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. 2020 Jul 8;31:106004. doi: 10.1016/j.dib.2020.106004

Dataset of allele and genotype frequencies of the three functionally significant polymorphisms of the MMP genes in Russian patients with primary open-angle glaucoma, essential hypertension and peptic ulcer

Oksana Minyaylo a, Dina Starikova a, Maria Moskalenko a, Irina Ponomarenko a, Evgeny Reshetnikov a,⁎, Volodymyr Dvornyk b, Mikhail Churnosov a
PMCID: PMC7365972  PMID: 32695863

Abstract

Data on the allele and genotype frequencies of the three functionally significant single nucleotide polymorphisms (SNPs) of the matrix metalloproteinases (MMP) genes (rs1799750 MMP1, rs3918242 and rs17576 MMP9) in Russian patients with primary open-angle glaucoma (POAG), essential hypertension (EH) and peptic ulcer (PU) are presented. Association studies identified these SNPs as possible significant markers associated with many multifactorial disorders, including POAG, EH, and PU. The frequencies of alleles and genotypes of the three SNPs in Russian patients with POAG, EH, and PU were presented separately for the entire study sample, females, and males, respectively. The data can be used as a reference for the Russian population.

Keywords: Single nucleotide polymorphism, Primary open-angle glaucoma, Essential hypertension, Peptic ulcer, MMP

Specifications Table

Subject Biology
Specific subject area Genetics
Type of data Table and figure
How data were acquired MALDI/TOF mass spectrometry using the Sequenom MassARRAY 4.0 platform (Agena Bioscience™)
Data format Raw and analyzed data
Parameters for data collection Whole blood (5 ml) was drawn to a plastic vial (VacutainerⓇ) containing 0.5 M EDTA (рН=8.0). Genomic DNA was isolated by the standard phenol-chloroform method. DNA samples were first checked for quality (concentration 10–15 ng/mL, purity А260/А280=1.7–2.0) and then used for genotyping. About 5% of blind replicate samples were used for genotyping quality control; the repeatability test indicated a 100% concordance rate.
Description of data collection The quality of isolated DNA was checked by the Nanodrop-2000 spectrophotometer. Genotyping was performed on the Sequenom MassARRAYⓇ iPLEX platform using the MALDI-TOF (matrix-assisted laser desorption/ ionization time-of-flight) mass spectrometry. Assay Design Suite 1.0 was used to design a multiplex genotyping assay (http://agenabio.com/assay-design-suite-10-software).
Data source location Belgorod, Russia
Data accessibility The data is available with this article
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Value of the data

  • •

    The frequencies of alleles and genotypes of rs1799750 MMP1, rs3918242 and rs17576 MMP9 in Russian patients with POAG, EH, and PU are presented separately for the entire cohort, male and female participants.

  • •

    The polymorphisms rs1799750 MMP1, rs3918242 and rs17576 MMP9 may be associated with POAG, EH, and PU.

  • •

    The data on the allele and genotype frequencies of the MMP genes can be used for meta-analyses of genetic studies on POAG, EH, and PU.

  • •

    The presented data of the MMP genes polymorphisms can serve as a reference for population and genetic association studies of the common disorders.

1. Data description

The dataset contains the raw data (supplementary Table), frequencies of alleles and genotypes (Table 1) for three SNPs of two MMP genes (rs1799750 MMP1, rs3918242 and rs17576 MMP9) in Russian patients diagnosed with POAG, EH, and PU. These polymorphisms were previously reported for their association with POAG, EH, and PU (Table 2) [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24], [25], [26], [27], [28], [29], [30], [31], [32], [33], [34], [35], [36], [37], [38], [39], [40], [41], [42], [43], [44], [45]. The studied SNPs manifest the regulatory potential (Table 3), which is evidenced by several eQTLs (Table 4) and splicing QTLs (Table 5). The allele and genotype frequencies are provided separately for the whole study cohort, females, and males, respectively. No significant differences in the frequencies of alleles and genotypes were found between the male and female participants for each of the studied diseases.

Table 1.

The frequencies of alleles and genotypes for SNPs rs1799750 MMP1, rs3918242 and rs17576 MMP9 in Russian patients with POАG, EH, and PU.

