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

87.7K
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....
87.7K
RNA-seq03:21

RNA-seq

9.3K
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...
9.3K
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

5.8K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
5.8K
Genome Annotation and Assembly03:36

Genome Annotation and Assembly

16.6K
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
16.6K
Sanger Sequencing01:57

Sanger Sequencing

800.5K
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...
800.5K

You might also read

Related Articles

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

Sort by
Same author

Serum metabolomic profiling and incident CKD among African Americans.

Clinical journal of the American Society of Nephrology : CJASN·2014
Same author

Copy number polymorphisms near SLC2A9 are associated with serum uric acid concentrations.

BMC genetics·2014
Same author

Pleiotropic genes for metabolic syndrome and inflammation.

Molecular genetics and metabolism·2014
Same author

Effects of long-term averaging of quantitative blood pressure traits on the detection of genetic associations.

American journal of human genetics·2014
Same author

Associations of NINJ2 sequence variants with incident ischemic stroke in the Cohorts for Heart and Aging in Genomic Epidemiology (CHARGE) consortium.

PloS one·2014
Same author

Gene-age interactions in blood pressure regulation: a large-scale investigation with the CHARGE, Global BPgen, and ICBP Consortia.

American journal of human genetics·2014
Same journal

Parent and professional experiences of a clinical trial of prenatal and postnatal stem cell therapy for severe osteogenesis imperfecta.

European journal of human genetics : EJHG·2026
Same journal

Scoping review and recommendations for development and delivery of education resources for reproductive genetic carrier screening.

European journal of human genetics : EJHG·2026
Same journal

Australian parents' perspectives on extended genomic screening: what information to return and when?

European journal of human genetics : EJHG·2026
Same journal

Perspectives on phenotype in genetic testing for early-onset atrial fibrillation.

European journal of human genetics : EJHG·2026
Same journal

Systematic analysis of homozygous autosomal copy number losses in exomes improves diagnostic yield and uncovers ultra-rare recessive disorders.

European journal of human genetics : EJHG·2026
Same journal

Decoding splicing variants in high-throughput sequencing: a functional validation approach integrating deep learning tools.

European journal of human genetics : EJHG·2026
See all related articles

Related Experiment Video

Updated: Apr 27, 2026

A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information
05:01

A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information

Published on: July 1, 2020

4.7K

Pathway analysis with next-generation sequencing data.

Jinying Zhao1, Yun Zhu1, Eric Boerwinkle2

  • 1Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA.

European Journal of Human Genetics : EJHG
|July 3, 2014
PubMed
Summary
This summary is machine-generated.

A new statistical method using smoothed functional principal component analysis (SFPCA) improves pathway association analysis for rare variants. This method offers higher power and correct error rates, outperforming existing approaches in genetic studies.

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

14.0K
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

10.0K

Related Experiment Videos

Last Updated: Apr 27, 2026

A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information
05:01

A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information

Published on: July 1, 2020

4.7K
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

14.0K
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

10.0K

Area of Science:

  • Genetics
  • Statistical Genetics
  • Bioinformatics

Background:

  • Pathway analysis is crucial for understanding genetic associations, but methods for rare variants are underdeveloped.
  • Current rare variant pathway analysis methods suffer from inflated false-positive rates and low power.
  • These limitations stem from an inability to account for gametic phase disequilibrium.

Purpose of the Study:

  • To develop a novel statistical method for pathway association analysis that effectively handles rare variants.
  • To address the limitations of existing methods, particularly their handling of gametic phase disequilibrium.
  • To improve the accuracy and power of pathway-based association tests using next-generation sequencing data.

Main Methods:

  • Developed a novel statistic based on smoothed functional principal component analysis (SFPCA).
  • The SFPCA-based statistic captures position-level variant information and accounts for gametic phase disequilibrium.
  • Evaluated the statistic through intensive simulations and application to exome sequencing data.

Main Results:

  • SFPCA-based statistic demonstrated correct type 1 error rates for rare, common, and combined variants.
  • The SFPCA statistic exhibited significantly higher power compared to 22 existing methods across all simulated scenarios.
  • Application to early-onset myocardial infarction (EOMI) exome data identified three significantly associated pathways.

Conclusions:

  • The SFPCA-based statistic is a robust and powerful tool for rare variant pathway association analysis.
  • This novel method overcomes key limitations of existing approaches, offering improved accuracy and discovery potential.
  • The SFPCA method shows promise for identifying genetic pathways in complex diseases using next-generation sequencing data.