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

Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

12.6K
Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...
12.6K
Multiple Allele Traits01:49

Multiple Allele Traits

32.7K
The Concept of Multiple Allelism
32.7K
Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

14.6K
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,...
14.6K
Epistasis Analysis01:09

Epistasis Analysis

4.9K
Although Mendel chose seven unrelated traits in peas to study gene segregation, most traits involve multiple gene interactions that create a spectrum of phenotypes. When the interaction of various genes or alleles at different locations influences a phenotype, this is called epistasis. Epistasis often involves one gene masking or interfering with the expression of another (antagonistic epistasis). Epistasis often occurs when different genes are part of the same biochemical pathway. The...
4.9K
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
Multiple Comparison Tests01:13

Multiple Comparison Tests

3.4K
Multiple comparison test, abbreviated as MCT, is a post hoc analysis generally performed after comparing multiple samples with one or more tests. An MCT will help identify a significantly different sample among multiple samples or a factor among multiple factors.
It would be easy to compare two samples using a significance alpha level of 0.05. In other words, there is only one sample pair to be compared. However, it would be difficult to identify a significantly different sample if the number...
3.4K

You might also read

Related Articles

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

Sort by
Same author

Threshold Effects, Cognitive Decline, and Longitudinal Changes in White Matter Hyperintensity Volume.

Stroke·2026
Same author

Discordance Between Perceived Risk and Cardiovascular Health in Women of Reproductive Age.

JACC. Advances·2026
Same author

Psychological Health, Polysocial Risk, and Cardiovascular Health Among Women of Reproductive Age.

JACC. Advances·2026
Same author

Rapid hepatitis C test and treat with peer support at opioid treatment programs (RAPID HCV): a hybrid effectiveness-implementation type 1 randomized control trial.

Lancet regional health. Americas·2026
Same author

Weight loss lifestyle intervention and bone health hormonal markers in type 2 diabetes: analysis from look AHEAD study.

Journal of the Endocrine Society·2026
Same author

Sex Hormones and Cardiovascular Risk in Type 2 Diabetes: Cohort Study of the Look AHEAD Trial.

Diabetes care·2026

Related Experiment Video

Updated: May 1, 2026

Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry
05:53

Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry

Published on: June 21, 2018

9.2K

A Simple Scalable Association Hypothesis Test Combining Gene-wide Evidence From Multiple Polymorphisms.

Dhananjay Vaidya1, Lisa R Yanek1, Rasika A Mathias1

  • 1Johns Hopkins School of Medicine, Department of Medicine, Baltimore, MD.

British Journal of Medicine and Medical Research
|April 2, 2014
PubMed
Summary

This study introduces a novel method for combining single-nucleotide polymorphism (SNP) data to provide gene-wide statistical evidence for high-density lipoprotein cholesterol (HDLC) associations. This approach enhances biological interpretation in genetic association scans.

Keywords:
Bonferronicombining evidencehypothesis tests

More Related Videos

Large-Scale Multi-Omics Genome-Wide Association Studies Mo-GWAS: Guidelines for Sample Preparation and Normalization
08:27

Large-Scale Multi-Omics Genome-Wide Association Studies Mo-GWAS: Guidelines for Sample Preparation and Normalization

Published on: July 27, 2021

4.6K
An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations
10:17

An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations

Published on: November 3, 2010

23.3K

Related Experiment Videos

Last Updated: May 1, 2026

Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry
05:53

Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry

Published on: June 21, 2018

9.2K
Large-Scale Multi-Omics Genome-Wide Association Studies Mo-GWAS: Guidelines for Sample Preparation and Normalization
08:27

Large-Scale Multi-Omics Genome-Wide Association Studies Mo-GWAS: Guidelines for Sample Preparation and Normalization

Published on: July 27, 2021

4.6K
An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations
10:17

An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations

Published on: November 3, 2010

23.3K

Area of Science:

  • Genetics
  • Statistical Genetics
  • Biostatistics

Background:

  • Single-nucleotide polymorphism (SNP) scans test gene-phenotype associations, but biological interpretation is limited to genes with multiple SNPs.
  • Current methods often lack the power to detect biologically relevant signals within genes.
  • High-density lipoprotein cholesterol (HDLC) is a key cardiovascular risk factor influenced by genetic variations.

Purpose of the Study:

  • To develop and validate a method for combining SNP-level evidence into gene-wide statistical evidence.
  • To improve the biological interpretability of genetic association studies.
  • To apply this method to identify genes associated with HDLC.

Main Methods:

  • Utilized a family-based study (N=1782) with 1000 phenotype-permuted datasets.
  • Calculated gene-wide p-values by summing correlated z-test statistics for 592 SNPs across 14 pre-selected genes.
  • Validated results using empirical distributions of chi-squared statistics and simulated data.

Main Results:

  • Identified the CETP gene as significantly associated with HDLC (p=4.0×10-5).
  • The PLTP gene showed borderline significance (p=6.7×10-3).
  • Gene-wide p-values were more significant than Bonferroni-corrected SNP p-values in 11 out of 14 genes.

Conclusions:

  • A simple, scalable method for generating gene-wide statistical evidence from SNP data has been validated.
  • This method enables biologically interpretable, high-throughput gene-wide hypothesis testing in genome-wide association scans.
  • Gene-wide association tests can facilitate replication across diverse populations with varying linkage disequilibrium structures.