Table II.

Regions of DNA copy number aberrations significantly associated with tumor size changes after NAC.

Cytoband	Start position	Candidate genes	Frequencies of DNA copy number aberrations			Average percentage of tumor volume reduction according to aberration			Raw p-value
			Loss	Normal	Gain	Loss	Normal	Gain
8q11.22	52402874	PXDNL	0	51	12	-	79.7	59.2	0.0248
8q12.3	65039478		0	50	13	-	79.4	56.3	0.0192
8q13.1	66247345		0	53	7	-	79.6	53.6	0.0286
8q13.2	69455939	C8orf34	0	54	9	-	79.6	48.2	0.0033
8q13.3	73392374		0	50	13	-	79.0	60.2	0.0479
8q21.11	76752408		0	49	8	-	79.8	48.2	0.0077
8q21.12	79843613	IL7	0	50	8	-	81.0	55.1	0.0183
8q24.23	137759202		0	32	18	-	84.2	62.0	0.0131
10q26.3	131211273	MGMT	0	53	10	-	72.0	93.2	0.0411
17p12	12773358	ELAC2	11	52	0	58.9	79.8	-	0.0222
17p12	12800643	ELAC2	10	52	0	59.3	79.8	-	0.0318
17q21.32	43988517	HOXB3, HOXB4, HOXB5, HOXB6, HOXB7, HOXB8, HOXB9	0	54	9	-	78.9	58.4	0.0381
17q21.32	44002448	HOXB3, HOXB4, HOXB5, HOXB6, HOXB7, HOXB8, HOXB9	0	54	9	-	78.9	58.4	0.0381
17q21.33	44810305	PHB	0	54	9	-	78.9	58.4	0.0381
17q21.33	44816025	PHB, NGF	0	54	9	-	78.9	58.4	0.0381
17q21.33	45062570	SPOP, SLC35B1	0	51	9	-	81.7	55.0	0.0035
17q21.33	45565237	PPP1R9B, SGCA, HILS1, COL1A1	0	53	10	-	79.9	56.2	0.0115
17q21.33	45661414	TMEM92	0	53	10	-	79.9	56.2	0.0115
17q21.33	45890171	CHAD, RSAD1, MYCBPAP, EPN3, SPATA20, CACNA1G	0	53	10	-	79.9	56.2	0.0115
17q21.33	45965729	EPN3, SPATA20, CACNA1G, ABCC3	0	53	10	-	79.9	56.2	0.0115
17q21.33	46222836	WFIKKN2, TOB1	0	52	11	-	79.6	59.7	0.0294
17q21.33	46255459	WFIKKN2, TOB,	0	52	11	-	79.6	59.7	0.0294
17q21.33	46490057	SPAG9, NME1	0	52	11	-	79.6	59.7	0.0294
17q21.33	46509890	SPAG9, NME1, MBTD1	0	52	11	-	79.6	59.7	0.0294