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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: May 28, 2026

A Next-generation Tissue Microarray (ngTMA) Protocol for Biomarker Studies

A Next-generation Tissue Microarray (ngTMA) Protocol for Biomarker Studies

Published on: September 23, 2014

A TMA de-arraying method for high throughput biomarker discovery in tissue research.

Yinhai Wang¹, Kienan Savage, Claire Grills

¹Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, United Kingdom. y.wang@qub.ac.uk

|October 22, 2011

Summary

This study introduces a robust algorithm for de-arraying Tissue MicroArrays (TMAs), accurately identifying and mapping individual cores from digital slides, even with significant distortions. This method enhances biomarker discovery by ensuring precise core localization.

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Production of Tissue Microarrays, Immunohistochemistry Staining and Digitalization Within the Human Protein Atlas

Production of Tissue Microarrays, Immunohistochemistry Staining and Digitalization Within the Human Protein Atlas

Published on: May 31, 2012

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Last Updated: May 28, 2026

A Next-generation Tissue Microarray (ngTMA) Protocol for Biomarker Studies

A Next-generation Tissue Microarray (ngTMA) Protocol for Biomarker Studies

Published on: September 23, 2014

Production of Tissue Microarrays, Immunohistochemistry Staining and Digitalization Within the Human Protein Atlas

Production of Tissue Microarrays, Immunohistochemistry Staining and Digitalization Within the Human Protein Atlas

Published on: May 31, 2012

Area of Science:

Digital pathology
Bioinformatics
Computational biology

Background:

Tissue MicroArrays (TMAs) are crucial for high-throughput biomarker discovery.
Manual TMA slide production introduces artefacts, distorting core layout and identification.
Irregularities like missing cores and grid rotation complicate associating cores with their original positions.

Purpose of the Study:

To develop a robust method for de-arraying TMAs.
To accurately identify and map individual TMA cores from digital slides.
To overcome challenges posed by artefacts and distortions in TMA slides.

Main Methods:

A three-phase TMA de-arraying method: core segmentation, gridding, and mapping.
Morphological operations for TMA core segmentation.
Delaunay Triangulation for TMA core gridding and index assignment.
Correlation of digital slide cores with TMAMap data.

Main Results:

High accuracy in TMA de-arraying: 99.84% core segmentation, 99.81% correct gridding, and 99.96% accurate mapping.
100% correct gridding achieved on 113 pseudo slides with various irregularities.
Successful identification and localization of TMA cores despite missing cores, rotation, and stretching.

Conclusions:

The developed algorithm offers a genuine and robust solution for TMA de-arraying.
Enables rapid identification and precise partitioning of TMA cores from digital slides.
Facilitates downstream analysis and enhances the reliability of biomarker discovery using TMAs.