Genome profiling of ERBB2-amplified breast cancers

BMC Cancer

Table 1 Genes altered by CNA with a frequency significantly different in ER+ and ER- ERBB2-amplified tumors.

ER status of ERBB2-amplified tumors	Targeted by gene CNA	Altered genes	Location	CNV, Type#
ER-	gain	*GDPD4*	11q13.5
		*PAK1*
		*CLNS1A*
ER+	gain	*ADAM5P*	8p11.23	*Variation_1197, CNV*
		*ADAM3A*		*Variation_1779, CNV*
		TRPS1*	8q23.3	*Variation_42116, InDel*
		*BC040336*
		*EIF3H*
		*AL713790*	8q24.11
		*SLC30A8*
		*MED30*
		*SAMD12*	8q24.12	*Variation_3145, CNV*
		*FAM91A1*	8q24.13
		*C8orf54*
		*C8orf78*
		*BC015129*
		*TMEM65*		*Variation_52365, CNV*
		*CR933665*
		*RNF139*		*Variation_28765, InDel*
		*TATDN1*
		*MTSS1*		Variation_43549, CNV
		*LOC157381*
		*SQLE*		*Variation_34021, InDel*
		*KIAA0196*
		*NSMCE2*		*Variation_41128, Indel*
		*TRIB1*
		*BC038572*	8q24.21
		*FAM84B*		*Variation_37296, Inversion*
		PVT1*		*Variation_8615, CNV*
		*BC009730*
	amplification	*C8ORFK23*	8q24.13
		*LOC650095*
		*LOC90110*	17q12	*Variation_5006, CNV*
		*FBXL20*		*CNVVariation_5006, CNV*
		*CASC3*	17q21.1
	gain or amplification	*ZNF572*	8q24.13
		*AK093407*
	loss or deletion	*SAMD11*	1p36.33	*Variation_30362, CNV*
		*AGRN*		*Variation_2294, CNV*
		*GNB1*		*Variation_3276, CNV*
		*AK128532*	1p36.32
		*RNF212*	4p16.3	*Variation_30190, CNV*
		*B4GALNT4*	11p15.5	*Variation_29880, CNV*

*TRPS1 and PVT1 gene expression was in proportion to their CNA
#The information about the presence of CNV and the type of genomic variations (CNV, InDel, inversion...) was extracted from hg17 and hg18.

ISSN: 1471-2407