Comparison of PrASE and Pyrosequencing for SNP Genotyping
2006 (English)In: BMC Genomics, ISSN 1471-2164, Vol. 7, 291- p.Article in journal (Refereed) Published
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.
Place, publisher, year, edition, pages
2006. Vol. 7, 291- p.
5, 10 methylenetetrahydrofolate reductase (FADH2); beta integrin; blood clotting factor 13; blood clotting factor 5; endothelial nitric oxide synthase; fibrinogen; plasminogen activator inhibitor 1; prothrombin; stromelysin; accuracy; article; automation; controlled study; gene cluster; gene technology; genetic polymorphism; genetic procedures; genetic susceptibility; genetic variability; genotype; human; intermethod comparison; microarray analysis; mutational analysis; parallel design; polymerase chain reaction; protease mediated allele specific extension; pyrosequencing; reproducibility; single nucleotide polymorphism; thrombosis
IdentifiersURN: urn:nbn:se:kth:diva-6968DOI: 10.1186/1471-2164-7-291ISI: 000242193100001ScopusID: 2-s2.0-34547926324OAI: oai:DiVA.org:kth-6968DiVA: diva2:11831
Tidigare titel: PrASE - An Accurate and Robust Genotyping Platform as Compared to DNA Sequencing
QC 201007142007-04-122007-04-122011-09-06Bibliographically approved