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) assaying a plurality of training breast cancer samples that have been classified according to breast cancer intrinsic subtype to detect the RNA expression level of at least 40 of the intrinsic genes listed in Table 1 and generating a gene expression profile based on said expression of said intrinsic genes, wherein each of the Luminal A (LumA), Luminal B (LumB), Basal-like (Basal), HER2-enriched (HER2), and Normal-like (Normal) intrinsic subtypes is represented in the plurality of breast cancer samples;   (b) constructing centroids for each of the breast cancer intrinsic subtypes in the training samples by comparing the 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;   (c) contacting said test sample with a plurality of nucleic acid probes arrayed on and attached to a solid substrate to form a plurality of hybridization complexes, wherein each complex within said plurality of complexes comprises at least one nucleic acid probe in the plurality of nucleic acid probes and at least one RNA transcript for at least one of at least 40 intrinsic genes listed in Table 1;   (d) contacting each of said plurality of complexes within at least one fluorescently labeled probe to form a plurality of fluorescently labeled complexes;   (e) detecting the fluorescently labeled complexes formed in step (d) to determine the RNA expression level of the at least 40 intrinsic genes and generating a gene expression profile based on said expression of said intrinsic genes;   (f) comparing the gene expression profile of the test sample to the centroids constructed in step (b);   (g) calculating the distance of the gene expression profile of the test sample to each of the centroids; and,   (h) assigning the test sample to one of the breast cancer intrinsic subtypes based upon the nearest centroid.   
     
     
         2 . A method of predicting response to neoadjuvant therapy in a subject having breast cancer comprising classifying said subject according to the method of  claim 1 , wherein the intrinsic tumor subtype is indicative of response to said therapy. 
     
     
         3 . The method of  claim 2 , wherein the therapy is neoadjuvant endocrine therapy, and the intrinsic subtype is predicted from a sample collected from said subject after initiation of said neoadjuvant endocrine therapy. 
     
     
         4 . The method of  claim 3 , wherein the sample is collected at least one month after initiation of said neoadjuvant endocrine therapy. 
     
     
         5 . 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. 
     
     
         6 . The method of  claim 5 , wherein said processing comprises normalization to a set of housekeeping genes. 
     
     
         7 . The method of  claim 6 , wherein said housekeeping genes are selected from MRPL19, PSMC4, SF3A1, PUM1, ACTB, GAPD, GUSB, RPLPO, and TFRC. 
     
     
         8 . 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. 
     
     
         9 . The method of  claim 1 , wherein the solid substrate is a microarray.