Breast cancer PAM50 signature: correlation and concordance between RNA-Seq and digital multiplexed gene expression technologies in a triple negative breast cancer series

Table 2 Risk of Recurrence (ROR) for the potential discordant sample calls

	Sample ID	ROR	ROR-Group	ROR-PS	ROR + PS-Group	Discordance
NanoString nCounter	HCSC-0027	51.10	med	43.42	med	NO
	HLPR-002	43.57	med	23.44	med	YES
	HUGM-0022	51.60	med	42.28	med	NO
	HUGM-0029	73.51	high	68.98	high	NO
	HUGM-0047	81.24	high	72.48	high	NO
	INEN-0017	66.66	high	55.051	high	NO
	INEN-0021	72.50	high	65.40	high	NO
RNA-Seq	HCSC-0027	35.25	med	33.04	med	NO
	HLPR-002	16.87	low	10.68	low	YES
	HUGM-0022	40.68	med	32.44	med	NO
	HUGM-0029	75.02	high	69.59	high	NO
	HUGM-0047	73.73	high	69.58	high	NO
	INEN-0017	62.68	high	52.98	high	NO
	INEN-0021	66.98	high	64.52	high	NO

These measures are extracted from the PAM50 assay outcome (Additional file 1: Table S1). Two measures regarding the risk of recurrence are reported: ROR, which takes into account only the subtype calling; and ROR + PS, which considers also the Proliferation Score. The latter is defined as the mean expression level for the proliferation genes: CCNB1, UBE2C, BIRC5, KNTC2, CDC20, PTTG1, RRM2, MKI67, TYMS, CEP55 and CDCA1. The ROR(+PS)-Group columns gives a categorical classification in terms of risk: high, medium (med) and low

ISSN: 1471-2164