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

You might also read

Related Articles

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

Sort by
Same author

Nest building as a missing piece in biparental care.

Biology letters·2026
Same author

Proton pencil beam scanning lattice radiotherapy: Technical implementation and comparison against photon-based delivery.

The British journal of radiology·2026
Same author

Clinical Outcomes of a Prosthetic Capsular Bag for Scleral Fixation of an Intraocular Lens in Eyes without Capsular Support.

Ophthalmology·2026
Same author

An inventory of emergency department information systems (EDIS) in Canada: Benchmarking system functionality and technology readiness.

CJEM·2026
Same author

Characterization of patient-derived site-specific <i>in vivo</i> models of pediatric-type diffuse high-grade glioma using magnetic resonance imaging.

Neuro-oncology advances·2026
Same author

Proton beam therapy for oropharyngeal cancer (TORPEdO): a phase 3, randomised controlled trial.

Lancet (London, England)·2026

Related Experiment Video

Updated: Mar 16, 2026

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
09:34

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

Published on: April 4, 2018

35.0K

OpEx - a validated, automated pipeline optimised for clinical exome sequence analysis.

Elise Ruark1, Márton Münz2, Matthew Clarke1

  • 1The Institute of Cancer Research, London, Division of Genetics &Epidemiology, Sutton SM2 5NG, UK.

Scientific Reports
|August 4, 2016
PubMed
Summary

OpEx is an open-source tool for accurate exome analysis, detecting small genetic variations like indels to clinical standards. It offers excellent performance, allowing labs to balance sensitivity and specificity for their needs.

More Related Videos

Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies
13:24

Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies

Published on: April 11, 2016

12.3K
Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing
11:02

Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing

Published on: October 18, 2013

20.0K

Related Experiment Videos

Last Updated: Mar 16, 2026

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
09:34

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

Published on: April 4, 2018

35.0K
Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies
13:24

Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies

Published on: April 11, 2016

12.3K
Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing
11:02

Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing

Published on: October 18, 2013

20.0K

Area of Science:

  • Genomics
  • Bioinformatics
  • Medical Genetics

Background:

  • Exome sequencing generates vast amounts of data requiring robust analysis tools.
  • Accurate detection of small-scale genetic variations is crucial for clinical diagnostics and research.
  • Existing tools may lack ease of use or comprehensive performance for diverse datasets.

Purpose of the Study:

  • To introduce OpEx, an open-source, user-friendly tool for optimized exome analysis.
  • To evaluate OpEx's performance in detecting small-scale variations, including indels, to clinical standards.
  • To demonstrate OpEx's suitability for both research and clinical exome sequencing laboratories.

Main Methods:

  • Development of the Optimised Exome analysis tool (OpEx).
  • Evaluation using three distinct datasets: ICR142 NGS validation series, ICR1000 UK exome series, and a clinical trio dataset.
  • Performance assessment focused on sensitivity, specificity, and false detection rate (FDR) for base substitutions and indels.

Main Results:

  • OpEx demonstrated excellent performance across all tested datasets.
  • Achieved high sensitivity (95%), specificity (97%), and a low FDR (3%) for small-scale variations.
  • The tool's output allows flexible optimization of sensitivity and specificity trade-offs based on specific requirements.

Conclusions:

  • OpEx is an accurate, easy-to-install, and use open-source tool for exome sequencing analysis.
  • It meets clinical standards for detecting small-scale variations, including indels.
  • OpEx is well-suited for research and clinical labs, especially those lacking dedicated bioinformatics expertise.