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Supplementary Material 1: Table S1. Distribution of genotypes of tSNPs in cases and controls

Supplementary Material 3: Table S3. Association between the 40 tSNPs in 4 genes and AIDS clinical stages

Supplementary Material 2: Table S2. Distribution of haplotypes of Chk1 and Cdc25C gene in cases and controls

Supplementary Material 4: Table S4. Association between the tSNPs and HIV-1 infection susceptibility in different subgroups divided by CD4+ T cell counts

Supplementary Material 5: Table S5. Gene-gene interaction models, as identified by GMDR

Additional file 2: Supplementary Table 1. Independent sample test of age.

Additional file 1: Supplementary Figure 1. Genotyping feasibility assessment of candidate SNPs. Priority "Fail" was not genotyped, and one of the linkage SNPs (red) was selected for genotyping. Supplementary Figure 2. P-P plot shows that the age is normally distributed. The data points all fall on the obliqueline of 45°, showing strong normality. Supplementary Figure 3. Association analysis of 14 SNPs with clinical test indexes in HCC patients. (A) Association analysis of 14 SNPs with AFP in HCC patients. (B) Association analysis of 14 SNPs with AST in HCC patients. (C) Association analysis of 14 SNPs with ALT in HCC patients. (D) Association analysis of 14 SNPs with AST/ALT ratios in HCC patients. Model 1 is the TCTTGC/TCTTGC+TCTTGC/T genetic model of rs10589312. Model 2 is the CC+C/CA genetic model of rs11438260. The values in red italics are statistically significant. The size of the indicator is represented by the median value (inter quartile range).

Background Polycystic kidney disease (PKD) is an inherited disease that is life‐threatening. Multiple cysts are present in the bilateral kidneys of PKD patients. The progressively enlarged cysts cause structural damage and loss of kidney function. Methods This study examined and analyzed 12 families with polycystic kidney disease. Whole exome sequencing (WES) or whole genome sequencing (WGS) of the probands was performed to detect the pathogenic genes. The candidate gene segments for lineal consanguinity in the family were amplified by the nest PCR followed by Sanger sequencing. The variants were assessed by pathogenic and conservational property prediction analysis and interpreted according to the American College of Medical Genetics and Genomics. Results Nine of the 12 pedigrees were identified the disease causing variants. Among them, four novel variants in PKD1, c.6930delG:p.C2311Vfs*3, c.1216T>C:p.C406R, c.8548T>C:p.S2850P, and c.3865G>A:p.V1289M (NM_001009944.2) were detected. After assessment, the four novel variants were considered to be pathogenic variants and cause autosomal dominant polycystic kidney disease in family. The detected variants were interpreted. Conclusion The four novel variants in PKD1, c.6930delG:p.C2311Vfs*3, c.1216T>C:p.C406R, c.8548T>C:p.S2850P, and c.3865G>A:p.V1289M (NM_001009944.2) are pathogenic variants and cause autosomal dominant polycystic kidney disease in family., This study examined and analyzed 12 families with polycystic kidney disease using whole exome sequencing or whole genome sequencing and several prediction tools. After assessment and interpretion, the four novel variants were considered to be pathogenic variants and cause autosomal dominant polycystic kidney disease in family. The present study enriched the knowledge of the pathogenicity for autosomal dominant polycystic kidney disease and would improve the understanding of this autosomal dominant disorder.