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Data from: Mannose-binding lectin gene polymorphisms in the East Siberia and Russian Arctic populations

Citation

Tereshchenko, Sergey; Smolnikova, Marina; Freidin, Maxim (2020), Data from: Mannose-binding lectin gene polymorphisms in the East Siberia and Russian Arctic populations, Dryad, Dataset, https://doi.org/10.5061/dryad.15dv41nvd

Abstract

Background: Mannose-binding lectin (MBL) encoded by MBL2 gene is a protein with the ability to form carbohydrate complexes with microbial wall promoting their subsequent elimination. Genetically determined levels of MBL can modify the risk and clinical characteristics of many infectious diseases. The frequency of MBL2 genotypes exhibits significant population differences. The data on the distribution of MBL2 genotypes among the aborigines of the Russian Arctic territories have not yet been published.

Methods: A total of 880 specimens of dried blood spots of the newborns were genotyped. The newborns represented four populations: Nenets, Dolgan-Nganasans, Mixed aboriginal population, and Russians (Caucasians, Krasnoyarsk). Six polymorphisms of the MBL2 gene were studied: rs11003125, rs7096206, rs7095891, rs5030737, rs1800450, and rs1800451.

Results: The frequency of the combined rare O allele (composed of the coding region variants rs5030737, rs1800450, and rs1800451) in the homozygous state was significantly higher in Russians: 10% vs 2% in Nenets and 1% in Dolgan-Nganosans (p<0.001 for Russians vs other populations). The frequency of the high-producing haplotype (HYPA) was 35.4% in the Russian newborns, in keeping with European populations (27-33%); 64% for Nenets and 56% for Dolgan-Nganasans, similar to the estimates obtained for Eskimos and North Amerinds (64-81%).

Conclusion: Our study results are in line with the hypothesis that human evolution has been moving in the direction of accumulation of the genotypes associated with low activity of the lectin complement activation pathway because of the prevalence of some intracellular infections such as tuberculosis, whereby low MBL activity may have a protective effect.

Methods

A total of 880 specimens of dried blood spots for the newborns obtained from the Krasnoyarsk Regional Consulting-Diagnostic Centre for Medical Genetics to study the prevalence of single nucleotide polymorphisms of MBL2 gene.

The demographic characteristics of the studied newborns according to the region of mother’s settlement was the same as in our previously published study,[28]. The newborns were split into four groups to study ethnic specificity of the MBL2 polymorphisms: (1) 260 from the Arctic region of mother's settlement, from villages with predominantly Nenets population (Nenets comprise 85% of the population); (2) 110 from the Arctic region of  mother's settlement, from villages with predominantly Dolgan-Nganasan population (Dolgan-Nganasans comprise 91% of the population); (3) 210 from the Arctic region of mother's settlement, from villages with mixed populations with various combination of indigenous and alien residents; (4) 300 newborns of European ancestry (Russians by self-reports of their mothers) from the city of Krasnoyarsk .

The study was approved by the Ethical Committee of the Scientific Research Institute of Medical Problems of the North (# 9 of 8.09.2014). Signed informed consent was obtained from parents of all participated children.

Blood Sample Collection and Genotyping

DNA was extracted using DIAtomTM DNA Prep kits (“Izogen”, Russia). Genotyping was carried out using restriction fragment lengths polymorphism approach (RFLP) and real-time polymerase chain reaction. Six polymorphisms of the MBL2 gene were studied: rs11003125, rs7096206, rs7095891, rs5030737, rs1800450 and rs1800451.

Genotyping of rs1800450 and rs1800451 polymorphisms was performed by RFLP approach. The relevant genomic fragment of 349 bp was amplified using the pair of oligonucleotide primers: forward 5'-TAGGACAGAGGGCATGCTC-3' and reverse 5'-CAGGCAGTTTCCTCTGGAAGG-3' (annealing temperature 60˚C). Restriction endonucleases AccB1 I (rs1800450) and Mbo II (rs1800451) for hydrolysis of the fragment followed by the electrophoresis in agarose gel with ethidium bromide to visualise the results. For rs1800450, AccB1 I endonuclease produces a single fragment of 349 bp for the B allele and two fragments of 260 and 89 bp for the A allele. For rs1800451, Mbo II endonuclease produces a single fragment of 349 bp for the A allele and two fragments of 270 and 79 bp for the C allele.

Four polymorphisms rs11003125, rs7096206, rs7095891 and rs5030737 were carried out using the real-time polymerase chain reaction approach. The nucleotide sequences of allele-specific probes are presented in Table 1.

Table 1. The nucleotide sequence of allele-specific probes used for genotyping

Polymorphism

The nucleotide sequence of allele-specific probes

Fluorophore – allele

rs11003125

F GGGCCAACGTAGTAAGAA

R GGAGTTTGCTTCCCCTTG

VIC-C/FAM-G

rs7096206

F GCGTTGCTGCTGGAAGAC

R CAATGCACGGTCCCATTTG

VIC-G/FAM-C

rs7095891

F GGGAAGGTTAATCTCAGTTAA

R CCAGGGATGGGTCATCTATT

VIC-A/FAM-G

rs5030737

F CTCCAGGCATCAACGGC

R CCAACACGTACCTGGTTC

VIC-T/FAM-C

 

Statistical Analysis

Differences in genotypic frequencies between the ethnic groups were assessed using the Pearson’s χ2 test. Haplotypes were assessed and compared between the populations using the haplo.stats package for R. Haplotype score test was applied with 1000 permutations to calculate p-values. Bonferroni correction for multiple testing was duly applied. Statistically significant differences were considered at p<0.05 after correction for multiple testing.

Usage Notes

Codes for "nationality" column: 

Nenets (1)

Dolgans-Nganasans (2)

 

Mixed Arctic population (3)

Russians (4)

 

 

Funding

This study was carried out under the state assignment (theme # 003) for Scientific Research Institute of Medical Problems of the North, Krasnoyarsk, Russia.