Table 2.

Genomic findings: copy number variants of interest

Gene	Chr	Copy change versus ploidy corrected model (i.e., 2n = 2)	Copy type	TCGA expression percentilea	Fold expression changeb
AKT3	1	+1 (HET)	Gain	21	−5.18
ERBB2	17	+8 (ALOH)	Amplif	98	32.73
GNAS	20	+1 (NLOH)	Gain	2	−1.55
PIK3CA	3	+1 (HET)	Gain	49	−1.40
RB1	13	−1 (DLOH)	Loss	88	1.76
TP53	17	−1 (DLOH)	Loss	21	−1.10
AR	X	+8 (NLOH)	Amplif	100	26.39
BIRC5	17	+5 (BCNA)	Amplif	100	40.87
BRCA2	13	−1 (DLOH)	Loss	94	2.21
CDK12	17	+8 (ALOH)	Amplif	99	5.00
CCNE2	8	+17 (ALOH)	Amplif	100	25.71

The key copy-number events in the tumor genome are listed, along with percentile values and fold changes calculated from the respective RPKMs.

The rows in bold highlight the genes of key interest in the genomic analysis.

AA, amino acid; ALOH, amplification with loss of heterozygosity; Alt, coverage of alternative allele; Alt_RNA, RNA reads mapping alternative allele; Amplif, amplification; BCNA, balanced amplification; Chr, chromosome; COSM, COSMIC Mutation ID (numeric ID listed; query as COSMxxxxx); DLOH, deletion with loss of heterozygosity; GoF, gain of function; HET, heterozygous; LoF, loss of function; NLOH, neutral with loss of heterozygosity; Ref, coverage of reference allele; Ref_RNA, RNA reads mapping reference allele; SNV, single-nucleotide variant; VUS, variant of unknown significance.

–, No RNA-seq reads mapped to this gene.

^aCalculated against TCGA Breast Cancer Compendium.

^bCalculated against Illumina BodyMap 2.0.