Targeted locus amplification to develop robust patient-specific assays for liquid biopsies in pediatric solid tumors.

ABSTRACT:

Background

Liquid biopsies combine minimally invasive sample collection with sensitive detection of residual disease. Pediatric malignancies harbor tumor-driving copy number alterations or fusion genes, rather than recurrent point mutations. These regions contain tumor-specific DNA breakpoint sequences. We investigated the feasibility to use these breakpoints to design patient-specific markers to detect tumor-derived cell-free DNA (cfDNA) in plasma from patients with pediatric solid tumors.

Materials and methods

Regions of interest (ROI) were identified through standard clinical diagnostic pipelines, using SNP array for CNAs, and FISH or RT-qPCR for fusion genes. Using targeted locus amplification (TLA) on tumor organoids grown from tumor material or targeted locus capture (

SUBMITTER: van Zogchel LMJ 

PROVIDER: S-EPMC10157037 | biostudies-literature | 2023

REPOSITORIES: biostudies-literature