Identification of a panel of sensitive and specific DNA methylation markers for lung adenocarcinoma

Tsou, Jeffrey A; Galler, Janice S; Siegmund, Kimberly D; Laird, Peter W; Turla, Sally; Cozen, Wendy; Hagen, Jeffrey A; Koss, Michael N; Laird-Offringa, Ite A

doi:10.1186/1476-4598-6-70

Molecular Cancer

Table 2 Frequency and median PMR values of AD, Adj NTL and NTL tissues for 28 loci

From: Identification of a panel of sensitive and specific DNA methylation markers for lung adenocarcinoma

HUGO^a	Frequency^b			Median^f			p-value^g
	AD^c n = 51	Adj NTL^d n = 38	NTL^e n = 11	AD n = 51	Adj NTL n = 38	NTL n = 11	AD vs All NTL	AD vs AdjNTL	AD vs matched NTL	BH-MC Threshold^h	Importance Measureⁱ
OPCML	98	79	36	107.15	8.93	10.02	9E-15	8E-13	2E-10	0.0025	7.38
CDX2	100^j	66	9	43.97	3.40	0.12	4E-13	2E-10	8E-10	0.0050	3.49
HOXA1	94	71	36	160.00	4.90	0.12	2E-12	2E-10	2E-10	N/A	8.52
CDKN2A EX2	100	100	82	191.07	46.17	27.39	6E-12	4E-10	1E-10	N/A	5.80
SFRP1	94^k	87	36	132.93	10.01	4.78	1E-10	2E-08	1E-09	0.0075	2.62
CDH13	78	45	0	39.65	4.95	78.05	4E-08	9E-07	2E-08	N/A	2.14
TWIST1	82	66	9	392.16	6.87	8.03	1E-07	8E-06	1E-07	0.0100	2.77
LZTS1	100	100	100	107.75	170.95	210.95	5E-06	0.0003	0.0262	0.0125	1.52
RASSF1	69^k	58	9	92.53	0.86	5.45	6E-05	0.0010	1E-07	N/A	1.83
SFRP4	67^k	42	9	3.25	1.03	8.71	0.0005	0.0052	0.0086	0.0150	0.39
SFRP5	90^k	92	45	14.38	5.78	4.59	0.0005	0.0095	0.0010	0.0175	0.72
ESR1	49^k	32	9	5.72	1.29	0.63	0.0049	0.0283	0.0007	N/A	0.33
CDH1	94	89	55	17.62	12.74	10.22	0.0092	0.0686	0.0151	N/A	0.51
SLC6A20	25	11	9	7.81	0.38	154.45	0.0426	0.0569	0.0244	0.0200	0.10
PGR	14	5	0	59.92	6.95	N/A	0.0850	0.1753	0.4375	0.0225	0.08
MT1A	100	100	100	104.45	108.58	112.44	0.2276	0.4283	0.7422	0.0250	0.84
MT2A	88	76	55	12.31	12.22	15.48	0.2650	0.4568	0.4622	0.0275	0.37
ATM	75	68	27	0.16	0.19	0.03	0.2954	0.9498	0.5131	0.0300	0.07
PTEN	29	26	0	1.21	0.85	N/A	0.3319	0.7976	0.8077	0.0325	0.07
SYK	29	24	18	0.42	0.15	3.34	0.4314	0.5002	0.8904	0.0350	0.07
CDKN2B	98	97	91	8.29	10.05	8.48	0.4400	0.2422	0.5335	0.0375	0.44
CYP1B1	29	26	18	1.80	1.26	0.13	0.4481	0.6565	0.1454	0.0400	0.11
CHFR	8	5	0	0.49	1.65	N/A	0.4560	0.6677	1.0000	0.0425	0.04
APC	80	97	82	15.10	4.60	10.81	0.5999	0.5923	0.0394	N/A	1.89
SOCS4	12^j	13	18	0.25	1.70	85.45	0.6040	0.7637	0.3125	0.0450	0.13
MGMT	16	18	0	224.53	9.22	N/A	0.7141	0.8988	0.2031	N/A	0.07
HMGA1	20^j	18	27	0.19	0.02	0.12	0.9642	0.7645	0.6221	0.0475	0.00001
VHL	0	0	0	N/A	N/A	N/A	1.0000	1.0000	1.0000	0.0500	0

^a HUGO, Human Genome Organization nomenclature sorted by AD vs All NTL p-value with the most significant at the top.
^bPercentage of samples with positive methylation value.
^cAD, Adenocarcinoma
^dAdj NTL, Adjacent non-tumor lung from adenocarcinoma patients
^eNTL, Non-tumor lung from non-cancer patients
^fMedian percent methylated reference calculated from positive methylation values
^gStatistically significant numbers are highlighted in bold; AD vs. all NTL and AD vs. AdjNTL: Wilcoxon rank sum test; AD vs. matched NTL: Wilcoxon signed rank test
^hBH-MC threshold, Benjamini- Hochberg multiple comparison threshold p-value
ⁱImportance Measure based on random forest analysis
^jn = 50
^kn = 49

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ISSN: 1476-4598

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