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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: Jul 17, 2026

Infinium Assay for Large-scale SNP Genotyping Applications

Infinium Assay for Large-scale SNP Genotyping Applications

Published on: November 19, 2013

Application of quantum dots to multicolor microarray experiments: four-color genotyping.

George Karlin-Neumann¹, Marina Sedova, Mat Falkowski

¹Affymetrix Inc., South San Francisco, CA, USA.

Methods in Molecular Biology (Clifton, N.J.)

|January 24, 2007

Summary

Quantum dots offer a superior solution for highly multiplexed genomics assays, overcoming signal-to-noise challenges. This advancement enables accurate, high-plex genotyping using a single excitation wavelength.

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Area of Science:

Genomics
Biotechnology
Analytical Chemistry

Background:

Highly multiplexed genomics assays require high signal-to-noise ratios for accurate marker scoring on microarray platforms.
Increasing target complexity often necessitates more assay material or increased marker activity, risking nonspecific binding and data degradation.

Purpose of the Study:

To investigate quantum dots as an alternative to organic dyes for high-plex microarray-based genomics assays.
To evaluate the accuracy and efficiency of quantum dot technology in achieving multiplexed genotyping.

Main Methods:

Utilized quantum dots as fluorescent reporters on a microarray-detection platform.
Developed and validated a four-color genotyping assay capable of scoring over 20,000 markers.
Employed a single excitation wavelength for all quantum dot reporters.

Main Results:

Quantum dots enabled highly multiplexed (>20,000-plex) genotyping with high accuracy.
Quantum dots provided a sufficient signal-to-noise ratio, overcoming limitations of organic dyes.
All quantum dot reporters were excitable by a single wavelength, simplifying the assay setup.

Conclusions:

Quantum dots are a successful alternative to organic dyes for advanced, highly multiplexed genomics.
The single-excitation property of quantum dots enhances the practicality and efficiency of high-plex assays.
This technology significantly improves data quality and information yield in complex genomic analyses.