Sensitive and Accurate Detection of Low-frequency Mutations via Pyrophosphorolysis-Activated Selective Amplification and MALDI-TOF-MS Single-Nucleotide Resolution Identification

Abstract

Nucleic acid mutation profiling is crucial for early screening, diagnosis, and prognosis of cancer patients. However, detecting rare mutations at low variant allele frequencies (VAFs) in clinical samples is often hindered by interference of abundant wild-type (WT) backgrounds as well as incorrect signal readout. To tackle this challenge, we propose a Hybrid Ultrasensitive Nucleic acid Targeted Enrichment and Readout (HUNTER) platform for highly sensitive, accurate and multiplexed detection of low-frequence single nucleotide variants (SNVs). HUNTER leverages pyrophosphorolysis-activated polymerization (PAP) based selective variant amplification to enhance the abundance of rare mutations for improved detection sensitivity. The matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) readout with single-nucleotide resolution further enables precise genotyping across multiple loci. Consequently, HUNTER can accurately detect SNVs as low as 3 copies, with a detection limit of 0.01% in a high-WT background. Additionally, HUNTER enables simultaneous detection of up to 10 target SNVs in a single pot. In clinical lung cancer samples, the HUNTER assay demonstrates 1.6- to 5-fold higher sensitivity compared to the conventional amplification refractory mutation system quantitative PCR (ARMS-qPCR), and maintains 100% specificity across diverse SNV types. With its high sensitivity, accuracy and multiplex capability, HUNTER is well-positioned to emerge as a groundbreaking tool for the detection of rare mutations in precision medicine.