Breast Cancer Table: Recurrent Genomic Alterations Detected by Chromosomal Microarray

Alteration	Relevant Gene(s)	CGC Evidence Level	Subgroup Association(s)
1q gain	unknown	2	Most common copy number alteration, often with 16q loss; all subtypes
8p11.2 amplification	FGFR1, ZNF703	2	METABRIC IntClust6, ER positive
8q24 amplification	MYC	2	METABRIC IntClust9, ER positive
9p24 amplification	JAK2, CD274, PDCD1LG2	2	Enriched in TNBC
10q23.3 loss or LOH	PTEN	2	Enriched in TNBC and in lobular carcinoma
11q13-q14 gain / amplification	CCND1, EMS1, and others	2	METABRIC IntClust2
16q loss / LOH	CDH1	2	METABRIC IntClust2, ER positive
17p loss / LOH	TP53	2	TNBC, basal-like intrinsic subtype
17q12 amplification	ERBB2 (HER2)	1	METABRIC IntClust5, HER2-enriched
17q21 amplification	TOP2A	2	METABRIC IntClust5, HER2-enriched
17q23 amplification (“17q distal amplicon”)	RPS6KB, others	2	METABRIC IntClust1
19q12	CCNE1	2	METABRIC IntClust5; HER2-enriched
20q gain; 20q13 amp	AURKA, GNAS, ZNF217	2	METABRIC IntClust1, ER Positive