Table 2 Top differentially methylated probes from conditional regression analysis

From: DNA methylation at birth in monozygotic twins discordant for pediatric acute lymphoblastic leukemia

Chr.

Position (hg19)

CpG name

UCSC RefGene name

Relation to Island region

Promoter associated

Mean beta (SD)

Mean delta-beta (SD)

Regression results

Coef.

FDR

14

73976155

cg07122798

HEATR4

Open sea

No

0.920 (0.025)

−0.00675 (0.0144)

−2.954

2.22E-05

19

51375975

cg19582822

KLK2

Open sea

No

0.852 (0.045)

0.0101 (0.0156)

1.833

1.83E-04

1

24104752

cg22131571

C1orf128

Island

Yes

0.069 (0.008)

−0.00512 (0.00873)

−2.918

1.83E-04

15

90447350

cg10093558

ARPIN; C15orf38-AP3S2

Open sea

No

0.942 (0.018)

0.00782 (0.0148)

2.029

1.83E-04

21

32649215

cg05299823

TIAM1

Open sea

No

0.944 (0.029)

0.00248 (0.00663)

3.157

6.19E-04

12

27462965

cg22709041

STK38L

Open sea

No

0.919 (0.014)

0.00511 (0.0117)

2.590

6.56E-04

2

111493356

cg09756855

ACOXL

Shelf

No

0.666 (0.027)

−0.0128 (0.0231)

−3.873

6.77E-04

1

27114177

cg12806381

PIGV

Island

No

0.071 (0.011)

0.00734 (0.0123)

2.036

6.77E-04

9

2717531

cg26428825

KCNV2

Shore

No

0.950 (0.015)

−0.00600 (0.0107)

−2.503

0.00217

17

79479583

cg05984533

ACTG1

Island

No

0.029 (0.006)

0.00336 (0.00718)

1.698

0.00217

1

101361740

cg16449184

EXTL2; SLC30A7

Island

Yes

0.053 (0.009)

−0.00564 (0.0117)

−2.446

0.00306

6

31934523

cg06250213

SKIV2L

Open sea

No

0.914 (0.014)

0.00738 (0.0172)

2.212

0.00318

2

170682238

cg23927974

METTL5

Shore

No

0.927 (0.012)

−0.00970 (0.0157)

−2.352

0.00331

21

43240484

cg14282798

PRDM15

Island

No

0.904 (0.015)

−0.0120 (0.0187)

−2.327

0.00362

19

14089711

cg18642503

RFX1

Island

No

0.056 (0.006)

−0.00349 (0.00656)

−3.349

0.00389

20

32700182

cg19881050

EIF2S2

Island

Yes

0.036 (0.006)

0.00430 (0.00814)

1.721

0.00425

5

131826485

cg06942904

IRF1

Island

Yes

0.066 (0.013)

0.00964 (0.0189)

1.901

0.00486

2

74919244

cg05363574

Intergenic

Open sea

No

0.955 (0.015)

−0.00366 (0.00620)

−3.168

0.00486

7

105679949

cg06475386

Intergenic

Open sea

No

0.940 (0.013)

0.00418 (0.0106)

3.164

0.00486

11

32915131

cg05662684

QSER1

Island

Yes

0.078 (0.007)

−0.00338 (0.00885)

−3.647

0.00486

  1. Conditional logistic regression analysis was used to assess for a relationship between leukemia status and DNA methylation at the 710,010 array probes included in the study, controlling for sex, array plate, nucleated cell proportions, and clustering by twin pair identity. The top 20 differentially methylated probes (DMPs) ranked by FDR-corrected conditional regression P value are shown out of a total of 240 significant (FDR < 0.05) DMPs. Probes without a genetic association are denoted as intergenic. Mean beta and delta-beta values are shown for twin pairs included in the conditional regression analysis (n = 37). Chr Chromosome. Coef Coefficient. FDR False discovery rate. SD Standard deviation. UCSC University of California Santa Cruz.
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