Table 5 CpG sites in 22 genes with a... | American Society of Hematology

Table 5

CpG sites in 22 genes with a correlation between methylation level and clinical outcome in the cell samples from patients with ALL

Gene*	CpG site location†		Fine & Gray P‡	N Beta value less than 0.25	N Beta value 0.25 to 0.75	N Beta value more than 0.75	Gray test P§
B-cell precursor ALL
ENSG00000167210	18	42 434 938	< .001	26	170	143	.007
LRP1B	2	142 605 338	< .001	210	112	17	.004
RUNDC3B	7	87 096 309	< .001	205	133	1	.032
ENSG00000167210	18	42 435 264	.001	87	73	179	.002
PAX8	2	113 752 043	.002	248	80	11	.081
SPON2	4	1 155 890	.003	251	72	16	.008
ENSG00000136315	14	20 457 591	.005	148	158	33	.004
ALDH1L1	3	127 382 460	.006	267	68	4	.119
CPVL	7	29 152 529	.007	185	108	46	.021
MUC4	3	197 023 530	.008	66	258	15	.172
PCDHGA12	5	140 790 293	.010	169	114	56	.087
High hyperdiploidy BCP
PAX8	2	113 752 043	.003	82	20	2	.089
CPNE7	16	88 170 539	.006	2	51	51	.046
COBL	7	51 352 477	.010	74	29	1	.090
t(12;21) BCP
C6orf47	6	31 738 119	< .001	3	44	26	< .001
RASAL1	12	112 057 868	.002	68	5	0	.140
CHST13	3	127 726 340	.003	9	41	23	.292
EFCAB4A	11	815 712	.004	5	67	1	.298
BDH2	4	104 241 438	.005	18	53	2	.379
CLEC10A	17	6 924 625	.007	6	53	14	.010
EVC	4	5 764 498	.009	7	55	11	.192
T-ALL
LRP1B	2	142 605 854	< .001	7	21	32	< .001
IGSF3	1	117 013 015	.006	2	29	29	.070

Gene*	CpG site location†		Fine & Gray P‡	N Beta value less than 0.25	N Beta value 0.25 to 0.75	N Beta value more than 0.75	Gray test P§
B-cell precursor ALL
ENSG00000167210	18	42 434 938	< .001	26	170	143	.007
LRP1B	2	142 605 338	< .001	210	112	17	.004
RUNDC3B	7	87 096 309	< .001	205	133	1	.032
ENSG00000167210	18	42 435 264	.001	87	73	179	.002
PAX8	2	113 752 043	.002	248	80	11	.081
SPON2	4	1 155 890	.003	251	72	16	.008
ENSG00000136315	14	20 457 591	.005	148	158	33	.004
ALDH1L1	3	127 382 460	.006	267	68	4	.119
CPVL	7	29 152 529	.007	185	108	46	.021
MUC4	3	197 023 530	.008	66	258	15	.172
PCDHGA12	5	140 790 293	.010	169	114	56	.087
High hyperdiploidy BCP
PAX8	2	113 752 043	.003	82	20	2	.089
CPNE7	16	88 170 539	.006	2	51	51	.046
COBL	7	51 352 477	.010	74	29	1	.090
t(12;21) BCP
C6orf47	6	31 738 119	< .001	3	44	26	< .001
RASAL1	12	112 057 868	.002	68	5	0	.140
CHST13	3	127 726 340	.003	9	41	23	.292
EFCAB4A	11	815 712	.004	5	67	1	.298
BDH2	4	104 241 438	.005	18	53	2	.379
CLEC10A	17	6 924 625	.007	6	53	14	.010
EVC	4	5 764 498	.009	7	55	11	.192
T-ALL
LRP1B	2	142 605 854	< .001	7	21	32	< .001
IGSF3	1	117 013 015	.006	2	29	29	.070

Gene symbol according to the HUGO Gene Nomenclature Committee (HGNC; http://www.genenames.org/).

†

Chromosome number and genomic coordinate of the C nucleotide in each CpG site (genome build 36).

‡

Unadjusted P value for relapse from the univariate regression analysis (Fine and Gray test) with methylation levels as independent variable.

Unadjusted P value from the Gray test of difference in probability of relapse between the three groups with methylation levels below 0.25, between 0.25 and 0.75, or above 0.75.

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