Diseases SNP genotype or allele
 All Male Female
n frequency n frequency n frequency
rs1799750
POAG 1G1G 152 0.2836 73 0.2968 79 0.2724
1G2G 267 0.4981 131 0.5325 136 0.4690
2G2G 117 0.2183 42 0.1707 75 0.2586
1G 571 0.5327 277 0.5630 294 0.5069
2G 501 0.4673 215 0.4370 286 0.4931
rs3918242
СС 385 0.7183 175 0.7114 210 0.7241
СТ 133 0.2482 65 0.2642 68 0.2345
ТТ 18 0.0335 6 0.0244 12 0.0414
С 903 0.8424 415 0.8435 488 0.8414
Т 169 0.1576 77 0.1565 92 0.1586
rs17576
AA 205 0.3825 110 0.4472 95 0.3276
GA 260 0.4851 108 0.4390 152 0.5241
GG 71 0.1324 28 0.1138 43 0.1483
A 670 0.6250 328 0.6667 342 0.5897
G 402 0.3750 164 0.3333 238 0.4103
EH rs1799750
1G1G 169 0.2721 65 0.2481 104 0.2897
1G2G 309 0.4976 140 0.5334 169 0.4707
2G2G 143 0.2303 57 0.2175 86 0.2396
1G 647 0.5209 270 0.5153 377 0.5251
2G 595 0.4791 254 0.4847 341 0.4749
rs3918242
СС 444 0.7150 189 0.7214 255 0.7103
СТ 149 0.2399 64 0.2443 85 0.2368
ТТ 28 0.0451 9 0.0343 19 0.0529
С 1037 0.8349 442 0.8435 595 0.8287
Т 205 0.1651 82 0.1565 123 0.1713
rs17576
AA 229 0.3688 100 0.3817 129 0.3593
GA 311 0.5008 131 0.5000 180 0.5014
GG 81 0.1304 31 0.1183 50 0.1393
A 769 0.6192 331 0.6317 438 0.6101
G 473 0.3808 193 0.3683 280 0.3899
РU rs1799750
1G1G 121 0.3033 45 0.2394 76 0.3602
1G2G 195 0.4887 98 0.5212 97 0.4597
2G2G 83 0.2080 45 0.2394 38 0.1801
1G 437 0.5476 188 0.5000 249 0.5901
2G 361 0.4524 188 0.5000 173 0.4099
rs3918242
СС 277 0.6942 129 0.6862 148 0.7014
СТ 115 0.2883 58 0.3085 57 0.2701
ТТ 7 0.0175 1 0.0053 6 0.0285
С 669 0.8383 316 0.8404 353 0.8365
Т 129 0.1617 60 0.1596 69 0.1635
rs17576
AA 142 0.3559 69 0.3670 73 0.3460
GA 184 0.4612 83 0.4415 101 0.4787
GG 73 0.1829 36 0.1915 37 0.1753
A 468 0.5865 221 0.5878 247 0.5853
G 330 0.4135 155 0.4122 175 0.4147
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Abbreviations: POAG - primary open-angle glaucoma, EH - essential hypertension, PU - peptic ulcer.

Table 2.

The literature data about associations of the studied polymorphisms of the ММР genes with POАG, PU and some digestive diseases (gastric and esophageal cancer), EH and IS with EH.

