Genome wide SNP comparative analysis between EGFR and KRAS mutated NSCLC and characterization of two models of oncogenic cooperation in non-small cell lung carcinoma

Blons, Hélène; Pallier, Karine; Le Corre, Delphine; Danel, Claire; Tremblay-Gravel, Maxime; Houdayer, Claude; Fabre-Guillevin, Elizabeth; Riquet, Marc; Dessen, Philippe; Laurent-Puig, Pierre

doi:10.1186/1755-8794-1-25

Table 3 Describes the population studied in terms of clinico-pathological features, gene mutations (EGFR, ERBB2, PIK3CA, KRAS, BRAF and TP53) as well as gene copy number (CCND1, CCNE1 and CDKN2A) analyzed by real time PCR.

From: Genome wide SNP comparative analysis between EGFR and KRAS mutated NSCLC and characterization of two models of oncogenic cooperation in non-small cell lung carcinoma

N°	Sex	Age at diagnosis	Smoker	TNM	Tumor Type	EGFR	TP53	KRAS	ERBB2	PIK3CA	STK11	CCND (2*2-DDCt)	CCNE1 (2*2-DDCt)	CDKN2A (2*2-DDCt)
2	F	49	Yes	T2N0	BAC	0	0	0	0	0	c650insG, pFs265X	2,42	2.32	0.53
3	F	61	Yes	T3N2	ADC	0	0	0	0	0	0	2,70	2.30	0.82
4	F	42	Yes	T1N0	ADC	0	C743G>T, pR248L	c34G>T pG12C	0	0	0	1,86	3.38	1.03
5	F	80	No	T4N2	ADC	0	0	0	0	0	0	1,82	2.05	0.90
6	F	41	Yes	T2N2	LCC	0	c358A>T, pK120X	0	0	0	0	3,16	2.19	2.38
7	F	39	Yes	T2Nx	LCC	0	c796G>T, pL266X	0	0	0	c153delG, pFs63X	3,13	2.36	3.42
8	F	69	No	T2N0	ADC/BAC	0	0	0	0	0	0	2.68	2.36	0.71
9	F	65	No	T2N1	ADC	0	c452454del, FsP153G	0	0	0	0	1.92	2.44	1.17
10	F	79	No	T4N0	ADC/BAC	L858R	0	0	0	0	0	2.68	2.92	0.33
12	F	52	Yes	T2N0	ADC/BAC	0	0	c35G>A pG12D	0	0	C508C>T, pQ170X	1.71	1.43	1.05
13	F	77	No	T2N0	ADC	0	0	0	0	0	0	2.28	2.26	1.22
15	F	73	Yes	T2N0	BAC	0	0	c35G>T pG12V	0	0	0	1.75	2.16	0.72
16	F	46	Yes	T2N0	ADC	0	c614A>G, pY205C	0	0	0	0	4.59	2.66	1.90
17	F	84	No	T2N0	ADC/BAC	L858R	0	0	0	0	0	1.84	1.97	0.90
18	F	65	No	T2N0	ADC/BAC	c2241_2258del p747-753del insQ747	c880delG, FsE294S	0	0	0	0	2.22	2.51	2.18
21	F	50	Yes	T2N0	ADC/BAC	0	0	c34G>T pG12C	0	0	0	2.15	2.75	1.73
22	F	78	Yes	T2N1	LCC	0	0	0	0	0	c595G>C, pE198Q	4.64	3.05	1.23
23	F	49	Yes	T2N0	LCC	0	0	0	0	0	c1072C>Q, pF354L	2.90	2.37	0.96
24	F	65	Yes	T2N0	BAC	0	c574C>T, PQ192X	c34G>T pG12C	0	0	0	1.82	2.34	1.77
25	F	55	No	T2N0	ADC/BAC	0	0	0	0	0	0	1.84	1.81	1.51
26	F	73	No	T2N2	ADC	0	c783-2A>G, SLPICEMUT	0	c2322_2323ins12, pM774_A775ins AYVM	0	0	2.60	3.56	1.68
29	F	61	No	T2N1	ADC	L858R	0	0	0	0	0	1.98	2.06	0.29
30	F	59	No	T4N2	ADC	L858R	c258-280del, FsA86A	0	0	0	0	2.31	1.47	0.59
