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

Next-generation Sequencing03:00

Next-generation Sequencing

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.
Sanger Sequencing01:57

Sanger Sequencing

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...
RNA-seq03:21

RNA-seq

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 microarray-based...

You might also read

Related Articles

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

Sort by
Same author

Predicting Clinical Sensitivities of PDGFRA Exon 18 Mutations to Imatinib and Avapritinib to Optimize Gastrointestinal Stromal Tumor Treatment.

Cancer research communications·2026
Same author

Clinical and molecular features of primary gliosarcoma with digital spatial whole-transcriptome analysis of glial and mesenchymal components.

Brain pathology (Zurich, Switzerland)·2026
Same author

Adjuvant Imatinib or Observation in Patients With Gastrointestinal Stromal Tumors With KIT Exon 9 Mutations.

JAMA oncology·2026
Same author

mSphere of Influence: Missing the trees for the forest.

mSphere·2026
Same author

Genomic and Molecular Associations with Preoperative Immune Checkpoint Inhibition in Patients with Stage III Clear Cell Renal Cell Carcinoma.

Cancers·2026
Same author

Enhancing Flexible Transfer of Fractions: The Role of Sequential and Simultaneous Games With Multiple Representations.

Cognitive science·2026

Related Experiment Video

Updated: May 15, 2026

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

Combining highly multiplexed PCR with semiconductor-based sequencing for rapid cancer genotyping.

Carol Beadling1, Tanaya L Neff, Michael C Heinrich

  • 1Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA.

The Journal of Molecular Diagnostics : JMD
|January 1, 2013
PubMed
Summary

This study presents a rapid semiconductor sequencing method for identifying cancer mutations in formalin-fixed, paraffin-embedded (FFPE) tissues. The assay requires minimal DNA and achieves high sensitivity and specificity for actionable mutation detection in clinical settings.

More Related Videos

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

Multi-Gene Single Nucleotide Polymorphism Detection in Gastric Cancer Based on Ion Semiconductor Sequencing Platform
06:21

Multi-Gene Single Nucleotide Polymorphism Detection in Gastric Cancer Based on Ion Semiconductor Sequencing Platform

Published on: May 10, 2024

Related Experiment Videos

Last Updated: May 15, 2026

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

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

Multi-Gene Single Nucleotide Polymorphism Detection in Gastric Cancer Based on Ion Semiconductor Sequencing Platform
06:21

Multi-Gene Single Nucleotide Polymorphism Detection in Gastric Cancer Based on Ion Semiconductor Sequencing Platform

Published on: May 10, 2024

Area of Science:

  • Oncology
  • Genomics
  • Molecular Diagnostics

Background:

  • Clinical cancer specimen analysis requires efficient identification of actionable mutations.
  • Formalin-fixed, paraffin-embedded (FFPE) tissues present challenges due to limited DNA quantity and quality.
  • Existing genotyping platforms need rapid turnaround times for clinical utility.

Purpose of the Study:

  • To develop and validate a semiconductor sequencing assay for detecting mutations in FFPE cancer specimens.
  • To assess the assay's performance regarding turnaround time, DNA input requirements, sensitivity, and specificity.
  • To evaluate the assay's suitability for routine clinical laboratory use.

Main Methods:

  • A single-tube, multiplexed panel targeting 46 cancer genes (190 amplicons) was designed for semiconductor sequencing.
  • DNA from FFPE specimens was sequenced using the multiplex panel, requiring only 10 ng of input DNA.
  • Assay performance was validated on 45 FFPE tumor specimens with known mutations, comparing results to a mass spectrometry-based platform.

Main Results:

  • The assay achieved average read depths of 2000× with >95% reads on target within 48 hours.
  • 100% sensitivity and 95.1% specificity were achieved for point mutation detection with an 8% mutant allele ratio cutoff.
  • All indels were detectable, with 6/9 indels ≤12 bp successfully called by variant caller software.

Conclusions:

  • Multiplex PCR and semiconductor-based sequencing offer a viable approach for mutation detection in clinical laboratories.
  • The assay's rapid turnaround time and low DNA input requirements address key challenges in FFPE specimen analysis.
  • This method facilitates routine identification of actionable mutations, supporting personalized cancer treatment.