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. 2018 Mar 6;13(2):163–172. doi: 10.1080/15592294.2017.1287654

Table 2.

The top DNA methylation loci associated with early spontaneous PTB in the discovery sample and their associations with PTB subtypes in the replication sample.

                    Further characterization
            Discovery
 Replication Early sPTBb
 Late sPTBc
 mPTBd
Namea CHR Position Gene Location Annotation βdiffe P βdiff P βdiff P βdiff P
cg13264543 6 7730937 BMP6 Body CDMR −4.4 2.0 × 10−6 −1.0 0.58 1.6 0.15 1.4 0.28
cg03915055 2 158301005 CYTIP TSS1500   −4.1 1.1 × 10−13 −2.7 0.03 −0.9 0.04 −3.3 4.3 × 10−7
cg06804705 21 40125580 LINC00114 TSS1500   −3.4 6.5 × 10−7 −4.6 0.002 −1.1 0.06 −4.2 0.001
cg14195992 8 48265917 KIAA0146 Body Enhancer, DHS −2.7 2.0 × 10−6 0.2 0.23 1.6 0.09 0.4 0.51
cg24892948 19 36001897 DMKN TSS1500   2.6 4.2 × 10−6 −4.0 0.02 −1.5 0.10 −1.0 0.25
cg03445220 1 244747323 C1orf101 Body   2.4 5.1 × 10−6 0.1 0.65 0.3 0.45 −0.6 0.57
cg11936089 11 64270294 NA NA Island 2.4 1.7 × 10−6 1.0 0.36 −1.5 0.10 −0.9 0.56
cg19226017 6 35697185 FKBP5 TSS1500   −2.2 1.1 × 10−6 −0.2 0.33 −0.1 0.67 −1.7 0.04
cg16187013 10 133949209 JAKMIP3 Body Island 2.1 6.3 × 10−7 −2.2 0.11 −0.7 0.57 −1.0 0.65

CDMR: cancer-specific differentially methylation regions; DHS: DNase I hypersensitive sites; PTB: preterm birth; mPTB: medically-indicated PTB; sPTB: spontaneous PTB at <37 weeks of gestation; early sPTB: spontaneous PTB at 24- 336/7 weeks of gestation. NA: not applicable. FDR: False discovery rate.

a

The table shows the top 9 FDR-significant loci with absolute DNA methylation changes >2% between mothers with early sPTBs and mothers with TBs in the discovery sample, which were sorted by this absolute methylation change.

b,c,dIn the replication and further characterization stage, b indicates 7 mothers with early sPTBs, c indicates 34 mothers with late PTBs and d indicates 14 mothers with early medically-indicated PTBs as the PTB cases compared to 54 TB controls.

e

βdiff reflects the DNA methylation changes (%) between mothers with PTBs (cases) and mothers with TBs (controls). The βdiff <0 means that the methylation level was lower in cases than in controls, while βdiff > 0 means the methylation level was higher in cases than in controls.