31	F	75	No	T2N2	ADC	c2240_2257del, p747-753del insS747	0	0	0	0	0	2.08	2.31	1.02
32	F	68	Yes	T2N0	ADC	0	c848G>C, pR283P	0	0	0	0	4.44	3.52	1.75
34	F	59	Yes	T2N2	SCC	0	0	0	0	0	0	5.62	2.21	1.31
36	F	70	No	T2N0	ADC	0	0	0	0	0	0	2.87	2.24	1.21
37	F	72	Yes	T1NO	SCC	0	0	0	0	0	0	2.17	2.00	1.62
38	F	60	Yes	T2N2	ADC	0	c747G>T, pR249S	c34G>T pG12C	0	0	0	2.41	2.48	0.81
39	F	75	No	T2N0	ADC/BAC	L858R	c189G>T, pE62X	0	0	0	0	0.91	2.04	0.92
41	F	56	No	T1NO	ADC/BAC	L858R	0	0	0	0	0	2.58	3.08	1.29
42	F	43	Yes	T2N0	ADC	0	0	c35G>T pG12V	0	0	c580G>T, pD194Y	1.84	2.49	1.01
43	F	72	No	T2N0	ADC	c2310insAGCGTGGAC p770insSVD	0	0	0	0	0	2.11	2.41	0.57
44	F	63	Yes	T2N0	LCC	0	c743G>T, pR248L	0	0	0	0	2.38	10.31	0.74
45	F	60	Yes	T2N0	ADC/BAC	0	c166G>T, pE56X	0	0	0	0	2.73	2.94	1.03
46	F	57	Yes	T2N0	ADC	0	0	0	0	0	0	2.39	2.67	0.70
48	F	49	Yes	T3N0	ADC	0	0	0	0	0	0	2.58	2.98	0.83
49	F	75	No	T2N0	BAC	c2237_2255delinsT, p746-752del insV746	0	0	0	0	0	1.77	2.20	1.58
50	F	42	Yes	T3N0	LCC	0	c814G>T, pV272L	0	0	0	0	6.26	3.13	2.40
51	F	51	Yes	n.d.	SCC	0	0	0	0	0	0	3.52	3.18	1.58
52	F	78	No	T2N2	ADC	0	0	0	0	0	0	1.77	2.13	1.79
53	F	55	Yes	T4NO	ADC/BAC	0	0	c34G>T pG12C	0	0	0	1.79	2.14	2.06
54	F	78	No	T2N0	ADC/BAC	c2239_2251delinsC, p747-751delinsP747	0	0	0	0	0	1.31	2.12	1.90
55	F	72	No	T2N2	ADC/BAC	L858R	COMPLEX INSDEL	0	0	0	0	1.65	1.81	1.72
57	M	85	Yes	T2N0	ADC	0	0	0	0	0	0	1.87	1.94	1.89
58	M	51	Yes	T2N0	ADC	0	c467G>C, pR156P	0	0	0	0	2.79	1.96	1.77
59	M	51	Yes	T2N0	ADC	0	0	c34G>T pG12C	0	0	0	2.10	1.39	1.92
60	M	71	Yes	T1NO	SCC	0	c-15-96del, Fs mutation	0	0	0	0	1.85	1.78	1.88
62	M	48	Yes	T4NO	ADC	0	C783-2A>G, SLPICEMUT	0	0	0	0	2.80	2.26	1.73
64	M	71	Yes	T3N1	ADC	0	c466-483del, FsI162H	0	0	0	0	2.86	2.12	0.69
65	M	49	Yes	T4NO	ADC/BAC	0	C817C>T, pR273C	0	0	0	0	2.33	2.24	2.02
66	M	56	Yes	T2N1	ADC	0	0	0	0	0	0	1.88	1.98	1.82
67	M	56	Yes	n.d.	ADC	0	0	c34G>T pG12C	0	0	0	3.25	2.84	1.93
68	M	58	Yes	T2N0	ADC	0	c818G>T, pR273L	c34G>T pG12C	0	0	0	3.26	1.86	1.44
69	M	72	Yes	T3N0	ADC	0	c610G>T, pE204X	0	0	0	0	3.17	1.55	2.19
70	M	71	Yes	T3N0		0	0	0	0	0	0	2.13	1.74	1.90
71	M	69	Yes	T3N1	ADC	0	C528C>G, pC176W	0	0	0	0	2.68	1.59	1.97
72	M	77	Yes	T3N2	SCC	0	c408DELA, FsQ136H	0	0	0	0	2.67	2.23	1.61
74	M	76	Yes	T2N0	SCC	0	c318G>C, pG105R	0	0	0	0	3.28	3.94	2.11
75	M	59	Yes	T3N2	SCC	0	c797delG, FsG266D	0	0	0	0	4.66	2.74	1.44
76	M	48	Yes	T3N0	ADC	0	0	c35G>T pG12V	0	0	0	2.32	2.92	1.90
78	M	67	Yes	T2N0	SCC	0	0	0	0	0	0	2.42	1.81	1.75
79	M	57	Yes	T2N0	ADC	0	c818G>T, pR273L	c34G>T pG12C	0	0	0	4.27	5.76	1.69