SNP Gene Number of publications in PubMed/PubMed Central Phenotype Association (significance) (associated allele) Reference
rs1799750 MMP1 70/119 POAG OR = 1.64, р = 0.01 [1]
POAG OR = 1.64, p = 0.002 [2]
POAG OR = 1.34, р = 0,017 (2 G) [3]
POAG OR = 2.04, р<0,001 (2 G) [4]
POAG OR = 1.35, p = 0.017 (2 G) [5]
POAG p>0.05 [6]
peptic ulcer OR = 3.46, p = 0.03 (1 G/1 G) [7]
gastric cancer OR = 3.34, р = 0.016 (2 G/2 G) [8]
gastric cancer OR = 1.05, р = 0.013 (2 G) [9]
IS with hypertension OR = 1.54, p = 0.005 (2 G) [10]
IS with hypertension OR>1; p<0.05 (2 G) [11]
IS with hypertension p>0.05 [12], [13], [14], [15], [16], [17]
essential hypertension in men OR = 2.58; р = 0.04 (together with rs11568818, rs1320632, rs11225395) [18]
essential hypertension in women p>0.05 [19]
rs3918242 MMP9 106/127 POAG OR = 1.63; р = 0.002 (Т) [20]
POAG OR = 1.55, p = 0.012 (T) [5]
POAG OR = 1.46, p = 0.032 (CT+TT) [21]
POAG p>0.05 [1,4,22]
peptic ulcer p>0.05 [7]
gastric cancer OR = 2.60; р<0.05 (together with rs17576 and rs17577) [23]
esophageal cancer OR = 2.71; р = 0.02 (СС) [24]
gastric cancer p>0.05 [25]
IS with hypertension OR = 2,76; р = 0.003 (ТT) [26]
IS with hypertension OR = 1,73; р<0,05 (Т) [27]
IS with hypertension OR = 2,20; р<0,05 (ТТ) [28]
IS with hypertension OR = 2,08; р = 0,016 (Т) [29]
IS with hypertension OR<1; р = 0.001 (CC) [30]
IS with hypertension OR>1; р = 0.009 (T) [31]
IS with hypertension OR = 5,53; р = 0,001 (СС) [32]
IS with hypertension OR = 1.43; р = 0.001 (Т) [33]
IS with hypertension OR = 5.47; р<0.05 (TТ) [34]
IS with hypertension OR = 1.27; р = 0.01 (T) [12]
IS with hypertension p>0.05 [35]
essential hypertension OR = 1.30; р = 0.002 [36]
isolated systolic hypertension OR>1; р = 0,009 (T) [37]
left ventricular hypertrophy in hypertensive patients OR>1; р = 0,0015 (together with rs2234681 and rs17576) [38]
hypertension of pregnancy OR<1; р = 0,007 (СС) [39]
essential hypertension in children OR>1; р<0.05 (ТТ) [40]
essential hypertension p>0.05 [41]
rs17576 MMP9 78/97 POAG OR = 1.96; р = 0.0005 (AG) [20]
POAG OR = 0.66; p = 0.03 (A) [21]
POAG OR = 1.53; p = 0.034 (GG) [42]
POAG in men OR = 0.56; р = 0,003 (together with rs2250889) [43]
POAG OR = 2.34; p = 0.01 (GG) [4]
POAG p>0.05 [6]
peptic ulcer OR = 0.49; p = 0.007 (AA) [7]
gastric cancer OR = 4.34; р<0.05 (Q) [23]
gastric cancer p>0.05 [44]
IS with hypertension OR = 0,91; р  = 0,04 (GG) [45]
IS with hypertension p>0.05 [15,26,29,30,31]
left ventricular hypertrophy in hypertensive patients OR>1; р = 0,0015 (together with rs2234681 and rs3918242) [38]
essential hypertension OR>1; р<0.05 (АА) [41]
isolated systolic hypertension p>0.05 [37]
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Abbreviations: POAG - primary open-angle glaucoma, EH - essential hypertension, IS - ischemic stroke, PU - peptic ulcer.

Table 3.

Regulatory effects of the 3 SNPs of the MMP genes (HaploReg, v4.1, update 05.11.2015) (https://pubs.broadinstitute.org/mammals/haploreg/haploreg.php).

graphic file with name fx1.gif
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Table 4.

The cis-eQTL values of the 3 SNPs of the MMP genes. (according to Genotype-Tissue Expression (GTEx) (http://www.gtexportal.org/)).

