Association between genetic variants involved in one-carbon metabolism and DNA methylation, and HCC risk

This study examined the association between common and rare variants in genes involved in one-carbon metabolism and DNA methylation, and risk for hepatocellular carcinoma (HCC). These data are from targeted exome sequencing of 67 candidate genes. The gene are ABCB1, ABCC1, ABCC2, AHCY, ALDH1L1, AMPD1, APOC3, AMT, ATIC, BHMT, CBS, CD320, CUBN, DHFR, DMGDH, DNMT1, DNMT3A, DNMT3B, FOLH1, FOLR1, FPGS, FTCD, GART, GGH, GIF, GNMT, ITPA, MAT1A, MAT2A, MAT2B, MMAB, MTFMT, MTHFD1, MTHFD1L, MTHFD2, MTHFD2L, MTHFR, MTHFS, MTR, MTRR, PNPLA3, SARDH, SHMT1, SHMT2, SLC19A1, SLC25A32, SLC46A1, TCN1, TCN2, TYMS, and TM6SF224,28-31, DNMT1, DNMT3A, DNMT3B, MeCP1, MeCP2, MBD1, MBD2, MBD3, MBD4, MBD5, MBD6, TET1, TET2, TET3, IDH1, and IDH2. Sequencing was performed on an Illumina NovaSeq 6000 platform with 150-bp paired-end reads. These variants had coverage >95% and median sequencing depth of1000x.