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

15.8K
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...
15.8K
Multiple Allele Traits01:49

Multiple Allele Traits

38.2K
The Concept of Multiple Allelism
38.2K
Genome Annotation and Assembly03:36

Genome Annotation and Assembly

21.1K
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.
21.1K
Trait and State Self-Esteem02:08

Trait and State Self-Esteem

11.5K
The term self-esteem is often used generically, to refer to how people feel about themselves. However, according to research, there are three distinct constructs that should not be used interchangeably (Brown & Marshall, 2006). 
11.5K
Polygenic Traits01:18

Polygenic Traits

69.2K
When more than one gene is responsible for a given phenotype, the trait is considered polygenic. Human height is a polygenic trait. Studies have uncovered hundreds of loci that influence height, and there are believed to be many more. Due to the high number of genes involved, as well as environmental and nutritional factors, height varies significantly within a given population. The distribution of height forms a bell-shaped curve, with relatively few individuals in the population at the...
69.2K
Genomics02:02

Genomics

40.9K
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...
40.9K

You might also read

Related Articles

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

Sort by
Same author

SPICE: A Robust Computational Framework for Identifying Copy Number Variations in Spatial Transcriptomics.

bioRxiv : the preprint server for biology·2026
Same author

Macrophage-Dependent Intercellular Crosstalk in Multiphenotypic Heart Failure With Preserved Ejection Fraction.

Journal of the American Heart Association·2026
Same author

mFABIO: An integrative multi-tissue TWAS fine-mapping approach to prioritize potentially causal genes and tissues underlying binary traits.

PLoS genetics·2026
Same author

Biological Age Acceleration and the Dynamic Progression of Cardiovascular-Kidney-Metabolic Diseases to Multimorbidity, Dementia and Mortality: A Prospective Cohort Study.

Geriatrics & gerontology international·2026
Same author

CEDR: robust consensus cancer subtyping with multi-omics data via ensemble dimensionality reduction.

Briefings in bioinformatics·2026
Same author

Exploring the Influence of Chemical Exposures in Breast Cancer Disparities: High-Throughput Transcriptomic Analysis in Normal Breast Cells from Diverse Donors.

bioRxiv : the preprint server for biology·2026

Related Experiment Video

Updated: Feb 15, 2026

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

4.9K

Identifying and exploiting trait-relevant tissues with multiple functional annotations in genome-wide association

Xingjie Hao1,2,3, Ping Zeng2,3, Shujun Zhang1

  • 1Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, Hubei, China.

Plos Genetics
|January 30, 2018
PubMed
Summary

We developed SMART, a new method to identify disease-relevant tissues using genomic data and omics annotations. This approach enhances the power of genetic association tests for complex traits.

More Related Videos

Genome-wide Analysis using ChIP to Identify Isoform-specific Gene Targets
11:19

Genome-wide Analysis using ChIP to Identify Isoform-specific Gene Targets

Published on: July 7, 2010

15.0K
Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics
08:09

Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics

Published on: June 17, 2012

20.6K

Related Experiment Videos

Last Updated: Feb 15, 2026

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

4.9K
Genome-wide Analysis using ChIP to Identify Isoform-specific Gene Targets
11:19

Genome-wide Analysis using ChIP to Identify Isoform-specific Gene Targets

Published on: July 7, 2010

15.0K
Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics
08:09

Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics

Published on: June 17, 2012

20.6K

Area of Science:

  • Genetics and Genomics
  • Bioinformatics
  • Statistical Genetics

Background:

  • Genome-wide association studies (GWASs) identify numerous disease-associated loci, but their biological functions and relevant tissues often remain unknown.
  • Understanding the biological mechanisms underlying trait associations requires identifying trait-specific tissues and conducting focused analyses.
  • Existing methods for integrating functional annotations with GWAS data have limitations in identifying trait-relevant tissues and improving association test power.

Purpose of the Study:

  • To develop a novel analytical procedure, Scalable Multiple Annotation integration for trait-Relevant Tissue identification and usage (SMART), for identifying trait-relevant tissues using multi-omics functional annotations and GWAS summary statistics.
  • To enhance the accuracy of trait-relevant tissue identification by incorporating multiple complementary functional annotations.
  • To leverage identified trait-relevant tissues for constructing more powerful SNP set association tests.

Main Methods:

  • Extended linear mixed models to incorporate multiple SNP functional annotations from omics studies with GWAS summary statistics.
  • Utilized a generalized estimating equation-based algorithm for parameter inference and a mixture modeling framework for trait-tissue relevance classification.
  • Developed a weighted sequence kernel association test (SKAT) incorporating identified trait-relevant tissues for enhanced association analysis.

Main Results:

  • Extensive simulations demonstrated SMART's improved accuracy in identifying trait-relevant tissues by effectively utilizing multiple annotations.
  • The SMART procedure successfully identified novel trait-tissue relevance across 43 traits from 28 GWASs, using tissue-specific annotations from ENCODE and Roadmap (105 tissues).
  • Demonstrated the utility of inferred trait-relevant tissues in constructing significantly more powerful SNP set association tests, as shown in the Wellcome Trust Case Control Consortium study.

Conclusions:

  • SMART provides a robust framework for integrating multi-omics functional annotations to identify trait-relevant tissues from GWAS data.
  • The method enhances our understanding of the biological underpinnings of complex traits by pinpointing informative functional annotations and their relationship to specific tissues.
  • SMART enables the development of more powerful genetic association tests by leveraging tissue-specific insights, advancing the field of genetic discovery.