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

100.8K
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....
100.8K
RNA-seq03:21

RNA-seq

12.4K
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...
12.4K
Sanger Sequencing01:57

Sanger Sequencing

777.7K
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...
777.7K
Genomics02:02

Genomics

41.7K
Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
41.7K
RACE - Rapid Amplification of cDNA Ends02:35

RACE - Rapid Amplification of cDNA Ends

7.5K
Rapid Amplification of cDNA Ends, or RACE, is one of the most effective methods to obtain a full-length cDNA from an mRNA sequence between a known internal region to the unknown sequence at the 5’ or 3’ end. The unknown region is cloned in the cDNA by a gene-specific primer that binds the known end, and a hybrid primer that attaches a predefined anchor sequence to the unknown end of the cDNA. The sequence in between is amplified by PCR with an anchor primer and a gene-specific...
7.5K
Synthetic Biology02:55

Synthetic Biology

5.8K
Synthetic biology is an interdisciplinary science that involves using principles from disciplines such as engineering, molecular biology, cell biology, and systems biology. It involves remodeling existing organisms from nature or constructing completely new synthetic organisms for applications such as protein or enzyme production, bioremediation, value-added macromolecule production, and the addition of desirable traits to crops, to name a few.
Golden rice
Golden rice is a genetically modified...
5.8K

You might also read

Related Articles

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

Sort by
Same author

Memory B cells in mature follicle-like tertiary lymphoid structures predict BCG response in non-muscle-invasive bladder cancer.

Scientific reports·2026
Same author

Rhodium Single-Atom Decorated CeO<sub>2</sub>:Yb,Er/Rh-ZnIn<sub>2</sub>S<sub>4</sub> With Enhanced Photo-Thermo-Electric Effects for Efficient H<sub>2</sub> Evolution and Biomass Valorization.

Small (Weinheim an der Bergstrasse, Germany)·2026
Same author

Understanding the chemistry of re-emerging proton batteries.

Chemical Society reviews·2026
Same author

Dual-Site Cooperativity in Ag/Cu-Ag<sub>2</sub>S Cocatalyst for CO<sub>2</sub> Activation and Deep Hydrogenation Towards 100%-Selective CH<sub>4</sub> Photoproduction.

Small (Weinheim an der Bergstrasse, Germany)·2026
Same author

BdXTH27 negatively regulates root development by modulating cell elongation in Brachypodium distachyon.

Biochemical and biophysical research communications·2026
Same author

Overcoming the Compatibility Challenge With a Biomimetic Mandala Heterostructure for Cross-Spectrum Electromagnetic Wave Absorption and Efficient Electrothermal Deicing.

Small (Weinheim an der Bergstrasse, Germany)·2026

Related Experiment Video

Updated: Mar 21, 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

12.3K

IntSIM: An Integrated Simulator of Next-Generation Sequencing Data.

Xiguo Yuan, Junying Zhang, Liying Yang

    IEEE Transactions on Bio-Medical Engineering
    |May 11, 2016
    PubMed
    Summary

    IntSIM is a novel simulation system for DNA sequencing data, capable of generating realistic data for germline and somatic variants, tumor purity, and genomic events. This tool enhances the evaluation of DNA variant discovery and tumor analysis methods.

    More Related Videos

    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
    High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq
    09:06

    High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

    Published on: October 5, 2018

    10.9K

    Related Experiment Videos

    Last Updated: Mar 21, 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

    12.3K
    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
    High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq
    09:06

    High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

    Published on: October 5, 2018

    10.9K

    Area of Science:

    • Genomics
    • Bioinformatics
    • Computational Biology

    Background:

    • Next-generation sequencing (NGS) generates vast amounts of data crucial for DNA variant discovery and tumor studies.
    • Computational tools are essential for analyzing NGS data, but require realistic simulated data for robust testing and development.
    • Existing simulation tools often lack the ability to model complex genomic features found in real-world data.

    Purpose of the Study:

    • To introduce IntSIM, an integrated simulation system designed to generate realistic DNA sequencing data.
    • To address limitations in current simulation tools by incorporating features like germline/somatic variants, tumor purity, and genomic event correlations.
    • To provide a valuable resource for evaluating computational methods in DNA variant detection and tumor analysis.

    Main Methods:

    • IntSIM simulates both germline and somatic DNA variants within the same sequence.
    • The system models tumor purity to generate sequencing reads from heterogeneous genomes and supports tumor-normal matched samples.
    • It incorporates Hidden Markov Models (HMMs) trained on real sequencing data to simulate correlations among Single Nucleotide Polymorphisms (SNPs) and Copy Number Variations/Alterations (CNVs/CNAs), including broad and focal events.

    Main Results:

    • Simulation data generated by IntSIM accurately reflect real-world sequencing data characteristics and align with specified input parameters.
    • IntSIM demonstrates superior performance compared to other simulation programs in scenarios involving heterozygous SNPs and CNVs/CNAs.
    • The system successfully achieves simulation functionalities not available in other existing programs.

    Conclusions:

    • IntSIM provides a powerful and versatile platform for simulating complex genomic data, essential for advancing DNA variant discovery and tumor analysis.
    • The realistic simulation capabilities of IntSIM are expected to significantly improve the performance evaluation of computational methods.
    • IntSIM offers a realistic assessment of how tumor purity impacts the identification of somatic mutations, a critical aspect of cancer research.