Sequential Analysis of cfDNA Reveals Clonal Evolution in Patients with Neuroblastoma Receiving ALK-Targeted Therapy

Area of Science:

• Oncology
• Genetics
• Molecular Biology

Background:

• Neuroblastoma is a pediatric cancer where sequential analysis of tumor genetics is crucial.
• Cell-free DNA (cfDNA) offers a non-invasive method to track genetic alterations in tumors.

Purpose of the Study:

• To assess the utility of cfDNA analysis for monitoring neuroblastoma patients treated with lorlatinib.
• To investigate tumor clonal evolution and resistance mechanisms using cfDNA.

Main Methods:

• Whole-genome sequencing (WGS) library construction and ALK-targeted digital droplet PCR (ddPCR) for hotspot mutations.
• Whole-exome sequencing (WES) of cfDNA to evaluate disease burden and clonal evolution.
• Comparison of cfDNA analysis with tumor and germline WES.

Main Results:

• Lorlatinib showed a 33% overall response rate, with higher efficacy in patients without MYCN amplification.
• ALK variant allele fractions (VAFs) in cfDNA correlated with clinical disease status, detecting relapse earlier than imaging.
• cfDNA WES identified new somatic mutations and clonal evolution, including alterations in TP53 and EGFR, during treatment resistance.

Conclusions:

• Combining cfDNA ddPCR and WES is clinically useful for monitoring neuroblastoma patients on ALK-targeted therapy.
• This approach facilitates the study of clonal evolution and resistance mechanisms.
• cfDNA analysis provides valuable insights into treatment response and disease progression.