Cell-free DNA ultra-low-pass whole genome sequencing distinguishes malignant peripheral nerve sheath tumor (MPNST) from its benign precursor lesion

Background: The leading cause of mortality for patients with the Neurofibromatosis type 1 (NF1) cancer predisposition syndrome is development of Malignant Peripheral Nerve Sheath Tumor (MPNST), an aggressive soft tissue sarcoma. In the setting of NF1, this cancer type frequently arises from within its common and benign precursor, plexiform neurofibroma (PN). Transformation from the benign PN to MPNST is challenging to diagnose due to difficulties in distinguishing cross-sectional imaging results and intralesional heterogeneity resulting in biopsy sampling errors. Methods and Findings: This multi-institutional study used ultra-low-pass whole genome sequencing (ULP-WGS) of plasma cell-free DNA (cfDNA) to distinguish between MPNST and PN in patients with NF1. Using copy number to estimate the fraction of plasma cfDNA originating from tumor (tumor fraction), we developed a noninvasive classifier which differentiates MPNST from PN with 91% specificity. Healthy controls without NF1 (subjects = 14, plasma samples= 14), PN (subjects = 45, plasma samples = 45), and MPNST (subjects = 14, plasma samples = 48) cohorts showed significant differences in tumor fraction in plasma (P = 0.006) as well as cfDNA fragment length (P < 0.001) with MPNST samples harboring shorter fragments and being enriched for tumor-derived cfDNA relative to PN and healthy controls. Mutational analysis demonstrated focal NF1 copy number loss in PN and MPNST patient plasma but not in healthy controls. Genomic alterations associated with malignant transformation (focal copy number gains in chromosome 8 and copy number losses in SUZ12, SMARCA2,CDKN2A/B, and chromosome arm 9p) were more prominently observed in MPNST plasma. Furthermore, the sum of longest tumor diameters (SLD) visualized by crosssectional imaging correlated significantly with paired tumor fractions in plasma from MPNST patients (ρ = 0.50, P = 0.0007). On case series analysis, tumor fraction levels in plasma correlated with treatment response to therapy and minimal residual disease (MRD) detection before relapse. Conclusions: Tumor fraction levels derived from copy number alteration analysis of plasma cfDNA using ULP-WGS significantly correlated with MPNST tumor burden, distinguished MPNST from its benign PN precursor, and correlated with treatment response. In the future, our findings could form the basis for improved early cancer detection and monitoring in high-risk cancer-predisposed populations.