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Open Access Methodology article

Comparison of PrASE and Pyrosequencing for SNP Genotyping

Max Käller14, Emilie Hultin1, Kristina Holmberg1, Marie-Louise Persson2, Jacob Odeberg13, Joakim Lundeberg1* and Afshin Ahmadian1

Author Affiliations

1 Department of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Center, Roslagstullsbacken 21, SE – 106 91 Stockholm, Sweden

2 Clinical Chemistry Laboratory, Blekinge Hospital, Karlskrona, Sweden

3 Department of Medicine, Atherosclerosis Research Unit, King Gustaf V Research Institute, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden

4 Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304, USA

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BMC Genomics 2006, 7:291  doi:10.1186/1471-2164-7-291

Published: 16 November 2006

Abstract

Background

There is an imperative need for SNP genotyping technologies that are cost-effective per sample with retained high accuracy, throughput and flexibility. We have developed a microarray-based technique and compared it to Pyrosequencing. In the protease-mediated allele-specific extension (PrASE), the protease constrains the elongation reaction and thus prevents incorrect nucleotide incorporation to mismatched 3'-termini primers.

Results

The assay is automated for 48 genotyping reactions in parallel followed by a tag-microarray detection system. A script automatically visualizes the results in cluster diagrams and assigns the genotypes. Ten polymorphic positions suggested as prothrombotic genetic variations were analyzed with Pyrosequencing and PrASE technologies in 442 samples and 99.8 % concordance was achieved. In addition to accuracy, the robustness and reproducibility of the technique has been investigated.

Conclusion

The results of this study strongly indicate that the PrASE technology can offer significant improvements in terms of accuracy and robustness and thereof increased number of typeable SNPs.