Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Comparing Copy Number Variations and SNPs

Comparing Copy Number Variations and SNPs

Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...

Genome-wide Association Studies-GWAS

Genome-wide Association Studies-GWAS

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...

Epistasis Analysis

Epistasis Analysis

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...

You might also read

Related Articles

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

Sort by

Same author

Cell-type-resolved genetic variation shapes inflammatory bowel disease risk.

Nature·2026

Same author

Design and interpretation of eQTL-GWAS colocalisation studies: Lessons from a large-scale evaluation.

PLoS genetics·2026

Same author

Altered B cell activation contributes to the immunopathogenesis of childhood arthritis-associated uveitis.

Nature communications·2026

Same author

High-resolution promoter interaction analysis implicates genes involved in the activation of Type 3 Innate Lymphoid Cells in autoimmune disease risk.

bioRxiv : the preprint server for biology·2026

Same author

Outcome-guided spike-and-slab Lasso Biclustering: A Novel Approach for Enhancing Biclustering Techniques for Gene Expression Analysis.

Statistics and computing·2025

Same author

Exploiting pleiotropy to enhance variant discovery with functional false discovery rates.

Nature computational science·2025

Same journal

Genetic survey of biomarkers at early and mid-pregnancy identifies pregnancy-specialized immune regulation.

PLoS genetics·2026

Same journal

Argonaute proteins orchestrate Meiotic Sex Chromosome Inactivation and timing of the spermatogenic transcriptional program.

PLoS genetics·2026

Same journal

Genome wide association study meta-analysis of neuropathologic lesions of Alzheimer's disease and related dementias in a multi-site autopsy cohort.

PLoS genetics·2026

Same journal

Microtubule stiffening by the doublecortin-domain protein ZYG-8 contributes to mitotic spindle orientation during zygote division in Caenorhabditis elegans.

PLoS genetics·2026

Same journal

Multiple instance fine-mapping: Predicting causal regulatory variants with a deep sequence model.

PLoS genetics·2026

Same journal

Nuclear ubiquitin-conjugating enzyme TrUbc4 and F-box protein TrFwd1-mediated modification of Cre1 in Trichoderma reesei establishes a regulatory mechanism for carbon catabolite repression.

PLoS genetics·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Oct 18, 2025

Tracking Drug-induced Changes in Receptor Post-internalization Trafficking by Colocalizational Analysis

Tracking Drug-induced Changes in Receptor Post-internalization Trafficking by Colocalizational Analysis

Published on: July 3, 2015

A more accurate method for colocalisation analysis allowing for multiple causal variants.

Chris Wallace^1,2

¹Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, United Kingdom.

|September 29, 2021

Summary

This summary is machine-generated.

Genome-wide association studies (GWAS) often find multiple causal variants. Combining the Sum of Single Effects (SuSiE) with colocalisation (coloc) improves accuracy for shared genetic variants, especially when multiple causal variants exist.

More Related Videos

Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA

Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA

Published on: August 21, 2016

Determining the Likelihood of Variant Pathogenicity Using Amino Acid-level Signal-to-Noise Analysis of Genetic Variation

Determining the Likelihood of Variant Pathogenicity Using Amino Acid-level Signal-to-Noise Analysis of Genetic Variation

Published on: January 16, 2019

Related Experiment Videos

Last Updated: Oct 18, 2025

Tracking Drug-induced Changes in Receptor Post-internalization Trafficking by Colocalizational Analysis

Tracking Drug-induced Changes in Receptor Post-internalization Trafficking by Colocalizational Analysis

Published on: July 3, 2015

Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA

Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA

Published on: August 21, 2016

Determining the Likelihood of Variant Pathogenicity Using Amino Acid-level Signal-to-Noise Analysis of Genetic Variation

Determining the Likelihood of Variant Pathogenicity Using Amino Acid-level Signal-to-Noise Analysis of Genetic Variation

Published on: January 16, 2019

Area of Science:

Genetics
Statistical Genetics
Bioinformatics

Background:

Genome-wide association studies (GWAS) frequently identify multiple, closely located causal variants.
Assessing shared causal variants between traits is crucial, but existing methods like colocalisation (coloc) assume a single causal variant per region.
This assumption limits the accuracy of coloc when multiple causal variants are present.

Purpose of the Study:

To evaluate the Sum of Single Effects (SuSiE) regression framework for enhancing colocalisation analyses.
To determine if SuSiE can improve the accuracy of coloc inference in the presence of multiple causal variants.

Main Methods:

Utilised the Sum of Single Effects (SuSiE) regression framework for fine-mapping genetic signals.
Integrated SuSiE with the colocalisation (coloc) method to assess shared causal variants.
Compared SuSiE-enhanced coloc performance against existing methods for handling multiple causal variants.

Main Results:

SuSiE enables simultaneous evaluation of evidence for multiple causal variants.
SuSiE separates statistical support for each variant conditionally.
Using SuSiE with coloc yields more accurate colocalisation inference compared to other multi-variant approaches.

Conclusions:

The Sum of Single Effects (SuSiE) framework is a valuable tool for fine-mapping in genetic studies.
Combining SuSiE with colocalisation (coloc) significantly optimizes the accuracy of colocalisation analyses.
This integrated approach is recommended for studies investigating shared causal variants when multiple causal variants are suspected.