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Related Concept Videos

DNA Microarrays02:34

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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Related Experiment Video

Updated: Jun 27, 2026

Infinium Assay for Large-scale SNP Genotyping Applications
13:33

Infinium Assay for Large-scale SNP Genotyping Applications

Published on: November 19, 2013

Whole-genome amplification enables accurate genotyping for microarray-based high-density single nucleotide

Farzana Jasmine1, Habibul Ahsan, Irene L Andrulis

  • 1Department of Health Studies, The University of Chicago, 5841 South Maryland Avenue, MC 2007, Chicago, IL 60637, USA.

Cancer Epidemiology, Biomarkers & Prevention : a Publication of the American Association for Cancer Research, Cosponsored by the American Society of Preventive Oncology
|December 10, 2008
PubMed
Summary

Whole-genome amplification using Multiple Displacement Amplification (MDA-WGA) is feasible for high-density SNP genotyping. MDA-WGA DNA products yield reproducible data comparable to genomic DNA for large-scale genetic studies.

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Last Updated: Jun 27, 2026

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Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry
05:53

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

Published on: June 21, 2018

Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Large-scale genome-wide association studies (GWAS) require substantial amounts of high-quality genomic DNA (gDNA).
  • Limited gDNA quantity and quality pose practical challenges in GWAS.
  • Whole-genome amplification (WGA) methods are explored to overcome these limitations.

Purpose of the Study:

  • To evaluate the feasibility of using Multiple Displacement Amplification (MDA) for whole-genome amplification (WGA) in high-density single nucleotide polymorphism (SNP) genotyping.
  • To compare the performance of MDA-WGA DNA with native gDNA in SNP genotyping arrays.

Main Methods:

  • Utilized the Affymetrix Early Access Mendel Nsp 250K GeneChip for genotyping 224,940 SNPs across 28 DNA samples.
  • Compared genotype call rates and concordance between 14 gDNA samples and their corresponding 14 MDA-WGA amplified samples.
  • Assessed reproducibility using duplicate samples and evaluated concordance on the Illumina Infinium 610 Quad platform.

Main Results:

  • Overall mean genotype call rates were comparable between gDNA (97.07%) and MDA-WGA samples (97.77%).
  • High concordance (97.74%) was observed between gDNA and MDA-WGA samples for overall genotypes.
  • Reproducibility of the genotyping platform was high (99.45%), and MDA-WGA DNA showed similar concordance on a different platform.

Conclusions:

  • MDA-WGA DNA is a viable and effective alternative to gDNA for high-density SNP genotyping in large-scale genetic studies.
  • The MDA method provides reproducible and high-quality data suitable for GWAS.
  • Despite minor copy number variations, MDA-WGA DNA ensures reliable genome-wide SNP genotyping analysis.