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DNA Microarrays

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...

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Updated: Aug 29, 2025

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

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

Published on: June 21, 2018

Multiplexed functional genomic assays to decipher the noncoding genome.

Yonatan A Cooper^1,2,3, Qiuyu Guo³, Daniel H Geschwind^1,4,5,6

¹Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.

Human Molecular Genetics

|September 3, 2022

Summary

This summary is machine-generated.

Identifying functional genetic variants linked to disease is challenging. New high-throughput experimental assays, like massively parallel reporter assays and CRISPR screens, offer powerful tools to characterize noncoding genetic variation at scale.

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Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq

Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq

Published on: March 12, 2021

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Last Updated: Aug 29, 2025

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

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

Published on: June 21, 2018

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

Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq

Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq

Published on: March 12, 2021

Area of Science:

Genomics
Genetic Variation
Disease Association

Background:

Linkage disequilibrium and incomplete regulatory annotation hinder functional noncoding variant identification.
Computational methods for variant prioritization have limited predictive power for disease association.

Purpose of the Study:

To describe two distinct, highly parallelized experimental approaches for characterizing human noncoding genetic variation.
To highlight the flexible implementation and advantages of these assays for large-scale functional genomics.

Main Methods:

Massively parallel reporter assays (MPRAs) for assessing regulatory element function.
CRISPR-based pooled screens for functional genetic screens.

Main Results:

These multiplexed assays enable the characterization of noncoding genetic variation at unprecedented scale.
Each approach offers unique advantages and limitations, underscoring the need for multimodal integration.

Conclusions:

Multiplexed assays of variant effects are crucial for experimentally characterizing noncoding genetic risk.
These methods will advance our understanding of disease mechanisms and improve predictive algorithms for genetic risk.