Chr SNP Reference allele Alternative allele Gene expression Effect Size (β) P-Value Tissue
11 rs1799750 TC T MMP1 −0.66 9.6E-84 Cells - Cultured fibroblasts
MMP1 −0.52 1.3E-25 Thyroid
MMP1 −0.42 1.9E-25 Lung
MMP1 −0.58 5.8E-23 Heart - Atrial Appendage
MMP1 −0.45 0.0000000000000000017 Adipose - Visceral (Omentum)
MMP1 −0.46 0.0000000000000066 Heart - Left Ventricle
MMP1 −0.36 0.000000000022 Nerve - Tibial
MMP1 −0.32 0.000000013 Esophagus - Muscularis
MMP1 −0.35 0.000000015 Artery - Aorta
MMP1 −0.28 0.000000024 Adipose - Subcutaneous
MMP1 −0.22 0.00000038 Artery - Tibial
MMP10 −0.19 0.0000025 Lung
MMP1 −0.3 0.0000028 Esophagus - Gastroesophageal Junction
MMP1 −0.28 0.0000075 Breast - Mammary Tissue
WTAPP1 −0.15 0.00004 Testis
20 rs3918242 C T SLC12A5 0.61 0.0000000000000000059 Lung
SLC12A5 0.8 0.0000000000000016 Adipose - Visceral (Omentum)
SLC12A5 0.6 0.000000000045 Adipose - Subcutaneous
SLC12A5 0.69 0.000000045 Breast - Mammary Tissue
SLC12A5 0.63 0.000000082 Artery - Aorta
SLC12A5 0.78 0.00000018 Spleen
SLC12A5 −0.61 0.00000019 Adrenal Gland
SNX21 0.21 0.00000099 Muscle - Skeletal
SLC12A5 0.45 0.0000029 Thyroid
SLC12A5 0.43 0.0000037 Nerve - Tibial
SLC12A5 0.43 0.0000038 Uterus
SLC12A5 0.41 0.0000053 Skin - Sun Exposed (Lower leg)
SLC12A5 0.48 0.00001 Skin - Not Sun Exposed (Suprapubic)
PLTP −0.25 0.000028 Nerve - Tibial
20 rs17576 A G SLC12A5 −0.57 0.0000000000043 Adrenal Gland
PLTP −0.26 0.00000000033 Lung
PLTP −0.32 0.000000026 Heart - Left Ventricle
PLTP −0.24 0.000000034 Nerve - Tibial
PLTP −0.2 0.00000021 Adipose - Subcutaneous
NEURL2 −0.3 0.00000026 Adipose - Visceral (Omentum)
PLTP −0.2 0.00000046 Thyroid
PLTP −0.19 0.00000055 Artery - Tibial
PLTP −0.37 0.00000066 Adrenal Gland
NEURL2 −0.24 0.0000015 Adipose - Subcutaneous
PLTP −0.25 0.000002 Artery - Aorta
NEURL2 −0.31 0.0000021 Artery - Aorta
PLTP −0.18 0.0000024 Adipose - Visceral (Omentum)
PLTP −0.3 0.0000025 Colon - Sigmoid
PLTP −0.22 0.0000033 Brain - Frontal Cortex (BA9)
PCIF1 0.35 0.0000041 Adrenal Gland
ZSWIM1 −0.26 0.0000068 Adipose - Visceral (Omentum)
RP3–337O18.9 −0.22 0.0000076 Lung
PLTP −0.32 0.0000091 Pituitary
SNX21 0.14 0.000012 Muscle - Skeletal
RP3–337O18.9 −0.2 0.000028 Adipose - Subcutaneous
NEURL2 −0.22 0.000036 Lung
NEURL2 −0.22 0.000073 Thyroid
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Table 5.

The sQTL values of the 3 SNPs of the MMP genes. (according to Genotype-Tissue Expression (GTEx) (http://www.gtexportal.org/)).

Chr SNP Reference allele Alternative allele Gene Symbol Intron Id Effect Size (β) P-Value Tissue
11 rs1799750 TC T WTAPP1 102,832,906:102,833,452:clu_16,168 −0.51 0.000000000065 Testis
20 rs3918242 C T CD40 46,126,741:46,128,138:clu_33,045 0.5 0.0000000029 Thyroid
CD40 46,126,741:46,128,138:clu_32,508 0.45 0.0000000067 Lung
CD40 46,126,741:46,128,138:clu_32,508 0.45 0.0000000067 Lung
SLC12A5 46,021,886:46,023,369:clu_29,529 0.79 0.0000000098 Pituitary
CD40 46,126,741:46,128,138:clu_27,442 0.49 0.00000041 Artery - Aorta
ACOT8 45,841,956:45,844,263:clu_24,540 0.58 0.0000011 Heart - Left Ventricle
CD40 46,126,741:46,128,138:clu_22,055 0.74 0.0000015 Cells - EBV-transformed lymphocytes
ACOT8 45,841,956:45,844,263:clu_27,123 0.49 0.0000041 Heart - Atrial Appendage
20 rs17576 A G SLC12A5 46,021,886:46,023,369:clu_29,529 0.63 0.0000000000093 Pituitary
SLC12A5 46,023,071:46,023,369:clu_24,852 −0.45 0.00000033 Brain - Cortex
SLC12A5 46,021,886:46,023,369:clu_26,648 0.46 0.000002 Brain - Cerebellum
SLC12A5 46,021,886:46,023,369:clu_53,353 0.38 0.000011 Testis
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2. Experimental design, materials, and methods

