Table 3.
Top selected CpGs and genes per subtype based on a one-vs.-rest CpG Site Selection with adjusted p-value threshold 0.05.
| Subtype | N CpG Sites (Adjusted p Value < 0.05) | N CpG Sites Unique to Subtype (N Genes) | Gene Names (CpG IDs) Unique to Subtype |
|---|---|---|---|
| Normal Karyotype | 569 | 6 (5) | ZNF793 (cg15139588), APBA2 (cg15605858), PRDM16 (cg02390319), PPP1R14A (cg02571816), ACCN1 (cg03745383) |
| MLL/KMT2A-rearranged | 873 | 59 (33) | KIAA1755 (cg14003035), PLAUR (cg27340480), PER3 (cg05803631), ASB2 (cg09341793), KLK4 (cg26827876), BARHL2 (cg18322569), L1TD1 (cg23049458), ARPC1B (cg10428938), ST8SIA6 (cg17256364), NKX6-2 (cg11174855), WNT5A (cg19554389), HOXA5 (cg12128839, cg25307665), NFIX (cg06744585), SNED1 (cg25241559, cg09991306), TNXB (cg12694372, cg10923662, cg16834823, cg01992382), MSX2 (cg06013117), MAPK8IP1 (cg08214808), BNIP3 (cg18477674), CASR (cg19108881), HECW1 (cg24384918), PCDHA1; PCDHA2; PCDHA3; PCDHA4; PCDHA5; PCDHA6; PCDHA7; PCDHA8 (cg19596110), PITX1 (cg00396667), KCNN1 (cg07857792), TMEM132D (cg20168964), NPSR1 (cg20276677), LOC732275 (cg16709904), NOM1 (cg02413092), SPEG (cg16440561), EDARADD (cg09164898), THBS4 (cg26286839), HOOK2 (cg06417478), LOC254559 (cg09969277), DCC (cg25204852) |
| mono7 | 330 | 24 (12) | BCL2 (cg25059899), ZNF577 (cg03562414, cg24794228, cg11269599, cg10635122), ZNF154 (cg21790626, cg27049766, cg26465391), ARRB2 (cg07971820, cg02286380), SKI (cg25139649), ERCC3 (cg06373940), RPTOR (cg09929238), FBXO47 (cg04120272), DLL1 (cg00084338), C1orf86; LOC100128003 (cg26227225), CYP1A1 (cg22549041), PLD6 (cg24578857, cg19093370) |
| inv(16)/CBFB-MYH11 | 571 | 22 (15) | DPF3 (cg13588403), IFLTD1 (cg13134916), BAHCC1 (cg06636541), LEPR (cg16987305), AFAP1 (cg22079161), PRHOXNB (cg20101529), ANK1 (cg19537719), SHISA6 (cg13330559), PRDM16 (cg03337482), MUC4 (cg05834845), C22orf34 (cg20744362), LY96 (cg23732024), ZNF423 (cg26929700, cg04086531), GNG7 (cg26988138), CNTD2 (cg08871608) |
| t(8;21)/RUNX1-RUNX1T1 | 723 | 27 (15) | SMTNL2 (cg13375589), TUSC1 (cg13811417), PDLIM3 (cg14632696), CYP27C1 (cg08022717), PCDHA1; PCDHA10; PCDHA11; PCDHA2; PCDHA3; PCDHA4; PCDHA5; PCDHA6; PCDHA7; PCDHA8; PCDHA9 (cg26514430), RYR2 (cg07790615), TACSTD2 (cg13443627), FBXL7 (cg26134895), VSTM2A (cg19868631), MARCH11 (cg25092681, cg01791874,cg00339556, cg16150752, cg17712694), IGSF21 (cg15564444), TTBK1 (cg16620382), SHROOM1 (cg21811204), ELOVL4 (cg04107099), SETDB1 (cg15448220) |
| t(15;17)/PML-RARA | 328 | 8 (8) | NFYC (cg16167741), C7orf50 (cg23657099), IGDCC4 (cg00776960), SETD7 (cg02409722), SCHIP1 (cg23553912), SYNE1 (cg02796568), WBSCR17 (cg02300154), C21orf7 (cg08854834) |