背景:患病率高达4%,室间隔缺损(VSD)是新生儿死亡的主要原因之一。VSD是一种常见的复杂遗传疾病,与许多遗传决定因素有关。转录因子包括T-BoxTBX5和NFATc1(活化T细胞的核因子,细胞质1),血管内皮生长因子(VEGF),ISLET1(由ISL1基因编码)和酶MTHFR,选择亚甲基四氢叶酸还原酶。遗传风险评分(GRS)是一种广泛接受的方法,用于将遗传数据转换为疾病易感性的预测和评估工具。
方法:本研究共招募了200名参与者,100名VSD患者和100名对照。使用四引物ARMSPCR和PCR-RFLP对ISL1:rs1017、NFATc1:rs7240256、VEGF:rs36208048、TBX5:rs11067075和MTHFR:rs1801133变体进行基因分型。对于统计分析,使用软件SPSS版本23。使用卡方(χ²)计算病例和对照的基因型频率,而使用SNPStats工具计算等位基因频率。使用二元逻辑回归检查GRS四分位数与VSD的关联。调整后的P值0.01用作所有分析的显著性阈值。
结果:ISL1(OD:0.242,CI:0.158-0.37,p值:2.15×10-4:),NFATc1(OD:2.53,CI:1.64-3.89,p值:2.11×10-5),发现TBX5(OD:2.24,CI:1.47-3.41,p值:1.6×10-4)和MTHFR(OD:10.46,CI:5.68-19.26,p值:2.09×10-9:)变异与VSD相关。相比之下,VEGF(OD:0.952,CI:0.56-1.62,p值:0.8921)变异与VSD无显著相关性.对于案例,平均GRS评分为3.78±1.285,而对照组为2.95±1.290(p值:0.479,CI:0.474-1.190).病例与对照组之间的GRS比较显示,病例的平均GRS为1.90±0.480,而对照组为1.68±0.490(p值:0.001,CI:0.086-0.354)。较高的四分位数在病例中更普遍,而较低的四分位数在对照中更普遍。
结论:这5个位点的GRS与VSD密切相关。此外,与单个SNP相比,遗传风险评分可以提供更好的变异与疾病之间关联的信息.我们还说明了GRS的累积功率比单个SNP效应更大。这是一项试点规模研究,样本量相对较小,其发现应以更大的样本量复制,以适应独特的当地巴基斯坦人口。
With prevalence up to 4%, Ventricular Septal Defect (VSD) is one of the leading causes of neonatal deaths. VSD is a common complex genetic disorder that has been associated with many genetic determinants. Variants from genes for the transcription factors including T-Box TBX5 and NFATc1 (nuclear factor of activated T cells, cytoplasmic 1), Vascular endothelial growth factor (VEGF), ISLET1 (encoded by the ISL1 gene) and enzyme MTHFR, a methylene tetrahydrofolate reductase were selected. Genetic risk score (GRS) is a widely accepted approach used to convert the genetic data into prediction and assessment tool for disease susceptibility.
A total of 200 participants were recruited for the current study, 100 VSD patients and 100 controls. Genotyping of the ISL1: rs1017, NFATc1: rs7240256, VEGF: rs36208048, TBX5: rs11067075, and MTHFR: rs1801133 variants was performed using tetra primer ARMS PCR and PCR-RFLP. For the statistical analysis, the software SPSS version 23 was used. Genotypic frequencies of cases and controls were calculated using chi-square (χ²) whereas allelic frequencies were calculated by using the SNPStats tool. The association of GRS quartiles with VSD was examined using binary logistic regression. Adjusted p-value 0.01 was used as significance threshold for all analyses.
The ISL1 (OD: 0.242, CI: 0.158-0.37, p-value: 2.15 × 10- 4 :), NFATc1 (OD: 2.53, CI: 1.64-3.89, p-value: 2.11 × 10- 5), TBX5 (OD: 2.24, CI: 1.47-3.41, p-value:1.6 × 10- 4) and MTHFR (OD: 10.46, CI: 5.68-19.26, p-value: 2.09 × 10- 9:) variants were found to be in association with VSD. In contrast, the VEGF (OD: 0.952, CI: 0.56-1.62, p-value: 0.8921) variant did not show significance association with the VSD. For cases, the mean GRS score was 3.78 ± 1.285 while in controls it was 2.95 ± 1.290 (p-value: 0.479, CI: 0.474-1.190). Comparison of GRS between cases and control showed that mean GRS of cases was 1.90 ± 0.480 while in controls it was 1.68 ± 0.490 (p-value: 0.001, CI: 0.086-0.354). Higher quartiles were more prevalent in cases whereas lower quartiles were more prevalent in controls.
GRS of these five loci was strongly associated with VSD. Moreover, genetic risk score can provide better information for the association between variants and disease as compared to a single SNP. We also illustrated that the cumulative power of GRS is greater over the single SNP effect. This is a pilot scale study with a relatively small sample size whose findings should be replicated in a larger sample size for the unique local Pakistani population.