2.1. Study subjects

The study cohort consisted of 1556 Russian participants, including 536 patients diagnosed with POAG (290 females and 246 males), 621 patients with EH (359 females and 262 males), and 399 patients with PU (211 females and 188 males). The study participants were clinically examined at the Department of Eye Microsurgery (patients with POAG), Department of Cardiology (patients with EH), and Department of Gastroenterology (patients with PU) of St. Iasaf Belgorod Regional Clinical Hospital. All participants were self-reported unrelated Russians born in Central Russia [46]. The study was approved by the Regional Ethics Committee of Belgorod State University. All participants signed an informed consent prior to the enrolment to this study.

2.2. DNA analysis

Phlebotomy was performed by a certified nurse. Blood (5 ml) was drawn from the ulnar vein to a plastic vial (VacutainerⓇ) with 0.5 M EDTA (рН = 8.0). Total genomic DNA was isolated from the buffy coat by the standard phenol-chloroform protocol [47] and then checked for quality using Nanodrop 2000 spectrophotometer (Thermo Scientific, Inc.). Only samples with А260/А280 = 1.7–2.0 were used for the analysis. The isolated DNA was stored at −80°С.

Three SNPs of the MMP genes (rs1799750 MMP1, rs3918242 and rs17576 MMP9) were selected for the analysis. The following selection criteria were applied [48,49]: 1) Previously reported associations with POAG, EH and PU (Table 2), 2) Regulatory potential (regSNP) (Table 3), 3) Effect on gene expression (eSNP) (Table 4), 4) Splicing QTLs (sSNP) (Table 5), and 5) MAF > 5%.

The selected loci were associated with POAG, EH and PU in previously published candidate gene association studies (Table 2) and have functional significance: significant regulatory potential (Table 3) (determined using the online tools HaploReg, v4.1 update 05.11.2015, https://pubs.broadinstitute.org/mammals/haploreg/haploreg.php), influence gene expression level (Table 4) and involved in splicing QTLs (Table 5) (determined using the GTExportal data, http://www.gtexportal.org/).

The DNA samples used for the analysis had concentration 10–15 ng/ml. A single well iPLEX SNP genotyping assay was designed using the Assay Design Suite 1.0 (http://agenabio.com/assay-design-suite-10-software). For this purpose, three SNPs of interest were retrieved from dbSNP of NCBI and imported into the software according to their IDs. DNA genotyping was performed on the MALDI‐TOF mass spectrometry iPLEX platform (Agena Bioscience Inc, San Diego, CA).

For quality control of genotyping, 5% of blind replicate samples were included. The concordance for replicate samples was 100%.

2.3. Statistical analysis

The studied SNPs were checked for their correspondence to the Hardy-Weinberg equilibrium (HWE) using the chi-square test. The frequencies of alleles and genotypes were analyzed for possible differences between the females and males in the study sample using the Kruskall-Wallis test.

Declaration of Competing Interest

The authors have no known competing financial interests or personal relationships that might have, or could be perceived to have influenced the results reported in this article.

Acknowledgments

The study of POAG and EH was supported by the grant of the President of the Russian Federation (NS-2609.2020.7).

Footnotes

Supplementary material associated with this article can be found, in the online version, at doi:10.1016/j.dib.2020.106004.

Appendix. Supplementary materials

mmc1.xls (182KB, xls)
mmc2.xml (379B, xml)

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mmc1.xls (182KB, xls)
mmc2.xml (379B, xml)

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