Genome-wide DNA methylation profiling integrated with gene expression profiling identifies PAX9 as a novel prognostic marker in chronic lymphocytic leukemia

Rani, Lata; Mathur, Nitin; Gupta, Ritu; Gogia, Ajay; Kaur, Gurvinder; Dhanjal, Jaspreet Kaur; Sundar, Durai; Kumar, Lalit; Sharma, Atul

doi:10.1186/s13148-017-0356-0

Table 3 Association of relative risk of treatment initiation, time to first treatment and overall survival with the mRNA expression of 17 genes selected for validation in early stage CLL patients (n = 93)

From: Genome-wide DNA methylation profiling integrated with gene expression profiling identifies PAX9 as a novel prognostic marker in chronic lymphocytic leukemia

Association of RR, TTFT and OS with mRNA expression
S No.	Parameter (cut off)		Treatment required		RR of treatment initiation			TTFT (in months)					OS (in months)
S No.			Yes	No	RR	95% CI	p value	Time	Events	HR	95% CI	p value	Time	Events	HR	95% CI	p value
1	CRY1 (0.678)	<0.678	16	31	1.91	1.221-3.006	0.01	83	13				NR	7
1		>0.678	30	16	1.91	1.221-3.006	0.01	19	28	3.53	1.789-6.987	<0.001	NR	11	2.22	0.857-5.754	0.1
2	MEIS1 (0.057)	<0.057	23	23	0.97	0.64-1.47	0.92	48	21				NR	9
2		>0.057	23	24	0.97	0.64-1.47	0.92	47	22	1.04	0.564-1.925	0.9	NR	9	1.06	0.421-2.707	0.89
3	ID4 (3.891)	<3.891	20	25	1.21	0.80-1.85	0.47	51	18				NR	11
3		>3.891	26	22	1.21	0.80-1.85	0.47	47	23	1.06	0.571-1.975	0.85	NR	7	1.85	0.654-5.245	0.25
4	TNRC18 (0.646)	<0.646	24	22	0.89	0.59-1.35	0.76	43	22				NR	11
4		>0.646	22	25	0.89	0.59-1.35	0.76	48	19	0.86	0.465-1.596	0.63	NR	7	0.64	0.248-1.657	0.36
5	NFATC1 (0.536)	<0.536	23	23	0.97	0.64-1.47	0.92	48	20				NR	7
5		>0.536	23	24	0.97	0.64-1.47	0.92	36	21	1.45	0.775-2.712	0.25	NR	11	0.95	0.364-2.503	0.93
6	CDK6 (0.247)	<0.247	22	23	1.02	0.67-1.54	0.92	48	21				NR	7
6		>0.247	24	24	1.02	0.67-1.54	0.92	47	22	1.05	0.570-1.945	0.87	NR	11	1.75	0.677-4.542	0.26
7	VIPR1 (7.21)	<7.210	19	26	1.33	0.87-2.03	0.25	48	17				NR	10
7		>7.210	27	21	1.33	0.87-2.03	0.25	36	24	1.6	0.857-2.997	0.14	NR	8	0.98	0.384-2.508	0.97
8	SPRY1 (0.08)	<0.080	24	25	0.91	0.60-1.38	0.84	51	16				NR	11
8		>0.080	22	24	0.91	0.60-1.38	0.84	29	25	1.77	0.949-3.335	0.07	NR	7	2.13	0.797-5.714	0.13
9	PAX9 (0.688)	<0.688	16	30	1.87	1.19-2.93	0.001	83	13				NR	5
9		>0.688	30	16	1.87	1.19-2.93	0.001	19	28	3.14	1.589-6.205	<0.001	NR	13	3.29	1.172-9.272	0.02
10	PMEPA1 (0.01)	<0.010	19	27	1.42	0.93-2.16	0.14	51	17				NR	5
10		>0.010	27	19	1.42	0.93-2.16	0.14	43	24	1.34	0.723-2.518	0.34	NR	13	1.97	0.698-5.565	0.2
11	TBX2 (0.085)	<0.085	24	21	0.87	0.583-1.322	0.68	48	21				NR	8
11		>0.085	22	25	0.87	0.583-1.322	0.68	47	22	0.96	0.523-1.792	0.92	NR	10	1.44	0.567-3.655	0.44
12	TSHZ3 (1.073)	<1.073	25	21	0.84	0.556-1.268	0.52	47	20				NR	8
12		>1.073	21	25	0.84	0.556-1.268	0.52	48	21	0.94	0.510-1.740	0.85	NR	10	1.38	0.546-3.511	0.49
13	BIK (0.438)	<0.438	19	26	1.33	0.87-2.04	0.25	43	16				NR	9
13		>0.438	26	20	1.33	0.87-2.04	0.25	47	24	1.23	0.652-2.330	0.52	NR	9	0.8	0.319-2.052	0.66
14	SPRY2 (5.464)	<5.464	22	23	1.02	0.67-1.55	0.92	48	19				NR	10
14		>5.464	23	23	1.02	0.67-1.55	0.92	48	21	0.86	0.459-1.614	0.64	NR	8	0.6	0.237-1.537	0.29
15	AXIN2 (5.979)	<5.979	23	22	0.93	0.61-1.41	0.92	29	21				NR	8
15		>5.979	22	24	0.93	0.61-1.41	0.92	59	19	0.73	0.393-1.375	0.34	NR	10	1.06	0.418-2.695	0.9
16	SOX7 (0.162)	<0.162	20	25	1.22	0.80-1.86	0.46	48	18				NR	10
16		>0.162	25	21	1.22	0.80-1.86	0.46	47	22	1.15	0.620-2.163	0.64	NR	8	0.68	0.270-1.744	0.43
17	RIC8B (1.741)	<1.741	19	24	1.22	0.80-1.87	0.46	48	17				NR	10
17		>1.741	26	22	1.22	0.80-1.87	0.46	43	23	1.08	0.577-2.028	0.81	NR	8	0.57	0.226-1.463	0.25

Abbreviations used: RR relative risk, TTFT time to first treatment, OS overall survival, NR not reached, HR hazard ratio
The statistically significant p values are shown in italics

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