Methods for assaying enriched nucleic acids

A method comprising:

• (a) providing a biological sample of a subject, and
• (b) assaying nucleic acid molecules derived from RNA expression products of said biological sample to determine RNA expression levels corresponding to genes of said subject wherein said assaying comprises use of capture probes having sequences complementary to said nucleic acid molecules derived from said RNA expression products;
• (c) generating a gene expression profile comprising RNA expression levels for a plurality of genes consisting of (i) 40 to 50 genes selected from ACTR3B, ANLN, BAG1, BCL2, BIRC5, BLVRA, CCNB1, CCNE1, CDC20, CDC6, CDCA1, CDH3, CENPF, CEP55, CXXC5, EGFR, ERBB2, ESR1, EXO1, FGFR4, FOXA1, FOXC1, GPR160, GRB7, HSPC150 (UBE2T), KIF2C, KNTC2, KRT14, KRT17, KRT5, MAPT, MDM2, MELK, MIA, MKI67, MLPH, MMP11, MYBL2, MYC, NAT1, ORC6L, PGR, PHGDH, PTTG1, RRM2, SFRP1, SLC39A6, TMEM45B, TYMS, and UBE2C and (ii) a set of housekeeping genes;
• (d) comparing said gene expression profile to each of a set of centroids, wherein said set of centroids correspond to a plurality of breast cancer intrinsic subtypes;
• and
• (e) assigning said biological sample to a breast cancer intrinsic subtype of said plurality of breast cancer intrinsic subtypes corresponding to a centroid among said set of centroids based at least upon a distance of said gene expression profile to said centroid.