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Comparison of GenFlex Tag array and Pyrosequencing in SNP genotyping
Daniel C Chen1, Janna Saarela, Ilpo Nuotio
1Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, California 90095-7088, USA.
The Journal of Molecular Diagnostics : JMD
|October 24, 2003
Summary
Pyrosequencing offers higher accuracy for single nucleotide polymorphism (SNP) genotyping compared to Affymetrix GenFlex Tag arrays, making it promising for diagnostics. However, it is less suitable for large-scale SNP profiling requiring multiplexing.
Area of Science:
- Genetics
- Molecular Biology
- Bioinformatics
Background:
- The Human Genome Project has identified millions of single nucleotide polymorphisms (SNPs), shifting research focus to high-throughput SNP genotyping.
- SNP profiling holds potential for future molecular diagnostics of complex traits, necessitating efficient and accurate genotyping methods.
- Cost-effectiveness drives the need for multiplexing capabilities in genotyping reactions.
Purpose of the Study:
- To compare the accuracy and efficiency of two SNP genotyping techniques: Affymetrix GenFlex Tag array and Pyrosequencing.
- To evaluate the suitability of these methods for potential diagnostic applications.
- To assess their performance in analyzing SNPs within a multiple sclerosis locus.
Main Methods:
- Comparison of Affymetrix GenFlex Tag array and Pyrosequencing against a tritium-based single nucleotide extension reaction reference method.
- Analysis of 14 single nucleotide polymorphisms (SNPs) in 96 related individuals from a multiple sclerosis fine mapping project.
- Evaluation of genotyping success rate and accuracy without extensive method optimization.
Main Results:
- Both GenFlex and Pyrosequencing successfully genotyped 11 out of 14 selected SNPs without extensive optimization.
- Pyrosequencing demonstrated higher accuracy compared to GenFlex, attributed to its single-stranded template in the extension reaction.
- The reference method confirmed the accuracy of the tested techniques.
Conclusions:
- Pyrosequencing shows significant potential for diagnostic applications due to its high accuracy in SNP genotyping.
- While accurate, Pyrosequencing is not ideal for large-scale SNP profiling where multiplexing is a key advantage.
- Further optimization could enhance the performance of both genotyping techniques.