Systematic assessment of prognostic gene signatures for breast cancer shows distinct influence of time and ER status

Table 1 Summary of gene signatures in the study and the annotation mapping coverage

Signature	Description	Validation	Training platform	Coverage (%)
Intrinsic [1, 21]	Intrinsic subtype	Ref. [2, 3]	Stanford cDNA array	410/549 (75%)
PAM50 [9]	PAM50 subtype	Ref. [9]	Agilent Human oligo array	42/50 (84%)
70gene [4]	MammaPrint	Ref. [5, 22–24]	Agilent 25 k Human oligo array	46/70 (65.7%)
76gene [6]	Veridex	Ref. [25, 26]	Affymetrix u133a GeneChip	76/76 (100%)
Hypoxia [30]	Hypoxia signature	Ref. [15, 30]	Stanford cDNA array	117/253 (46.2%)^a
WR [28]	Wound response	Ref. [15, 29]	Stanford cDNA array	298/380 (78.4%)
GGI [7]	Genomic Grade Index	Ref. [17, 27]	Affymetrix u133a GeneChip	128/128 (100%)
RS [12]	OncoType DX Recurrent Score	Ref. [12, 31]	qRT-PCR	21/21 (100%)
EP [32]	EndoPredict risk score	Ref. [32, 40]	qRT-PCR	11/11 (100%)

^aThe original study [30] reported 168 UniGene IDs annotated from 253 clones in the Hypoxia signature, of which 117 clones mapped to the Affy probes (46.2%). Considering these mapped clones represented 116 unique Unigene clusters (under UniGene Build Number 222), the mapping coverage for this signature on the studied data is higher than the percentage reported here.

ISSN: 1471-2407