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 <i>MBL2</i> 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 c...
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| Format: | Article |
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MDPI AG
2021-02-01
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| Series: | Diagnostics |
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| Online Access: | https://www.mdpi.com/2075-4418/11/2/301 |
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| author | Jana Mrazkova Petr Sistek Jan Lochman Lydie Izakovicova Holla Zdenek Danek Petra Borilova Linhartova |
| author_facet | Jana Mrazkova Petr Sistek Jan Lochman Lydie Izakovicova Holla Zdenek Danek Petra Borilova Linhartova |
| author_sort | Jana Mrazkova |
| collection | DOAJ |
| description | Mannose-binding lectin (MBL) deficiency caused by the variability in the <i>MBL2</i> 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 <i>MBL2</i> 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 <i>MBL2</i> 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. |
| first_indexed | 2024-03-09T00:54:41Z |
| format | Article |
| id | doaj.art-9fc89a6b9c3f43d0a710d858c33d4144 |
| institution | Directory Open Access Journal |
| issn | 2075-4418 |
| language | English |
| last_indexed | 2024-03-09T00:54:41Z |
| publishDate | 2021-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Diagnostics |
| spelling | doaj.art-9fc89a6b9c3f43d0a710d858c33d41442023-12-11T16:59:11ZengMDPI AGDiagnostics2075-44182021-02-0111230110.3390/diagnostics11020301A SNaPshot Assay for Determination of the Mannose-Binding Lectin Gene Variants and an Algorithm for Calculation of Haplogenotype CombinationsJana Mrazkova0Petr Sistek1Jan Lochman2Lydie Izakovicova Holla3Zdenek Danek4Petra Borilova Linhartova5Department of Pathophysiology, Faculty of Medicine, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech RepublicSecondary Technical School Brno, Purkynova, a Contributory Organization, Purkynova 97, 612 00 Brno, Czech RepublicDepartment of Pathophysiology, Faculty of Medicine, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech RepublicDepartment of Pathophysiology, Faculty of Medicine, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech RepublicDepartment of Pathophysiology, Faculty of Medicine, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech RepublicDepartment of Pathophysiology, Faculty of Medicine, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech RepublicMannose-binding lectin (MBL) deficiency caused by the variability in the <i>MBL2</i> 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 <i>MBL2</i> 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 <i>MBL2</i> 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.https://www.mdpi.com/2075-4418/11/2/301mannose-binding lectinmannose-binding lectin gene (<i>MBL2</i>)SNaPshot assaysingle nucleotide polymorphismgenotypingHaplogenotype Calculator |
| spellingShingle | Jana Mrazkova Petr Sistek Jan Lochman Lydie Izakovicova Holla Zdenek Danek Petra Borilova Linhartova A SNaPshot Assay for Determination of the Mannose-Binding Lectin Gene Variants and an Algorithm for Calculation of Haplogenotype Combinations Diagnostics mannose-binding lectin mannose-binding lectin gene (<i>MBL2</i>) SNaPshot assay single nucleotide polymorphism genotyping Haplogenotype Calculator |
| 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 | mannose-binding lectin mannose-binding lectin gene (<i>MBL2</i>) SNaPshot assay single nucleotide polymorphism genotyping Haplogenotype Calculator |
| url | https://www.mdpi.com/2075-4418/11/2/301 |
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