80	M	58	Yes	T1N2	ADC	0	0	c35G>A pG12D	0	0	0	6.36	1.66	1.47
82	M	62	Yes	T2N1	SCC	0	0	0	0	0	0	2.24	1.88	1.84
83	M	51	Yes	T3N0	ADC	0	C139-140DEL, pFsP47G c844C>T, pR282W	c34G>C pG12R	0	0	C521A>G, pM174R	1.87	2.38	1.98
84	M	67	Yes	T4N2	SCC	0	0	0	0	0	0	2.49	2.19	1.98
85	M	56	Yes	T2N0	ADC	0	C577C>G, pH193D	0	0	0	0	2.53	2.56	2.09
86	M	74	Yes	T1NO	SCC	0	0	0	0	0	0	2.19	2.04	1.84
87	M	52	Yes	T2N1	ADC	0	c595G>T, pG199X	0	0	0	c126-149del, pFsmutation	2.38	2.61	1.98
88	M	75	Yes	T4N1	SCC	0	C586C>T, pR196X	0	0	c1633G>A, pE545K	0	2.88	3.89	0.28
89	M	83	Yes	T4N1	SCC	0	c560-lG>T, SPLICEMUT	0	0	0	0	2.37	1.77	1.73
92	M	83	Yes	T2N0	SCC	0	0	0	0	0	0	1.31	0.66	1.86
93	M	50	No	T2N0	ADC	0	n.d.	0	0	0	0	3.81	1.44	1.72
94	M	73	Yes	T3N2	SCC	0	c785G>T, pG262V	0	0	0	0	1.40	1.53	1.31
95	M	64	Yes	T2N1	SCC	0	0	0	0	0	0	2.40	2.28	1.92
96	M	67	Yes	T2N2	SCC	0	c438G>A, pW146X	0	0	0	0	4.16	2.87	1.71
97	M	81	Yes	T4N2	ADC	0	0	0	0	0	0	7.44	2.68	1.64
98	M	57	Yes	T2N0	ADC	0	0	0	0	0	0	2.41	2.16	2.13
99	M	69	Yes	T2N1	SCC	0	C586C>T, pR196X	0	0	0	0	2.85	6.96	1.14
100	M	74	Yes	T3N2	SCC	0	0	0	0	0	0	2.69	2.42	1.73
101	M	51	No	T4N2	ADC	0	0	0	0	0	0	2.44	1.95	1.9
102	M	61	Yes	T2N0	SCC	0	c578A>G, pH193R	0	0	0	0	6.13	1.94	1.89
103	M	52	Yes	T2N0	ADC	0	0	0	0	0	0	2.42	1.34	1.87
104	M	75	Yes	T2N0	ADC	0	0	0	0	0	0	1.38	1.35	2.18
105	M	71	Yes	T2N0	ADC	0	C832DELC, pFsP278L	0	0	0	0	5.13	2.04	1.75
106	M	56	Yes	n.d.	SCC	0	C906DELG, pFsS303A	0	0	0	0	2.66	2.87	1.71
107	M	54	Yes	T1NO	ADC	0	c460G>A, pG154I	c34G>T pG12C	0	0	0	2.50	0.81	0.55
108	M	57	Yes	T3N1	SCC	P753L	C902DELC, pFsP301Q	0	0	0	0	6.91	1.55	1.09
109	M	52	Yes	T2N0	ADC	0	0	c34G>T pG12C	0	0	0	1.48	1.79	1.65
110	M	75	Yes	T1N1	SCC	0	0	0	0	0	0	3.11	1.71	1.97
111	M	65	Yes	T2N2	ADC	0	0	0	0	0	0	1.41	1.58	2.00
112	M	51	Yes	T1NO	ADC	0	0	c34G>T pG12C c35G>T pG12V	0	0	0	2.65	2.73	1.49
134	F	62	No	T2N0	ADC	L858R	c503A>T, pH168L	0	0	0	0	2.00	13.47	2.13
135	F	72	No	T1NO	BAC	c2237_2255delinsT, p746-752del insV746	0	0	0	0	0	1.31	1.16	0.46
143	F	55	Yes	T2N0	ADC/BAC	0	0	c34G>T pG12C	0	0	0	1.99	2.10	1.83
177	F	67	Yes	T2N0	ADC/BAC	0	0	c35G>A pG12D	0	0	0	2.00	1.94	1.71
246	F	44	Yes	T2N2	ADC	0	0	c34G>T pG12C	0	0	0	2.25	2.59	1.78

For quantitative PCR, an inferred copy number ≥ 4 defines an amplification of target and an inferred copy number ≤ 0.6 defines homozygous deletion. Tumors analyzed by Xba1 50000 SNPs array (Affymetrix) are underlined.

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