Gene expression profiles to predict breast cancer outcomes

Abstract

Methods for classifying and for evaluating the prognosis of a subject having breast cancer are provided. The methods include prediction of breast cancer subtype using a supervised algorithm trained to stratify subjects on the basis of breast cancer intrinsic subtype. The prediction model is based on the gene expression profile of the intrinsic genes listed in Table 1. This prediction model can be used to accurately predict the intrinsic subtype of a subject diagnosed with or suspected of having breast cancer. Further provided are compositions and methods for predicting outcome or response to therapy of a subject diagnosed with or suspected of having breast cancer. These methods are useful for guiding or determining treatment options for a subject afflicted with breast cancer. Methods of the invention further include means for evaluating gene expression profiles, including microarrays and quantitative polymerase chain reaction assays, as well as kits comprising reagents for practicing the methods of the invention.

What is claimed is: 
     
         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 to generate a first gene expression profile, 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;   b) 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 GSEI0886 in the National Center for Biotechnology Information Gene Expression Omnibus utilizing a nearest centroid algorithm;   c) contacting said test sample with a composition comprising a plurality of fluorescently labeled nucleic acid probes of at least 500 nucleotides in length to form a plurality of hybridization complexes, wherein each complex within said plurality of complexes comprises at least one probe in the plurality of probes and at least one RNA transcript for at least one of at least 40 intrinsic genes listed in Table 1;   d) detecting the fluorescently labeled nucleic acid probes in the complexes formed in step (c) to determine the RNA expression level of the at least 40 intrinsic genes;   e) generating a second gene expression profile based on said expression of said intrinsic genes in the test sample;   f) comparing the second gene expression profile of the test sample to each of the centroids constructed in step (b) by calculating the distance of the second gene expression profile of the test sample to each of the centroids; and,   g) classifying the test sample as one of the breast cancer intrinsic subtypes having the nearest calculated distance.   
     
     
         2 . The method of  claim 1 , wherein data obtained from the gene expression profiles for the training samples and the gene expression profile for the test sample are processed via normalization methods prior to analysis. 
     
     
         3 . The method of  claim 2 , wherein said processing comprises normalization to a set of housekeeping genes. 
     
     
         4 . The method of  claim 3 , wherein said housekeeping genes are selected from MRPL19, PSMC4, SF3A1, PUM1, ACTB, GAPD, GUSB, RPLPO, and TFRC. 
     
     
         5 . The method of  claim 1 , wherein the expression profile is based on the RNA expression of at least 45 of the intrinsic genes listed in Table 1. 
     
     
         6 . 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 to generate a first gene expression profile, 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;   b) constructing centroids for each of the breast cancer intrinsic subtypes in the training samples utilizing a nearest centroid algorithm;   c) contacting the test sample with a composition comprising a plurality of fluorescently labeled nucleic acid probes of at least 500 nucleotides in length to form a plurality of hybridization complexes, wherein each complex within said plurality of complexes comprises at least one probe in the plurality of probes and at least one RNA transcript for at least one of at least 40 intrinsic genes listed in Table 1;   d) detecting the fluorescently labeled nucleic acid probes in the complexes formed in step (c) to determine the RNA expression level of the at least 40 intrinsic genes;   e) generating a second gene expression profile based on said expression of the intrinsic genes in the test sample;   f) comparing the second gene expression profile of the test sample to each of the centroids constructed in step (b) by calculating the distance of the second gene expression profile of the test sample to each of the centroids; and,   g) classifying the test sample as one of the breast cancer intrinsic subtypes having the nearest calculated distance.