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Weiskirchen, R. et al.

Ralf Weiskirchen, Carmen G. Tag, Senait Mengsteab, Axel M. Gressner, Catherine J. E. Ingram, Dallas M. Swallow,

Pitfalls in LightCycler diagnosis of the single-nucleotide polymorphism 13.9 kb upstream of the lactase gene that is associated with adult-type hypolactasia.

BACKGROUND: Patients presenting with symptoms of lactose intolerance are in some centres routinely tested for a single-nucleotide polymorphism C-13910T, which is located upstream of the lactase gene (LCT) and is tightly associated with genetically determined lactase persistence/non-persistence. Typing of this polymorphism enables differential diagnosis for genetic versus secondary causes of lactose intolerance. Several PCR-based methods have been established as tests for this SNP. In particular, automated genotyping assays conducted on LightCycler platforms provide a rapid, labour-saving means for routine high-throughput analysis of this variant. Recently, several novel allelic variants have been identified in non-European populations. Three of these variants occur in close proximity to C-13910T, but their effect on the genetic test is unknown. METHODS: Here we analyse whether the occurrence of C-13907G, T-13913C, and T-13915G, affect the diagnostic accuracy of C-13910T typings obtained using the LightCycler MutaREAL lactase real-time PCR kit. RESULTS: Genotyping of DNA samples harbouring respective variants or combinations thereof significantly influenced the LightCycler analysis. Some allelic combinations generated melting profiles that prevented the correct assignment of C-13910T. CONCLUSIONS: We conclude that genotyping of the C-13910T variant with the MutaREAL lactase real-time PCR kit in non-Europeans is prone to error and should be omitted.[1]

References

Pitfalls in LightCycler diagnosis of the single-nucleotide polymorphism 13.9 kb upstream of the lactase gene that is associated with adult-type hypolactasia. Weiskirchen, R., Tag, C.G., Mengsteab, S., Gressner, A.M., Ingram, C.J., Swallow, D.M. Clin. Chim. Acta (2007) [Pubmed]

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