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Nonsense-mediated mRNA Decay

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The Upf proteins that carry out nonsense-mediated decay (NMD) are found in all eukaryotic organisms, including humans. Each protein has an individual role, but they need to work in collaboration. Upf1 is an ATP-dependent RNA helicase that unwinds the RNA helix. Because Upf1 can unwind any RNA, Upf2 and Upf3 are required to help Upf1 discriminate between nonsense and normal mRNAs.
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Updated: May 7, 2026

Detection of Rare Mutations in CtDNA Using Next Generation Sequencing

Detection of Rare Mutations in CtDNA Using Next Generation Sequencing

Published on: August 24, 2017

MUTE-Seq: An Ultrasensitive Method for Detecting Low-Frequency Mutations in cfDNA With Engineered Advanced-Fidelity

Sunghyeok Ye¹, Jin-Soo Kim², Myungshin Kim^3,4

¹GeneCker, Seoul, 04793, South Korea.

Advanced Materials (Deerfield Beach, Fla.)

|August 22, 2025

Summary

This summary is machine-generated.

A new method, MUTE-Seq, uses a precise CRISPR tool (FnCas9-AF2) to detect low-frequency cancer mutations. This technique enhances early cancer detection and monitoring, including minimal residual disease in Acute Myeloid Leukemia.

Keywords:

CRISPR/Cas9 FnCas9 cell‐free DNA circulating tumor DNA liquid biopsy

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Detection and Monitoring of Tumor Associated Circulating DNA in Patient Biofluids

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Published on: June 8, 2019

Area of Science:

Molecular Biology
Genetics
Biotechnology

Background:

CRISPR-Cas9 technology offers precise genome editing capabilities.
Accurate detection of low-frequency cancer mutations is crucial for early diagnosis and treatment.
Existing methods face challenges with specificity and sensitivity in detecting rare mutations.

Purpose of the Study:

To develop a highly sensitive method for detecting low-frequency cancer mutations.
To engineer an advanced-fidelity Cas9 variant with improved specificity.
To demonstrate the clinical utility of the developed method for cancer monitoring.

Main Methods:

Development of Mutation tagging by CRISPR-based Ultra-precise Targeted Elimination in Sequencing (MUTE-Seq).
Engineering of an advanced-fidelity FnCas9 variant (FnCas9-AF2) for precise discrimination of DNA mismatches.
Application of MUTE-Seq for enrichment of mutant DNA by selective cleavage of wild-type DNA.
Testing MUTE-Seq on minimal residual disease monitoring in Acute Myeloid Leukemia patients.
Multiplexed application of MUTE-Seq on cell-free DNA from non-small cell lung cancer and pancreatic cancer patients.

Main Results:

FnCas9-AF2 demonstrated significantly lower off-target effects than existing high-fidelity Cas9 variants.
MUTE-Seq enabled sensitive detection of low-frequency cancer-associated mutant alleles.
Successful monitoring of minimal residual disease in Acute Myeloid Leukemia patients.
Improved sensitivity in simultaneous mutant detection using multiplexed MUTE-Seq on cfDNA from NSCLC and pancreatic cancer patients.
Demonstrated clinical utility for early-stage cancer detection with low circulating tumor DNA.

Conclusions:

MUTE-Seq, powered by FnCas9-AF2, offers a sensitive and precise tool for detecting cancer mutations.
The method shows significant potential for early cancer diagnosis, prognosis, and treatment planning.
MUTE-Seq can be applied to various cancer types and sample matrices, including cfDNA.
This technology could advance molecular diagnostics for a range of cancers.