1. Combination of real-time PCR and sequencing to detect multiple clinically relevant genetic variations in the lactase gene.
- Author
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Brasen CL, Frischknecht L, Ørnskov D, Andreasen L, and Madsen JS
- Subjects
- Alleles, Denmark epidemiology, Gene Expression, Gene Frequency, Genetic Testing, Genotype, Humans, Lactase deficiency, Lactose Intolerance epidemiology, Lactose Intolerance physiopathology, Phenotype, Prevalence, Real-Time Polymerase Chain Reaction, Sequence Analysis, DNA, Software, Lactase genetics, Lactose Intolerance diagnosis, Lactose Intolerance genetics, Polymorphism, Single Nucleotide, Promoter Regions, Genetic
- Abstract
Background: Lactase persistence is an autosomal dominant trait commonly distributed in Europe as well as some parts of east Africa and the Arabian Peninsula. Using real-time PCR to detect the -13910C > T variant common in the European population is a reliable analysis although other variants in the probe-binding site may cause errors in analysis. The aim of this study was to determine the prevalence of the variants in a Danish cohort examined for lactose intolerance as well as to improve the real-time PCR analysis for detection of the different variants., Methods: We genotyped 3395 routine samples using real-time PCR for the -13910C > T-variant. All consecutive samples identified as -13910CC were sequenced using Sanger Sequencing. Using the SDS software we examined various quality value settings to improve on the genetic analysis., Results: Using real-time PCR resulted in 100% successful genotyping of the -13910C > T variant. By using a quality value of 99% and sequencing the undetermined samples we improved the ability of the assay to identify variants other than -13910C > T. This resulted in a reduction of the diagnostic error rate by a factor of 2.4 while increasing the expenses only 3%., Conclusions: We conclude that using a quality value of 99% in the SDS software significantly improves the diagnostic efficiency of the real-time PCR assay for detecting variants associated to lactase persistence.
- Published
- 2017
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