Identification of novel candidate target genes, including EPHB3, MASP1 and SSTat 3q26.2–q29 in squamous cell carcinoma of the lung

Table 3 BAC clones with significant frequency differences between SCC and AC subtypes of NSCLC

BAC clone	Regions	Gene contained in clones	% of gain in SCCs^‡	% of gain in AC^†	p-value*
Gains ^¶
BAC13_I04	2q14.2		55	7	0.046
BAC215_M07	3q26.2	EVI1	77	29	0.007
BAC28_H10	3q26.2	MDS1	45	7	0.034
BAC127_C12	3q26.32	PIK3CA, KCNMB3	50	14	0.050
BAC78_P09	3q26.2	LOC389174	45	7	0.034
BAC97_L20	3q27.1	EPHB3	32	0	0.039
BAC187_G13	3q27.3	MASP1	45	7	0.034
BAC195_F06	3q27.3	SST	32	0	0.039
BAC62_G09	3q28		64	7	0.002
BAC29_O18	3q28	TP73L	45	7	0.034
BAC74_E06	3q28		50	7	0.015
BAC143_F11	3q28	FGF12	45	7	0.034
BAC144_N20	3q28	LPP	48	0	0.032
BAC95_M19	3q29	OPA1	55	7	0.046
BAC96_C05	3q29	KIAA0226, LOC220729, LOC440996, LOC440997, LOC440998	45	7	0.034
BAC42_D19	7q22.1	TRRAP	0	29	0.023
BAC141_P01	7q22.1	ZKSCAN1, ZNF38, ZNF3	0	29	0.023
BAC118_C23	12p13.2	CDKN1B, DKFZP434F0318	50	0	0.003
BAC26_P09	12p13.32	TSPAN9, LOC399986, LOC441627	59	7	0.001
BAC159_B18	12p13.33	LOC440123, SLC6A12, SLC6A13	45	0	0.002
BAC179_J19	12p13.33	SLC6A12, SLC6A13	32	0	0.003
BAC18_B14	19p13.3	SCHC2, C19orf19, MADCAM1, C19orf20, CDC34, GZMM, BSG	41	0	0.008
Losses ^§
BAC83_J18	3p26.2	LOC440943	36	0	0.018
BAC229_D19	3p26.3	CCR2, CCRL2, APOD	45	0	0.005
BAC57_A15	15q22.2	RORA	5	36	0.033
BAC175_C05	15q25.2	DNM1DN11-6, LOC388160, LOC440300, LOC388152, LOC161527, LOC440301, LOC159170	5	36	0.033
BAC169_L10	16p13.11		55	7	0.046
BAC130_G23	17p11.2		64	36	0.039

Abbreviations: ^†AC, Adenocarcinoma; ^‡SCC, Squamous cell carcinoma; * P values from Fisher's exact test on categorized log2 ratio values. ^¶Alterations were defined by log2 ratio thresholds of 0.25 for copy number gain. Using this threshold, we generated a frequency table. ^§Alterations were defined by log2 ratio thresholds of – 0.25 for copy number loss. Using this threshold, we generated a frequency table.

ISSN: 1471-2407