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

Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

18.5K
A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
18.5K
Next-generation Sequencing03:00

Next-generation Sequencing

98.8K
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....
98.8K
Nucleotide Excision Repair01:08

Nucleotide Excision Repair

40.9K
Overview
40.9K
Nucleotide Excision Repair01:38

Nucleotide Excision Repair

5.3K
DNA Distortion and Damage
Cells are regularly exposed to mutagens—factors in the environment that can damage DNA and generate mutations. UV radiation is one of the most common mutagens and is estimated to introduce a significant number of changes in DNA. These include bends or kinks in the structure, which can block DNA replication or transcription. If these errors are not fixed, the damage can cause mutations, which in turn can result in cancer or disease depending on which sequences are...
5.3K
Cluster Sampling Method01:20

Cluster Sampling Method

14.8K
Appropriate sampling methods ensure that samples are drawn without bias and accurately represent the population. Because measuring the entire population in a study is not practical, researchers use samples to represent the population of interest.
To choose a cluster sample, divide the population into clusters (groups) and then randomly select some of the clusters. All the members from these clusters are in the cluster sample. For example, if you randomly sample four departments from your...
14.8K
Vesicular Tubular Clusters01:45

Vesicular Tubular Clusters

3.2K
After budding out from the ER membrane, some COPII vesicles lose their coat and fuse with one another to form larger vesicles and interconnected tubules called vesicular tubular clusters or VTCs. These clusters constitute a compartment at the ER-Golgi interface known as ERGIC (Endoplasmic Reticulum Golgi Intermediate Compartment). The ERGIC is a mobile membrane-bound cargo transport system that sorts proteins secreted from ER and delivers them to the Golgi.
With the help of motor proteins such...
3.2K

You might also read

Related Articles

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

Sort by
Same author

Men and women differ in their diurnal expression of monocyte peroxisome proliferator-activated receptor-α in the fed but not in the fasted state.

FASEB journal : official publication of the Federation of American Societies for Experimental Biology·2015
See all related articles

Related Experiment Video

Updated: Feb 11, 2026

Genotyping Single Nucleotide Polymorphisms in the Mitochondrial Genome by Pyrosequencing
07:24

Genotyping Single Nucleotide Polymorphisms in the Mitochondrial Genome by Pyrosequencing

Published on: February 10, 2023

2.0K

ShRangeSim: Simulation of Single Nucleotide Polymorphism Clusters in Next-Generation Sequencing Data.

Markus Boenn1,2,3

  • 11 Institute of Computer Science, Martin Luther University Halle-Wittenberg , Halle/Saale, Germany .

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
|April 17, 2018
PubMed
Summary

Simulating next-generation sequencing (NGS) data with genomic variations is crucial for evaluating analysis pipelines. Existing methods fail to model single nucleotide polymorphism (SNP) clusters, suggesting the need for overdispersion-aware distributions.

Keywords:
SNP clusternext-generation sequencingoverdispersionsimulation

More Related Videos

Author Spotlight: Genetic Profiling for Fluorouracil Response in Gastric Cancer
06:21

Author Spotlight: Genetic Profiling for Fluorouracil Response in Gastric Cancer

Published on: May 10, 2024

1.3K
The Visual Colorimetric Detection of Multi-nucleotide Polymorphisms on a Pneumatic Droplet Manipulation Platform
10:01

The Visual Colorimetric Detection of Multi-nucleotide Polymorphisms on a Pneumatic Droplet Manipulation Platform

Published on: September 27, 2016

8.0K

Related Experiment Videos

Last Updated: Feb 11, 2026

Genotyping Single Nucleotide Polymorphisms in the Mitochondrial Genome by Pyrosequencing
07:24

Genotyping Single Nucleotide Polymorphisms in the Mitochondrial Genome by Pyrosequencing

Published on: February 10, 2023

2.0K
Author Spotlight: Genetic Profiling for Fluorouracil Response in Gastric Cancer
06:21

Author Spotlight: Genetic Profiling for Fluorouracil Response in Gastric Cancer

Published on: May 10, 2024

1.3K
The Visual Colorimetric Detection of Multi-nucleotide Polymorphisms on a Pneumatic Droplet Manipulation Platform
10:01

The Visual Colorimetric Detection of Multi-nucleotide Polymorphisms on a Pneumatic Droplet Manipulation Platform

Published on: September 27, 2016

8.0K

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Genomic variations are key to understanding host-pathogen interactions and diseases like cancer.
  • Next-generation sequencing (NGS) data analysis pipelines are essential for detecting these variations.
  • Simulated NGS data aids in evaluating and validating these analysis pipelines.

Purpose of the Study:

  • To identify limitations in current methods for simulating NGS data with genomic variations.
  • To address the failure of existing approaches in modeling single nucleotide polymorphism (SNP) clusters.
  • To propose improved statistical models for simulating SNP cluster enrichments.

Main Methods:

  • Applied two count data distributions to publicly available genomic variation datasets.
  • Evaluated the ability of these distributions to model SNP cluster sizes.
  • Focused on overdispersion-aware distributions for modeling count data.

Main Results:

  • Existing methods for simulating NGS data with genomic variations do not accurately model SNP clusters.
  • SNP clusters represent local enrichments of single nucleotide polymorphisms.
  • Overdispersion-aware distributions show promise for modeling the sizes of SNP clusters.

Conclusions:

  • Current simulation approaches for NGS data and genomic variations are inadequate for modeling SNP clusters.
  • Accurate modeling of SNP clusters requires distributions that account for overdispersion.
  • The findings suggest specific statistical distributions for more robust NGS data simulation in genomic variation studies.