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

J 2021

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

MRÁZKOVÁ, Jana, Petr SISTEK, Jan LOCHMAN, Lydie IZAKOVIČOVÁ HOLLÁ, Zdeněk DANĚK et. al.

Basic information

Original name

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

Authors

MRÁZKOVÁ, Jana (203 Czech Republic, belonging to the institution), Petr SISTEK (203 Czech Republic), Jan LOCHMAN (203 Czech Republic, belonging to the institution), Lydie IZAKOVIČOVÁ HOLLÁ (203 Czech Republic, belonging to the institution), Zdeněk DANĚK (203 Czech Republic, belonging to the institution) and Petra BOŘILOVÁ LINHARTOVÁ (203 Czech Republic, belonging to the institution)

Edition

Diagnostics, Basel, MDPI, 2021, 2075-4418

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10606 Microbiology

Country of publisher

Switzerland

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 3.992

RIV identification code

RIV/00216224:14110/21:00120096

Organization unit

Faculty of Medicine

DOI

http://dx.doi.org/10.3390/diagnostics11020301

UT WoS

000622433400001

Keywords in English

mannose-binding lectin; mannose-binding lectin gene (MBL2); SNaPshot assay; single nucleotide polymorphism; genotyping; Haplogenotype Calculator; haplogenotypes

Abstract

V originále

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.

Links

LM2015085, research and development project

Name: CERIT Scientific Cloud (Acronym: CERIT-SC)

Investor: Ministry of Education, Youth and Sports of the CR, CERIT Scientific Cloud

NU20-08-00205, research and development project

Name: Molekulární etiopatogeneze apikální periodontitidy a odontogenních cyst

Investor: Ministry of Health of the CR, Subprogram 1 - standard

NV17-30439A, research and development project

Name: Moderní biotechnologické a behaviorální přístupy ve výzkumu zubního kazu a strategie jeho prevence

90042, large research infrastructures

Name: CESNET II

Citovat

MRÁZKOVÁ, Jana, Petr SISTEK, Jan LOCHMAN, Lydie IZAKOVIČOVÁ HOLLÁ, Zdeněk DANĚK and Petra BOŘILOVÁ LINHARTOVÁ. A SNaPshot Assay for Determination of the Mannose-Binding Lectin Gene Variants and an Algorithm for Calculation of Haplogenotype Combinations. Diagnostics. Basel: MDPI, 2021, vol. 11, No 2, p. 1-17. ISSN 2075-4418. Available from: https://dx.doi.org/10.3390/diagnostics11020301.

@article{1767999,
   author = {Mrázková, Jana and Sistek, Petr and Lochman, Jan and Izakovičová Hollá, Lydie and Daněk, Zdeněk and Bořilová Linhartová, Petra},
   article_location = {Basel},
   article_number = {2},
   doi = {http://dx.doi.org/10.3390/diagnostics11020301},
   keywords = {mannose-binding lectin; mannose-binding lectin gene (MBL2); SNaPshot assay; single nucleotide polymorphism; genotyping; Haplogenotype Calculator; haplogenotypes},
   language = {eng},
   issn = {2075-4418},
   journal = {Diagnostics},
   title = {A SNaPshot Assay for Determination of the Mannose-Binding Lectin Gene Variants and an Algorithm for Calculation of Haplogenotype Combinations},
   url = {https://www.mdpi.com/2075-4418/11/2/301},
   volume = {11},
   year = {2021}
}

TY  - JOUR
ID  - 1767999
AU  - Mrázková, Jana - Sistek, Petr - Lochman, Jan - Izakovičová Hollá, Lydie - Daněk, Zdeněk - Bořilová Linhartová, Petra
PY  - 2021
TI  - A SNaPshot Assay for Determination of the Mannose-Binding Lectin Gene Variants and an Algorithm for Calculation of Haplogenotype Combinations
JF  - Diagnostics
VL  - 11
IS  - 2
SP  - 1-17
EP  - 1-17
PB  - MDPI
SN  - 20754418
KW  - mannose-binding lectin
KW  - mannose-binding lectin gene (MBL2)
KW  - SNaPshot assay
KW  - single nucleotide polymorphism
KW  - genotyping
KW  - Haplogenotype Calculator
KW  - haplogenotypes
UR  - https://www.mdpi.com/2075-4418/11/2/301
N2  - 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.
ER  -

MRÁZKOVÁ, Jana, Petr SISTEK, Jan LOCHMAN, Lydie IZAKOVIČOVÁ HOLLÁ, Zdeněk DANĚK and Petra BOŘILOVÁ LINHARTOVÁ. A SNaPshot Assay for Determination of the Mannose-Binding Lectin Gene Variants and an Algorithm for Calculation of Haplogenotype Combinations. \textit{Diagnostics}. Basel: MDPI, 2021, vol.~11, No~2, p.~1-17. ISSN~2075-4418. Available from: https://dx.doi.org/10.3390/diagnostics11020301.

Detailed Information on Publication Record