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A SNaPshot Assay for Determination of the Mannose-Binding Lectin Gene Variants and an Algorithm for Calculation of Haplogenotype Combinations

Mannose-binding lectin (MBL) deficiency caused by the variability in the MBL2 gene is responsible for the susceptibility to and severity of various infectious and autoimmune diseases. A combination of six single nucleotide polymorphisms (SNPs) has a major impact on MBL levels in circulation. The aim...

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Autores principales: Mrazkova, Jana, Sistek, Petr, Lochman, Jan, Izakovicova Holla, Lydie, Danek, Zdenek, Borilova Linhartova, Petra
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7918147/
https://www.ncbi.nlm.nih.gov/pubmed/33668563
http://dx.doi.org/10.3390/diagnostics11020301
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author Mrazkova, Jana
Sistek, Petr
Lochman, Jan
Izakovicova Holla, Lydie
Danek, Zdenek
Borilova Linhartova, Petra
author_facet Mrazkova, Jana
Sistek, Petr
Lochman, Jan
Izakovicova Holla, Lydie
Danek, Zdenek
Borilova Linhartova, Petra
author_sort Mrazkova, Jana
collection PubMed
description Mannose-binding lectin (MBL) deficiency caused by the variability in the MBL2 gene is responsible for the susceptibility to and severity of various infectious and autoimmune diseases. A combination of six single nucleotide polymorphisms (SNPs) has a major impact on MBL levels in circulation. The aim of this study is to design and validate a sensitive and economical method for determining MBL2 haplogenotypes. The SNaPshot assay is designed and optimized to genotype six SNPs (rs1800451, rs1800450, rs5030737, rs7095891, rs7096206, rs11003125) and is validated by comparing results with Sanger sequencing. Additionally, an algorithm for online calculation of haplogenotype combinations from the determined genotypes is developed. Three hundred and twenty-eight DNA samples from healthy individuals from the Czech population are genotyped. Minor allele frequencies (MAFs) in the Czech population are in accordance with those present in the European population. The SNaPshot assay for MBL2 genotyping is a high-throughput, cost-effective technique that can be used in further genetic-association studies or in clinical practice. Moreover, a freely available online application for the calculation of haplogenotypes from SNPs is developed within the scope of this project.
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spelling pubmed-79181472021-03-02 A SNaPshot Assay for Determination of the Mannose-Binding Lectin Gene Variants and an Algorithm for Calculation of Haplogenotype Combinations Mrazkova, Jana Sistek, Petr Lochman, Jan Izakovicova Holla, Lydie Danek, Zdenek Borilova Linhartova, Petra Diagnostics (Basel) Article Mannose-binding lectin (MBL) deficiency caused by the variability in the MBL2 gene is responsible for the susceptibility to and severity of various infectious and autoimmune diseases. A combination of six single nucleotide polymorphisms (SNPs) has a major impact on MBL levels in circulation. The aim of this study is to design and validate a sensitive and economical method for determining MBL2 haplogenotypes. The SNaPshot assay is designed and optimized to genotype six SNPs (rs1800451, rs1800450, rs5030737, rs7095891, rs7096206, rs11003125) and is validated by comparing results with Sanger sequencing. Additionally, an algorithm for online calculation of haplogenotype combinations from the determined genotypes is developed. Three hundred and twenty-eight DNA samples from healthy individuals from the Czech population are genotyped. Minor allele frequencies (MAFs) in the Czech population are in accordance with those present in the European population. The SNaPshot assay for MBL2 genotyping is a high-throughput, cost-effective technique that can be used in further genetic-association studies or in clinical practice. Moreover, a freely available online application for the calculation of haplogenotypes from SNPs is developed within the scope of this project. MDPI 2021-02-13 /pmc/articles/PMC7918147/ /pubmed/33668563 http://dx.doi.org/10.3390/diagnostics11020301 Text en © 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Mrazkova, Jana
Sistek, Petr
Lochman, Jan
Izakovicova Holla, Lydie
Danek, Zdenek
Borilova Linhartova, Petra
A SNaPshot Assay for Determination of the Mannose-Binding Lectin Gene Variants and an Algorithm for Calculation of Haplogenotype Combinations
title A SNaPshot Assay for Determination of the Mannose-Binding Lectin Gene Variants and an Algorithm for Calculation of Haplogenotype Combinations
title_full A SNaPshot Assay for Determination of the Mannose-Binding Lectin Gene Variants and an Algorithm for Calculation of Haplogenotype Combinations
title_fullStr A SNaPshot Assay for Determination of the Mannose-Binding Lectin Gene Variants and an Algorithm for Calculation of Haplogenotype Combinations
title_full_unstemmed A SNaPshot Assay for Determination of the Mannose-Binding Lectin Gene Variants and an Algorithm for Calculation of Haplogenotype Combinations
title_short A SNaPshot Assay for Determination of the Mannose-Binding Lectin Gene Variants and an Algorithm for Calculation of Haplogenotype Combinations
title_sort snapshot assay for determination of the mannose-binding lectin gene variants and an algorithm for calculation of haplogenotype combinations
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7918147/
https://www.ncbi.nlm.nih.gov/pubmed/33668563
http://dx.doi.org/10.3390/diagnostics11020301
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