Patent ID: 9631239
Date: 2017-04-25
CPC Classifications: C12Q,G16B

Claim:
1. A method of classifying a breast cancer intrinsic subtype in a test sample comprising: (a) detecting the RNA expression level of at least 40 of the intrinsic genes listed in Table 1 in a plurality of training breast cancer samples that have been classified according to breast cancer intrinsic subtype; (b) generating a first gene expression profile based on said expression of said intrinsic genes, wherein each of the Luminal A (LumA), Luminal B (LumB), Basal-like (Basal), and HER2-enriched (HER2) intrinsic subtypes is represented in the plurality of training breast cancer samples; (c) constructing centroids for each of the breast cancer intrinsic subtypes in the training samples by comparing the first gene expression profile of the training samples to the gene expression data deposited as accession number GSE10886 in the National Center for Biotechnology Information Gene Expression Omnibus utilizing a nearest centroid algorithm; (d) performing a reverse-transcriptase polymerase chain reaction (RT-PCR) with primers specific for at least 40 intrinsic genes listed in Table 1 from a test sample obtained from a subject to generate a complementary DNA molecule (cDNA) for each of the at least 40 intrinsic genes; (e) detecting the cDNA generated in step (d) to determine the expression level of the at least 40 intrinsic genes; (f) generating a second gene expression profile based on said expression of said intrinsic genes in the test sample; (g) comparing the second gene expression profile of the test sample to the each of the centroids constructed in step (c) by calculating the distance of the second gene expression profile to each of the centroids; and (h) assigning the test sample to one of the breast cancer intrinsic subtypes having the nearest calculated distance.