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Genotyping of Single Nucleotide Polymorphisms in DNA Isolated from Serum Using Sequenom MassARRAY Technology
Tess V Clendenen1, Justin Rendleman1, Wenzhen Ge1
1Department of Population Health, New York University School of Medicine, New York, New York, United States of America.
Plos One
|August 15, 2015
Summary
DNA from serum can reliably genotype single nucleotide polymorphisms (SNPs) in large epidemiologic studies. This method offers a viable alternative when high-quality DNA sources are limited, ensuring accurate genetic analysis.
Area of Science:
- Genetics and Genomics
- Epidemiology
- Biotechnology
Background:
- Large epidemiologic studies require extensive exposure data for gene-environment interaction assessment.
- Limited DNA quantity from serum or plasma samples poses a challenge in these studies.
Purpose of the Study:
- To evaluate the reliability and accuracy of genotyping single nucleotide polymorphisms (SNPs) using DNA isolated from serum.
- To assess the feasibility of using serum DNA for large-scale genetic studies.
Main Methods:
- Genotyping of 81 SNPs using Sequenom multiplex SNP genotyping technology.
- Comparison of DNA from serum with DNA from high-quality sources (clots, cell precipitates) from 158 participants.
- Analysis of call frequencies and genotype concordance across different sample types.
Main Results:
- 74% of SNPs achieved high call frequencies (≥95%) with serum DNA, comparable to clot/precipitate DNA (85%).
- 95% of SNPs showed high genotype concordance (>98%) across serum, clot, and precipitate DNA.
- High DNA purity was not essential for successful genotyping.
Conclusions:
- Multiplex SNP genotyping using DNA from serum is reliable for large-scale epidemiologic studies.
- Serum DNA provides a practical alternative for genetic analysis when high-quality DNA is scarce.
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