Table 4. Technical validation of Infinium HumanMethylation450 BeadChip data using pyrosequencing.
| Infinium HumanMethylation450 BeadChip data | Pyrosequencing data | Correlation between the two methods | ||||||||||
| Gene symbol | Probe ID | Non-diabetic DNA meth (%) | T2D DNA meth (%) | Delta DNA meth (%) | P-value | q-value | Non-diabetic DNA meth (%) | T2D DNA meth (%) | Delta DNA meth (%) | P-value | rho | P-value |
| CDKN1A | cg21091547 | 69.2±5.1 | 61.0±5.7 | −8.2 | 3.7×10−6 | 0.0091 | 75.8±6.2 | 66.2±8.2 | −9.5 | 1.3×10−3 | 0.84 | 1.2×10−13 |
| PDE7B | cg27306443 | 23.3±6.0 | 16.5±3.8 | −6.8 | 2.1×10−6 | 0.0076 | 12.5±4.2 | 8.5±2.8 | −4.0 | 5.1×10−3 | 0.89 | 6.3×10−17 |
| SEPT9 | cg19654743 | 65.9±7.1 | 58.0±7.1 | −7.8 | 2.5×10−5 | 0.018 | 84.2±6.1 | 76.2±9.5 | −8.0 | 6.0×10−3 | 0.93 | 1.8×10−21 |
| IRS1 | cg04751089 | 40.0±6.3 | 33.1±4.4 | −6.9 | 5.5×10−5 | 0.025 | 39.9±8.3 | 31.3±5.3 | −8.6 | 1.3×10−5 | 0.90 | 2.8×10−18 |
| HDAC7 | cg20995304 | 77.5±5.5 | 71.1±7.0 | −6.4 | 2.8×10−4 | 0.048 | 80.3±6.4 | 71.4±9.3 | −8.9 | 5.5×10−3 | 0.94 | 2.1×10−22 |
| THADA | cg01649611 | 71.0±4.9 | 63.2±5.9 | −7.8 | 5.4×10−8 | 0.0031 | 77.2±8.6 | 69.1±9.6 | −8.1 | 8.6×10−3 | 0.85 | 4.1×10−14 |
| PTPRN2 | cg15572489 | 64.0±8.1 | 55.5±7.5 | −8.4 | 2.5×10−5 | 0.018 | 63.7±7.8 | 53.9±9.7 | −9.7 | 4.1×10−3 | 0.90 | 4.2×10−17 |
q-values are based on a FDR analysis. Correlations between Infinium HumanMethylation450 BeadChip data and pyrosequencing data were analyzed using Spearman's test. Rho represents the correlation coefficient.