Ultrasensitive Detection of Rare Mutations via Amplifying–Cleaving–Enriching in Acute Myeloid Leukemia

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Abstract
Background: Detecting low-frequency mutations is crucial for predicting prognosis and monitoring minimal residual disease (MRD) in acute myeloid leukemia (AML). However, the presence of abundant wild-type sequences hinders the detection of rare mutant alleles. We present a highly sensitive method called ACE (Amplifying–Cleaving–Enriching) to selectively enrich mutant sequences. Methods: ACE includes three steps: (1) initial PCR amplification using biotin-labeled primers, (2) cleavage of wild-type sequences with a specific restriction enzyme, and (3) enrichment of undigested mutant alleles via streptavidin-labeled magnetic beads. Results: Using two rounds of ACE, we achieved over 80,000-fold enrichment of mutant sequences carrying FLT3-TKD, enabling the detection of mutant alleles at levels as low as 0.0001% in AML patient blood samples. Additionally, the ACE method can be adapted to nearly any driver mutation by introducing wild-type-specific restriction sites through PCR with mismatched primers, which has been validated in the IDH1 mutation. Furthermore, the ACE method can be flexibly integrated into conventional detection techniques including Sanger sequencing, quantitative real-time PCR, allele-specific PCR, and even with advanced techniques like droplet digital PCR. Conclusions: ACE significantly enhances the sensitivity of existing techniques for rare mutation detection and holds potential for broad clinical applications.
Funding Information
  • National Natural Science Foundation of China (82372312)
  • National Natural Science Foundation of China (82202579)
  • National Natural Science Foundation of China (82370164)
  • Science, Technology and Innovation Commission of Shenzhen Municipality (JCYJ20250604143719026)
  • Science, Technology and Innovation Commission of Shenzhen Municipality (JCYJ20220530144814032)
  • Science, Technology and Innovation Commission of Shenzhen Municipality (JCYJ20230807110419040)
  • Science, Technology and Innovation Commission of Shenzhen Municipality (JCYJ20240813150301002)
  • Science, Technology and Innovation Commission of Shenzhen Municipality (JCYJ20240813150249043)
  • Science, Technology and Innovation Commission of Shenzhen Municipality (JCYJ20250604143719025)
  • Guangdong Provincial Key Laboratory of Digestive Cancer Research (2021B1212040006)

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