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Ribosome Profiling

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Related Experiment Video

Updated: Apr 15, 2026

A Robust Polymerase Chain Reaction-based Assay for Quantifying Cytosine-guanine-guanine Trinucleotide Repeats in Fragile X Mental Retardation-1 Gene

A Robust Polymerase Chain Reaction-based Assay for Quantifying Cytosine-guanine-guanine Trinucleotide Repeats in Fragile X Mental Retardation-1 Gene

Published on: September 16, 2019

Targeted long-read sequencing for high-resolution repeat profiling in myotonic dystrophy type 1.

Yoojung Han^1,2, Ja-Hyun Jang³, Hyeshik Chang^4,5,6

¹Center for RNA Research, Institute for Basic Science, Seoul, Republic of Korea.

Experimental & Molecular Medicine

|April 13, 2026

Summary

This summary is machine-generated.

Diagnosing large repeat expansions in genetic disorders is challenging. A new Cas9-targeted nanopore sequencing workflow and RepeatLab pipeline accurately detect these expansions and methylation patterns, improving diagnosis for conditions like myotonic dystrophy type 1.

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Area of Science:

Genomics
Molecular Diagnostics
Bioinformatics

Background:

Tandem repeat expansion disorders pose diagnostic challenges, especially with expansions over 200 repeats.
Conventional methods like Southern blot and PCR often lack sensitivity for large expansions.

Purpose of the Study:

To develop and validate a novel Cas9-targeted nanopore sequencing workflow and analysis pipeline (RepeatLab).
To enable accurate repeat-length estimation, structural assessment, and methylation profiling for tandem repeat expansion disorders.

Main Methods:

Utilized Cas9-targeted nanopore sequencing for high-resolution analysis of repeat regions.
Developed RepeatLab, an automated pipeline for repeat-length calling, structure assessment, and methylation analysis.
Incorporated an alternative basecalling strategy and a robust repeat-length calling algorithm for extended repeats.

Main Results:

Demonstrated improved sensitivity and accuracy for large repeat expansions in 13 myotonic dystrophy type 1 samples.
The workflow achieved a turnaround time under 24 hours with costs comparable to standard assays.
Successfully profiled methylation near the DMPK repeat region, identifying five CpG site groups.

Conclusions:

The integrated Cas9-targeted nanopore sequencing and RepeatLab workflow provides a rapid, cost-effective, and scalable diagnostic solution.
This approach enhances diagnostic capabilities for tandem repeat expansion disorders, including myotonic dystrophy type 1.
The methylation profiling offers potential for more nuanced clinical evaluations.