Data to genetic risk assessment on high-density cholesterol level associated polymorphisms in Hungarian general and Roma populations

Data obtained by genotyping single nucleotide polymorphisms (SNPs) related to high-density lipoprotein cholesterol (HDL-C) levels were utilized in Genetic Risk Score [unweighted (GRS) and weighted (wGRS)] computation on Hungarian general and Roma populations. The selection process of the SNPs as well as the results obtained are published in our research article (Piko et al., 2017) [1]. Linkage analyses were performed by study groups. Study populations were stratified by quintiles of weighted Genetic Risk Score. Multivariate linear regression analyses were performed using Genetic Risk Scores and HDL-C levels as dependent variables; and ethnicity, sex and age as independent variables. The study subjects were categorized into quintiles according their wGRS values. Associations of Genetic Risk Scores with plasma HDL-C levels (as a continuous variable) were observed in both populations. Finally, the two populations were merged and analyzed together by multivariate logistic regression where reduced plasma HDL-C level was the dependent variable; while ethnicity, age and sex were the independent ones.

plasma HDL-C level was the dependent variable; while ethnicity, age and sex were the independent ones. &

Value of the data
Several studies describe the health status of the Roma, which constitutes the largest ethnic minority in Europe however studies focusing on their genetic predisposition to common chronic diseases are scarce.
Genetic background of atherosclerosis among Roma as well as the general Hungarian population can be studied separately or in international cohort.
Genetic risk score assessment can be further utilized to compare susceptibility to reduced HDL-C level among different population groups.

Data
Distribution of SNPs related to HDL-C level were analysed in the Hungarian Roma and general populations and weighted Genetic Risk Scores were defined and used to categorize the population into quintiles.

Subjects
Study involved subjects of samples investigated during recent cross sectional surveys [2,3]. The Roma sample is representative to the Roma population living settlements in North-East Hungary in terms of age and sex and includes 646 individuals (Roma). The "General" sample consisting of 1542 individuals representative for the Hungarian general population in terms of geographic, age and sex distributions.

DNA extraction
DNA was isolated using a MagNA Pure LC system (Roche Diagnostics, Basel, Switzerland) with a MagNA Pure LC DNA Isolation Kit-Large Volume according to the manufacturer's instructions. Extracted DNA was eluted in 200 µl MagNA Pure LC DNA Isolation Kit-Large Volume elution buffer.

SNP selection
A systematic literature review on the PubMed, HuGE Navigator and Ensembl databases was conducted to identify SNPs most strongly associated with HDL-C metabolism ( Table 1 and Fig. 1). The selection process of the SNPs is demonstrated in detail in our research article [1].

Genotyping
Genotyping was performed on a MassARRAY platform (Sequenom Inc., San Diego, CA, USA) with iPLEX Gold chemistry. Validation, concordance analysis and quality control were conducted by the facility according to their protocols.

Statistical analyses
Two-sided t tests were used to compare the distribution of genetic risk scores in populations. To reveal the association between genetic risk, serum HDL-C level and ethnicity several statistical models were used (Tables 2-6).    Table 3 Output of multiple regression models using unweighted and weighted genetic risk scores as dependent variable and ethnicity, age and sex as independent variables. Multivariate regression analysis using age, sex as covariates did not change the inference neither for the GRS nor for wGRS. Table 4 Proportion of subjects with reduced plasma HDL-C level in the General and Roma populations according to wGRS quintiles. Average HDL-C level (mmol/l)  Table 5 Association of GRSs with plasma HDL-C a level by study groups. The association of GRS and wGRS with plasma HDL-C level were evaluated under unadjusted regression models (Model I and III) and under regression models adjusted for age and sex (Model II and IV) separately in Roma and general subjects. In all models the HDL-C was the dependent variable, the GRS/wGRS were the independent variables. 95% CI: 95% confidence interval a HDL-C values were non-normally distributed and were transformed using a two-step approach suggested by Templeton [4].

Ethical approval
All procedures performed in studies involving human participants were in accordance with the ethical standards of the institutional and/or national research committee and with the 1964 Helsinki declaration and its later amendments or comparable ethical standards. This article does not contain any studies with animals performed by any of the authors. Table 6 The association of HDL-C level with genetic risk scores adjusted by ethnicity, sex and age.