32 CSF specimens demonstrated 78% and 90% PPA for aneuploidy and gene-level CNVs, respectively. Clinical impact of Belay Ascent was demonstrated, with 243 production cases able to inform the diagnosis and management of CNS tumors with high accuracy.
Conclusions:
Given the paucity of cells in CSF, limiting the use of karyotyping, CMA, IHC, and FISH, the Belay Ascent test provides a highly sensitive novel minimally invasive method for the evaluation of chromosome aneuploidy and gene-level CNVs in CSF.
Figure 1: Schema of study (A). Equivalence (B), validation (C), and production cohort specifics (D) with concordance results.
Figure 2: Aneuploidy plot of 32 samples in the validation cohort showing chromosomal arm-level loss/gains detected by Belay Ascent. Cohort had previous tumor profiling results using immunohistochemistry (IHC), chromosomal microarray (CMA), fluorescence in situ hybridization (FISH), or targeted next-generation sequencing (NGS). Legend: gain—increase in chromosome arm number; loss—deletion of chromosome arm; not reportable—no change in chromosome arm number. X-axis lists the specimen ID, and Y-axis shows the chromosome arm number evaluated.
