2.1 Study Design
In this study, body circumference (neck circumference, waist circumference, hip circumference) and testosterone level were used as exposure factors, and single nucleotide polymorphisms (SNPs) loci significantly associated with the above exposure factors were selected as instrumental variables(IVs), and the outcome variable was MAFLD, and the causal association analysis between exposure and outcome was performed using a two-sample MR analysis approach based on a publicly available genome wide association study (GWAS) database of large samples, and Cochran Q test to assess heterogeneity, and finally sensitivity analysis to verify the reliability of the causal association results. MR analysis needs to satisfy the following three core hypotheses: ①there is a strong association between instrumental variable Z and exposure factor X; ②instrumental variable Z is not associated with any confounding factor U of the exposure-outcome association; and ③the instrumental variable Z does not affect the outcome Y, except possibly by association with the exposure X. The two-sample MR study model is shown in Figure 1.
2.2 Data sources
Three important body circumferences (neck circumference, waist circumference, and hip circumference) and serum testosterone levels were used as exposure factors, SNPs significantly associated with the above exposure factors were used as IVs, and the outcome factor was MAFLD. The pooled data used to conduct the two-sample MR study were obtained from the IEU Open GWAS database (https://gwas.mrcieu.ac.uk/ ), neck circumference (GWAS ID: ebi-a-GCST90017134), waist circumference (GWAS ID: ukb-a-382), hip circumference (GWAS ID: ukb-a-388), testosterone (GWAS ID: ebi-a-GCST90012102), and MAFLD (GWAS ID: finn-b-NAFLD), all of the above databases were European populations or mixed populations. All datasets used in this study were from the public domain, and summary information is presented in Table 1.
TABLE 1 Summary of the GWAS included in this two-sample MR study
Variable
|
ID
|
Sample size
|
Number of SNPs
|
Consortium
|
Population
|
Sex
|
Year
|
Neck circumference
|
ebi-a-GCST90017134
|
6358
|
7297174
|
-
|
Mixed
|
Males and Females
|
2021
|
Waist circumference
|
ukb-a-382
|
336639
|
10894596
|
Neale Lab
|
European
|
Males and Females
|
2017
|
Hip circumference
|
ukb-a-388
|
336601
|
10894596
|
Neale Lab
|
European
|
Males and Females
|
2017
|
Testosterone levels
|
ebi-a-GCST90012102
|
188507
|
16139906
|
-
|
European
|
Males and Females
|
2020
|
MAFLD
|
finn-b-NAFLD
|
218792
|
16380466
|
-
|
European
|
Males and Females
|
2021
|
2.3 Selection of instrumental variables
SNPs with significant correlation with body circumference and testosterone level (P < 5. 0×10-8 ) were screened, and the interference of linkage disequilibrium (LD) was excluded (16), setting parameter r2 = 0. 001, kb = 10000, and the echo SNPs were excluded, and the SNPs with significant heterogeneity were excluded by heterogeneity test, If the number of SNPs filtered according to the above criteria is large, each SNP should be queried on the PhenoScanner website (http://www.phenoscanner.medschl.cam.ac.uk/), SNPs affected by confounding factors that violated Mendelian randomization core hypothesis②and③were excluded, and finally valid SNPs significantly associated with exposure factors that met Mendelian core hypothesis were obtained as IVs.F > 10 indicates the absence of weak instrumental variable bias, which is calculated as follows: , where N is the sample size of the exposed database, k is the number of SNPs, and R2 is the proportion of variance explained by SNPs in the exposed database. R2 is calculated as , where EAF is the effect allele frequency, β is the allele effect value, and SD is the standard deviation.
2.4 Statistical analysis for Mendelian randomization
We used the TwoSampleMR package (version 0.5.6) in R program (version 4.2.1) to integrate and analyze the data. In this study, inverse variance weighted (IVW) (17) was used as the main analysis method, while MR-Egger regression (18), weighted median estimator (WME) (19), simple mode and weighted mode (20) were used together for MR analysis. The principle of IVW is to weight the inverse of the variance of each IV as the weight while ensuring that all IVs are valid, the regression does not consider the intercept term, and the final result is the weighted average of the effect values of all IVs. The major difference between MR-Egger regression and IVW is that the regression takes into account the presence of the intercept term, and in addition, it also uses the inverse of the ending variance as a weight for the fit. The WME is defined as the median of the weighted empirical density function of the ratio estimates, which allows consistent estimation of causality if at least half of the valid instruments are present in the analysis.
2.5 Heterogeneity and sensitivity test
There may be heterogeneity in the 2-sample MR analysis due to differences in analysis platforms, experimental conditions, including populations and SNPs, which may bias the estimation of causal effects. Therefore, the main IVW and MR-Egger methods were tested for heterogeneity in this study. The heterogeneity test was used to test the differences between individual IVs, and Cochran's Q statistic and P-value were used to determine whether there was heterogeneity, and P < 0.1 represented the presence of heterogeneity; Pleiotropy test mainly tests the presence of horizontal pleiotropy for multiple IVs (21), and the P-value of the pleiotropy test was used in this study to measure whether there was pleiotropy in the analysis, if P > 0.05, it is considered that the possibility of pleiotropy in the causal analysis is weak; Leave-one-out sensitivity test is mainly to calculate the MR results of the remaining IVs after eliminating them one by one (22), if the estimated MR results of other IVs after eliminating one IV are very different from the total results, it means that the MR results are sensitive to that IV. The presence of pleiotropy in the analysis was also determined in this study using the MR-pleiotropy residual sum outlier (MR-PRESSO) (23).