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De Luca P, Iaconis D, Biffali E, Enza C, de Magistris L, Riegler G, Pappalardo D, Amato MR, Iardino P, Montanino C, De Felice B. Development of a novel SNP assay to detect lactase persistence associated genetic variants. Mol Biol Rep 2021; 48:7087-7093. [PMID: 34515921 PMCID: PMC8572811 DOI: 10.1007/s11033-021-06698-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 08/31/2021] [Indexed: 10/29/2022]
Abstract
BACKGROUND In adulthood the activity of the lactase enzyme is inherited as autosomal dominant form associated to Single nucleotide polymorphisms (SNPs). The present research was aimed to develop a novel genetic method to test lactase non persistence more powerfully. METHODS AND RESULTS In our study, we selected eight different SNPs that are associated with lactase persistence from Caucasian, Arabian Bedouins, sub-Saharian Africans and Asian populations to set up an approach to detect all the eight different SNPs at the same time in the same sample. This technique is centred on the identification of SNPs with a single nucleotide primer extension method using Sanger sequencing and capillary electrophoresis. CONCLUSIONS Our method allowed us to check the genotype asset of eight SNPs related to lactase persistence simultaneously and in a very efficient manner. It could be applied to a higher number of SNPs in a single reaction.
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Affiliation(s)
- Pasquale De Luca
- Department of Research Infrastructures for Marine Biological Resources (RIMAR), Sequencing and Molecular Analyses Center, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy.
| | - Daniela Iaconis
- Department of Research Infrastructures for Marine Biological Resources (RIMAR), Sequencing and Molecular Analyses Center, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
| | - Elio Biffali
- Department of Research Infrastructures for Marine Biological Resources (RIMAR), Sequencing and Molecular Analyses Center, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
| | - Coluccia Enza
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, 81100, Caserta, Italy
| | - Laura de Magistris
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, 81100, Caserta, Italy
| | - Gabriele Riegler
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, 81100, Caserta, Italy
| | - Diego Pappalardo
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, 81100, Caserta, Italy
| | - Maria Rosaria Amato
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, 81100, Caserta, Italy
| | - Patrizia Iardino
- UOC Clinic and Molecular Pathology, University of Campania Luigi Vanvitelli, 81100, Caserta, Italy
| | - Concetta Montanino
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DISTABIF), University of Campania Luigi Vanvitelli, Via Vivaldi 43, 81100, Caserta, Italy
| | - Bruna De Felice
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DISTABIF), University of Campania Luigi Vanvitelli, Via Vivaldi 43, 81100, Caserta, Italy.
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Real-time PCR based detection of the lactase non-persistence associated genetic variant LCT-13910C>T directly from whole blood. Mol Biol Rep 2019; 46:2379-2385. [PMID: 30790118 DOI: 10.1007/s11033-019-04696-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 02/09/2019] [Indexed: 01/20/2023]
Abstract
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.
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Lactase persistence genotyping on whole blood by loop-mediated isothermal amplification and melting curve analysis. Clin Chim Acta 2018; 482:50-56. [PMID: 29596814 DOI: 10.1016/j.cca.2018.03.029] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 03/23/2018] [Accepted: 03/24/2018] [Indexed: 01/14/2023]
Abstract
BACKGROUND The lactase persistence phenotype is controlled by a regulatory enhancer region upstream of the Lactase (LCT) gene. In northern Europe, specifically the -13910C > T variant has been associated with lactase persistence whereas other persistence variants, e.g. -13907C > G and -13915 T > G, have been identified in Africa and the Middle East. The aim of the present study was to compare a previously developed high resolution melting assay (HRM) with a novel method based on loop-mediated isothermal amplification and melting curve analysis (LAMP-MC) with both whole blood and DNA as input material. METHODS To evaluate the LAMP-MC method, we used 100 whole blood samples and 93 DNA samples in a two tiered study. First, we studied the ability of the LAMP-MC method to produce specific melting curves for several variants of the LCT enhancer region. Next, we performed a blinded comparison between the LAMP-MC method and our existing HRM method with clinical samples of unknown genotype. RESULTS The LAMP-MC method produced specific melting curves for the variants at position -13909, -13910, -13913 whereas the -13907C > G and -13915 T > G variants produced indistinguishable melting profiles. CONCLUSION The LAMP-MC assay is a simple method for lactase persistence genotyping and compares well with our existing HRM method.
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