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Next-generation Sequencing

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Related Experiment Video

Updated: May 9, 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

Profiling short tandem repeats from short reads.

Melissa Gymrek¹, Yaniv Erlich

¹Harvard-MIT Division of Health Sciences and Technology, MIT, Cambridge, MA, USA.

Methods in Molecular Biology (Clifton, N.J.)

|July 23, 2013

Summary

Short tandem repeats (STRs) are crucial for genetics research. Our lobSTR algorithm accurately profiles STR variations from high-throughput sequencing data, overcoming alignment and noise challenges.

Area of Science:

Genetics
Bioinformatics

Background:

Short tandem repeats (STRs), or microsatellites, are vital in medical genetics, forensics, and population genetics.
High-throughput sequencing (HTS) offers potential for large-scale STR profiling but faces challenges with alignment and noise.

Purpose of the Study:

To present lobSTR, an algorithm for accurate STR profiling from HTS data.
To provide guidance on using lobSTR for calling STR variations and assessing call quality.

Main Methods:

Development of the lobSTR algorithm to address gapped alignment and noise issues in STR profiling.
Application of lobSTR to high-throughput sequencing datasets for STR variation analysis.

Main Results:

lobSTR enables accurate profiling of STRs from short reads, overcoming previous technical hurdles.

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The algorithm facilitates the diagnosis of call quality in STR variation analysis.

Conclusions:

lobSTR is an effective tool for accurate STR variation calling from HTS data.
The methodology aids researchers in leveraging HTS for comprehensive STR analysis in various genetic fields.