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

Search research articles

Related Experiment Video

Updated: Dec 29, 2025

QTL Mapping and CRISPR/Cas9 Editing to Identify a Drug Resistance Gene in Toxoplasma gondii

QTL Mapping and CRISPR/Cas9 Editing to Identify a Drug Resistance Gene in Toxoplasma gondii

Published on: June 22, 2017

Allele-Specific QTL Fine Mapping with PLASMA.

Austin T Wang¹, Anamay Shetty², Edward O'Connor³

¹Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.

American Journal of Human Genetics

|February 1, 2020

Summary

Related Concept Videos

You might also read

Related Articles

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

Sort by

Same author

DPP9-mediated inflammasome repression protects against checkpoint inhibitor lung toxicity.

bioRxiv : the preprint server for biology·2026

Same author

Data-driven RNA phenotyping captures genetically regulated dimensions of the transcriptome.

American journal of human genetics·2026

Same author

Leveraging tumor dynamics to discover mutations influencing progression and treatment response for precision oncology.

Genome medicine·2026

Same author

Using the biopsychosocial model of challenge and threat to understand stress-induced alcohol consumption.

Psychology of addictive behaviors : journal of the Society of Psychologists in Addictive Behaviors·2026

Same author

Systemic Glucocorticoid Immunosuppression and Survival Among Immune Checkpoint Inhibitor Recipients.

JAMA network open·2026

Same author

Somatic mutations reveal hyperactive Notch signaling in prurigo nodularis.

JCI insight·2026

This summary is machine-generated.

We developed PLASMA, a new method for pinpointing causal variants in genetic data. PLASMA integrates quantitative trait locus (QTL) and allele-specific (AS) QTL signals, improving accuracy and reducing the number of candidate variants for molecular trait studies.

Area of Science:

Genomics
Statistical Genetics
Molecular Biology

Background:

Identifying causal variants for molecular traits like gene expression is challenging using traditional quantitative trait locus (QTL) associations.
Allele-specific (AS) QTLs offer a robust measure of cis-regulation, but existing fine-mapping methods struggle to utilize AS-QTL signals effectively due to linkage disequilibrium (LD) complexities.

Purpose of the Study:

To introduce PLASMA (Population Allele-Specific Mapping), a novel fine-mapping method designed to integrate both QTL and AS-QTL data for enhanced causal variant detection.
To demonstrate PLASMA's superior performance in prioritizing causal variants across diverse genetic architectures through simulations and real-world data applications.

Main Methods:

Developed PLASMA, a statistical method that combines traditional QTL and allele-specific QTL (AS-QTL) information.

Keywords:

ChIP-seq QTL RNA-seq allele-specific causal variant cis-regulation fine-mapping gene regulation regulatory variant

More Related Videos

High-throughput DNA Extraction and Genotyping of 3dpf Zebrafish Larvae by Fin Clipping

High-throughput DNA Extraction and Genotyping of 3dpf Zebrafish Larvae by Fin Clipping

Published on: June 29, 2018

Robust 3D DNA FISH Using Directly Labeled Probes

Robust 3D DNA FISH Using Directly Labeled Probes

Published on: August 15, 2013

Related Experiment Videos

Last Updated: Dec 29, 2025

QTL Mapping and CRISPR/Cas9 Editing to Identify a Drug Resistance Gene in Toxoplasma gondii

QTL Mapping and CRISPR/Cas9 Editing to Identify a Drug Resistance Gene in Toxoplasma gondii

Published on: June 22, 2017

High-throughput DNA Extraction and Genotyping of 3dpf Zebrafish Larvae by Fin Clipping

High-throughput DNA Extraction and Genotyping of 3dpf Zebrafish Larvae by Fin Clipping

Published on: June 29, 2018

Robust 3D DNA FISH Using Directly Labeled Probes

Robust 3D DNA FISH Using Directly Labeled Probes

Published on: August 15, 2013

Validated PLASMA through extensive simulations assessing its accuracy in prioritizing causal variants under various genetic scenarios.

Applied PLASMA to RNA-seq data from 524 kidney tumors and H3K27AC ChIP-seq data from 28 prostate tumors to evaluate its performance on real biological data.

Main Results:

Simulations confirmed PLASMA's ability to accurately prioritize causal variants across a wide range of genetic architectures.
In kidney tumor RNA-seq data, PLASMA identified causal variants with higher power at 50 samples compared to conventional QTL mapping at 500 samples.
PLASMA achieved a significant reduction in median credible set size (6.9-fold) for prostate tumor ChIP-seq data compared to existing methods, with enriched functional annotations.

Conclusions:

PLASMA effectively integrates AS activity with traditional QTL data, substantially improving the accuracy and efficiency of causal variant detection in molecular trait studies.
The method enhances the power of fine mapping, enabling more precise identification of regulatory variants with fewer candidate markers.
PLASMA represents a significant advancement for genetic studies aiming to understand the molecular basis of complex traits and diseases.