Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

RNA-seq03:21

RNA-seq

10.4K
RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
10.4K
Next-generation Sequencing03:00

Next-generation Sequencing

92.8K
The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
92.8K
Sanger Sequencing01:57

Sanger Sequencing

758.4K
DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
758.4K

You might also read

Related Articles

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

Sort by
Same author

Genome misassembly detection using Stash: A data structure based on stochastic tile hashing.

PloS one·2026
Same author

Detection of repeat expansion variants using next generation sequencing: A points to consider statement of the American College of Medical Genetics and Genomics (ACMG).

Genetics in medicine : official journal of the American College of Medical Genetics·2026
Same author

Efficacy and safety evaluation of artificial intelligence-identified antimicrobial peptides targeting avian pathogenic Escherichia coli in broiler chickens.

Journal of animal science and biotechnology·2026
Same author

Genomic newborn screening: a scoping review of the field's evolution and associated ethical, legal, and social implications.

European journal of human genetics : EJHG·2026
Same author

AIEdit: Alignment-free genome assembly polisher trained on spaced seed match patterns.

PLoS computational biology·2026
Same author

Inherited TBX4 frameshifting variants predicted to escape nonsense mediated decay in two families with variable phenotypes, including lethal lung developmental disorders.

Human genomics·2026

Related Experiment Video

Updated: Sep 20, 2025

Amplification, Next-generation Sequencing, and Genomic DNA Mapping of Retroviral Integration Sites
09:31

Amplification, Next-generation Sequencing, and Genomic DNA Mapping of Retroviral Integration Sites

Published on: March 22, 2016

17.8K

Linked-read sequencing for detecting short tandem repeat expansions.

Readman Chiu1, Indhu-Shree Rajan-Babu2,3, Inanc Birol4,5

  • 1Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, V5Z 4S6, Canada.

Scientific Reports
|June 7, 2022
PubMed
Summary

Barcode linked-read sequencing (BLRS) improves detection of large short tandem repeat (STR) expansions. This method enhances STR genotyping accuracy compared to standard short-read sequencing, overcoming mapping challenges.

More Related Videos

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER
14:06

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Published on: June 23, 2012

15.3K
Rare Event Detection Using Error-corrected DNA and RNA Sequencing
10:36

Rare Event Detection Using Error-corrected DNA and RNA Sequencing

Published on: August 3, 2018

12.2K

Related Experiment Videos

Last Updated: Sep 20, 2025

Amplification, Next-generation Sequencing, and Genomic DNA Mapping of Retroviral Integration Sites
09:31

Amplification, Next-generation Sequencing, and Genomic DNA Mapping of Retroviral Integration Sites

Published on: March 22, 2016

17.8K
Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER
14:06

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Published on: June 23, 2012

15.3K
Rare Event Detection Using Error-corrected DNA and RNA Sequencing
10:36

Rare Event Detection Using Error-corrected DNA and RNA Sequencing

Published on: August 3, 2018

12.2K

Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Standard short-read sequencing struggles with accurately detecting and sizing short tandem repeat (STR) expansions due to mapping difficulties with repetitive sequences.
  • Accurate genotyping of large STR expansions (over 1 kb) is crucial for understanding genetic variations and associated diseases.

Purpose of the Study:

  • To explore the utility of barcode linked-read sequencing (BLRS) for improving the detection and genotyping of large STR expansions.
  • To develop and evaluate a novel algorithm leveraging BLRS barcodes for accurate STR distance estimation and genotyping.

Main Methods:

  • Utilized barcode linked-read sequencing (BLRS) to capture long-range sequence information.
  • Developed a novel algorithm for STR genotyping using BLRS barcode data for distance estimation.
  • Validated the approaches using simulated and experimental genomic data from multiple BLRS platforms.

Main Results:

  • BLRS, combined with barcode and phasing information, significantly improved STR genotype accuracy compared to standard short-read sequencing.
  • The novel algorithm demonstrated effectiveness in genotyping large STR expansions that are challenging for existing methods.
  • Identified coverage bias in extremely GC-rich STRs as a limitation of BLRS.

Conclusions:

  • Barcode linked-read sequencing (BLRS) offers a powerful strategy for enhancing the accuracy of short tandem repeat (STR) expansion genotyping.
  • The developed algorithm provides a valuable tool for sizing large STR expansions, overcoming limitations of current sequencing technologies.
  • BLRS is a promising approach for genotyping a wide range of STR loci, despite limitations with highly GC-rich regions.