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

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.


Specifications
Biology Specific subject area Genetics Type of data Raw and analyzed data Parameters for data collection Whole blood (5 ml) was drawn to a plastic vial (Vacutainer R ) 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-20 0 0 spectrophotometer. Genotyping was performed on the Sequenom MassARRAY R 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 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 metaanalyses 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.

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 )   . 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.

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  ( continued on next page ) Abbreviations: POAG -primary open-angle glaucoma, EH -essential hypertension, IS -ischemic stroke, PU -peptic ulcer.      Table 5 The sQTL values of the 3 SNPs of the MMP genes. (according to Genotype-Tissue Expression (GTEx) ( http://www.gtexportal.org/ )). 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.
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%.

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.