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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: Mar 31, 2026

Genome-Wide Analysis of DNA Methylation in Gastrointestinal Cancer

Genome-Wide Analysis of DNA Methylation in Gastrointestinal Cancer

Published on: September 18, 2020

From DNA Methylation Microarray to Digital PCR: A Stepwise Strategy for Tissue Specific cfDNA Biomarker Development.

David H Murray^1,2, Nicky Boulter¹, Shanon Ranjit¹

¹Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia.

Journal of Clinical Laboratory Analysis

|March 30, 2026

Summary

This summary is machine-generated.

A new method uses DNA methylation data to create PCR-based biomarkers for kidney-specific cell-free DNA (cfDNA). This approach enables rapid, cost-effective monitoring of acute kidney injury in transplant recipients.

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Area of Science:

Biomarkers
Molecular Diagnostics
Genomics

Background:

Cell-free DNA (cfDNA) is a promising biomarker for organ injury.
Current cfDNA tissue-of-origin analysis relies on genome-wide sequencing, limiting clinical scalability.

Purpose of the Study:

To develop a scalable workflow for creating PCR-based tissue-specific cfDNA biomarker assays.
To establish a kidney-specific cfDNA biomarker for monitoring acute kidney injury.

Main Methods:

Translated public DNA methylation data into PCR-compatible assays.
Identified kidney-specific hypermethylated regions using microarray data.
Developed and validated a digital PCR assay targeting a PAX2-associated differentially methylated region (DMR).

Main Results:

The PAX2 methylation marker showed high specificity for kidney tissue.
The marker was undetectable in healthy donor plasma and pre-transplant samples.
Robust detection of the marker in post-transplant plasma indicated acute kidney injury.

Conclusions:

A scalable method for developing PCR-based cfDNA biomarkers was established.
The kidney-specific assay facilitates rapid, cost-effective organ injury monitoring.
This strategy has potential applications in nephrology, oncology, and transplant medicine.