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Table 2 Significant DMPs associated with aGVHD severity status

From: A donor-specific epigenetic classifier for acute graft-versus-host disease severity in hematopoietic stem cell transplantation

Rank DMP Adj. P value Δβ-value Chr. Position Gene Feature CpG context LOOCV
1 cg20475486 1.38 × 10−3 −0.180 14 70,317,075 IGR Island 85
2 cg10399005 1.62 × 10−4 −0.162 14 70,316,898 IGR Island 85
3 cg16925210 1.60 × 10−5 0.130 2 216,946,718 PECR TSS200 Island 85
4 cg00762468 7.61 × 10−6 0.066 16 103,568 POLR3K 1stExon Island 85
5 cg26758857 1.07 × 10−7 −0.062 22 36,649,135 APOL1 5′UTR 85
6 cg21752471 8.92 × 10−4 −0.061 5 133,861,794 PHF15 TSS200 Island 85
7 cg21459486 5.14 × 10−4 −0.060 13 112,885,426 IGR 85
8 cg16495818 2.05 × 10−5 −0.055 11 73,306,367 FAM168A 5′UTR Shelf 85
9 cg16276523 5.29 × 10−4 −0.094 1 161,049,579 PVRL4 Body Island 84
10 cg19558933 5.11 × 10−3 −0.129 11 134,632,242 IGR Island 82
11 cg00087067 9.63 × 10−3 0.071 5 5,265,509 ADAMTS16 Body 82
12 cg14099595 1.62 × 10−2 0.067 5 145,717,283 POU4F3 TSS1500 Shore 82
13 cg07464977 6.69 × 10−3 −0.062 5 2,097,136 IGR 82
14 cg11364888 8.50 × 10−3 −0.055 12 116,920,304 IGR 82
15 cg24599107 9.57 × 10−3 −0.073 1 161,049,443 PVRL4 Body Island 81
16 cg07280807 8.94 × 10−3 −0.151 14 70,317,239 IGR Island 80
17 cg14546466 2.49 × 10−2 −0.077 2 11,796,974 IGR Island 80
18 cg03481039 8.60 × 10−3 −0.065 11 116,662,012 APOA5 Body Shore 80
19 cg03896685 2.62 × 10−2 −0.062 7 65,512,561 IGR Shelf 80
20 cg00245850 1.78 × 10−2 0.060 8 143,925,513 GML Body 80
21 cg09284655 1.17 × 10−2 −0.152 14 70,317,228 IGR Island 79
22 cg10287485 2.20 × 10−2 0.090 11 69,473,145 IGR Shelf 79
23 cg19704238 1.55 × 10−2 0.058 10 85,900,022 GHITM 5′UTR Shore 79
24 cg09282654 3.33 × 10−2 0.070 7 123,563,992 SPAM1 TSS1500 75
25 cg16701890 3.57 × 10−2 0.064 2 119,906,008 IGR 73
26 cg04664342 3.80 × 10−2 −0.107 17 4,685,905 TM4SF5 Body Island 65
27 cg20307347 4.06 × 10−2 −0.119 2 231,734,563 ITM2C Body Shelf 58
28 cg19311448 4.17 × 10−2 −0.075 2 11,797,017 IGR Island 45
29 cg09852744 4.55 × 10−2 0.058 6 158,732,256 TULP4 TSS1500 39
30 cg16398628 4.46 × 10−2 0.090 10 91,011,689 LIPA TSS200 Island 32
31 cg20585841 4.57 × 10−2 −0.164 8 102,729,926 NCALD Body 21
  1. DMPs achieving a P value <0.05 after Bonferroni correction and a DNA methylation difference of at least ±5 % are reported. DMPs are ranked according to their recurrence in the LOOCV, for which a total of 85 iterations were performed, and their absolute DNA methylation difference. DNA methylation differences were calculated as follows: mean β-values of HSCT donors matched to recipients with severe aGVHD – mean β-values of HSCT donors matched to recipients with no/mild aGVHD. The four highlighted DMPs on chromosome 14q24.2 form a region with consistent DNA hypomethylation in graft donors matched to recipients with severe aGVHD compared to donors paired with recipients with no/mild aGVHD (Fig. 2a). Chromosomal positions are reported in genome build = hg19