Quantification of intrinsic subtype ambiguity in Luminal A breast cancer and its relationship to clinical outcomes

Table 4 Molecular characteristics of Luminal A breast cancers in the METABRIC cohort classified by subtype purity, n = 674

	Distance ratio tertiles
	T1 n = 223	T2 n = 222	T3 n = 229	P, T1 vs T3
HER2 gain^a (%)	7%	9%	17%	0.001
High proliferation (AURKA)	5%	25%	41%	< 0.001
Proliferation Score, PAM50 (mean)	8.99	9.05	9.09	< 0.001
Recurrence Score, PAM50 (mean)	28.60	57.43	75.65	< 0.001
Risk of recurrence, PAM50
Low	52%	10%	3%	< 0.001
Intermediate	38%	28%	8%
High	10%	62%	89%
Mutational load^b (mean)	5.46	5.80	5.44	0.919
MATH score^c (mean)	0.30	0.30	0.33	0.238
Somatic mutations (%)
TP53	7%	10%	20%	< 0.001
PIK3CA	68%	59%	45%	< 0.001
CBFB	14%	7%	5%	0.003

^aHER2 gain or loss determined by HER2_SNP6 DNA microarray
^bNumber of mutations among 172 selected genes sequenced
^cMATH score = mad(vaf)/median(vaf); where mad = median absolute deviation and vaf = variant allele frequency (intratumor heterogeneity based on variation in mutant allele frequency, see Mroz EA, Oral Oncol 2013)

ISSN: 1471-2407