Real-time PCR based detection of the lactase non-persistence associated genetic variant LCT-13910C>T directly from whole blood

Mol Biol Rep. 2019 Apr;46(2):2379-2385. doi: 10.1007/s11033-019-04696-9. Epub 2019 Feb 21.


Primary hypolactasia is the main cause of lactose intolerance in adults. It is strongly associated with the single genetic variant LCT-13910C>T, located upstream of the lactase encoding gene. Consequently, analysis of LCT-13910C>T has been recommended as a direct genetic test for the trait. The aim of our study was to develop a TaqMan probe based real-time PCR protocol for the detection of the LCT-13910C>T variant directly from whole blood, circumventing DNA isolation. The LCT-13910C>T variant was determined using the DirectBlood Genotyping PCR Kit (myPOLS Biotec, Konstanz, Germany) together with an in-house TaqMan primer-probe assay. Validity and specificity of the assay was evaluated using EDTA anti-coagulated whole blood samples and corresponding DNA samples. Results from real-time PCR were compared with results obtained by Sanger sequencing from 105 blinded whole blood samples. Validity and specificity of the assay using whole blood were comparable to those using purified genomic DNA as substrate in PCR. Genetic analysis of blood samples were in complete agreement with results obtained by Sanger sequencing. In conclusion, we present a reliable real-time PCR protocol for the detection of the LCT-13910C>T variant directly from whole blood further facilitating diagnosis of primary hypolactasia in symptomatic patients.

Keywords: Direct blood PCR; LCT-13910C>T; Lactose intolerance; Locked nucleic acids; Primary hypolactasia; Real-time PCR; TaqMan probe.

MeSH terms

  • Adult
  • Female
  • Genetic Testing / methods
  • Genotype
  • Humans
  • Lactase / deficiency
  • Lactase / genetics*
  • Lactase / metabolism
  • Lactose Intolerance / diagnosis*
  • Lactose Intolerance / genetics*
  • Male
  • Phenotype
  • Polymorphism, Single Nucleotide / genetics
  • Real-Time Polymerase Chain Reaction / methods
  • Reproducibility of Results
  • Sensitivity and Specificity


  • Lactase

Supplementary concepts

  • Lactose Intolerance, Adult Type