Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Fragmentation Analysis of the MYC Enhancer in Cell-Free DNA by qPCR for Early Detection of Hepatocellular Carcinoma.

Hepatology research : the official journal of the Japan Society of Hepatology·2026

Same author

Consistency versus variability: Contrasting microbial ecological strategies of anaerobic digestion and activated sludge systems in full-scale Baijiu distillery wastewater treatment plants.

Water research·2026

Same author

gSV: a general structural variant detector using the third-generation sequencing data.

Briefings in bioinformatics·2026

Same author

Spatially differentiated conductive materials enable synergistic optimization of methane production and ARGs suppression in two-phase anaerobic treatment of antibiotic wastewater.

Water research·2026

Same author

Trait-Based Optimization of Plant Density in Drip-Fertigated Wheat: Yield Formation and Nitrogen-Radiation-Water Use Efficiency Responses of Varieties Contrasting in Individual Spike Productivity.

Plants (Basel, Switzerland)·2026

Same author

LSTM-based prediction and early warning of nitrogen removal in a partial denitrification-anammox bioreactor for municipal wastewater.

Journal of environmental management·2026

Same journal

RankVar: machine learning-based variant ranking and reinterpretation for rare genetic diseases.

Genome medicine·2026

Same journal

Multi-omics profiles of sex hormone-binding globulin are associated with subclinical atherosclerosis in men with HIV.

Genome medicine·2026

Same journal

Multi-modal data integration reveals functionally credible predictive biomarkers in ovarian cancer.

Genome medicine·2026

Same journal

Human cancer genomes harbor the mutational signature of tobacco-specific nitrosamines NNN and NNK.

Genome medicine·2026

Same journal

Identification and functional characterization of regulatory variants in DPP9 associated with COVID-19 severity.

Genome medicine·2026

Same journal

De novo variants in NPTN cause a neurodevelopmental disorder with autism and neuroplastin-PMCA hypofunction.

Genome medicine·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Dec 16, 2025

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

Interrogating the "unsequenceable" genomic trinucleotide repeat disorders by long-read sequencing.

Qian Liu¹, Peng Zhang², Depeng Wang²

¹Institute for Genomic Medicine, Columbia University, New York, NY, 10032, USA.

Genome Medicine

|July 20, 2017

Summary

This summary is machine-generated.

Repeat expansion disorders are difficult to diagnose. A new algorithm, RepeatHMM, uses long-read sequencing to accurately count trinucleotide repeats, enabling the study of previously unsequenceable genetic diseases.

Keywords:

Long-read sequencing Microsatellites Nanopore PacBio RepeatHMM Trinucleotide repeat disorders Trinucleotide repeats

More Related Videos

Ultra-long Read Sequencing for Whole Genomic DNA Analysis

Ultra-long Read Sequencing for Whole Genomic DNA Analysis

Published on: March 15, 2019

A Strategy to Identify de Novo Mutations in Common Disorders such as Autism and Schizophrenia

A Strategy to Identify de Novo Mutations in Common Disorders such as Autism and Schizophrenia

Published on: June 15, 2011

Related Experiment Videos

Last Updated: Dec 16, 2025

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

Ultra-long Read Sequencing for Whole Genomic DNA Analysis

Ultra-long Read Sequencing for Whole Genomic DNA Analysis

Published on: March 15, 2019

A Strategy to Identify de Novo Mutations in Common Disorders such as Autism and Schizophrenia

A Strategy to Identify de Novo Mutations in Common Disorders such as Autism and Schizophrenia

Published on: June 15, 2011

Area of Science:

Genomics
Bioinformatics
Genetic Diseases

Background:

Microsatellite expansion, particularly trinucleotide repeat expansions (TREs), underlies numerous genetic disorders.
Traditional sequencing methods like Sanger and short-read sequencing struggle to accurately quantify these repeat expansions.
This limitation hinders the diagnosis and study of TRE-associated diseases.

Purpose of the Study:

To develop a novel algorithm for accurately estimating repeat counts from long-read sequencing data.
To address the limitations of current sequencing technologies in analyzing TREs.
To enable the interrogation of previously unsequenceable genomic regions associated with TRE disorders.

Main Methods:

Development of RepeatHMM, a novel algorithm utilizing long-read sequencing data.
Evaluation using simulated data, amplicon sequencing data from patients with TRE disorders, and whole-genome sequencing data.
Comparison of RepeatHMM performance against existing methods.

Main Results:

RepeatHMM demonstrated superior performance in estimating repeat counts compared to other approaches.
The algorithm successfully analyzed data from both PacBio and Oxford Nanopore long-read sequencing platforms.
Accurate repeat count estimation was achieved even for complex microsatellite regions.

Conclusions:

Long-read sequencing combined with RepeatHMM provides a reliable method for quantifying microsatellite repeat counts.
This approach overcomes previous technical barriers, allowing for the investigation of trinucleotide repeat expansion disorders.
RepeatHMM facilitates the study and potential diagnosis of genetic diseases caused by TREs.