Cell-type-specific patterns of gene expression

摘要

Among the methods, compositions, combinations and kits provided herein are those for determining gene expression levels in one or more cell types in heterogeneous cell samples, for identifying genes differentially expressed in different cell types, and for detecting a cell type in a sample from a subject. Also provided herein are methods, compositions, combinations and kits for determining gene expression levels in cells corresponding to phenotypes, and for identifying a phenotype of a subject by detecting differentially expressed genes.

主权项

1. A method of determining gene expression levels in prostate tissue samples from subjects diagnosed as having prostate cancer, comprising the steps of:
(a) assaying the relative content of malignant and non-malignant cells within each of two or more heterogeneous prostate tissue samples from subjects diagnosed as having prostate cancer, wherein at least two of the samples do not contain the same relative content of malignant and non-malignant cells, and wherein the assaying is done without physically separating the malignant from the non-malignant cells in the sample; (b) measuring the overall level of each of a plurality of different RNA expression analytes extracted from each prostate tissue sample without physically separating the malignant from the non-malignant cells in the sample, such that each measured level corresponds to the combined expression of an RNA expression analyte in malignant and nonmalignant cells; (c) determining a linear or non-linear regression relationship between the relative content of malignant and non-malignant cells in each sample and the measured overall levels of the plurality of different RNA analytes in each sample to provide a quantitative relationship therebetween; (d) using the regression relationship determined in step (c) to calculate the level of each of the plurality of different RNA expression analytes in the malignant cells and in the non-malignant cells separately, wherein the calculated levels of analytes correspond to the gene expression levels; and (e) outputting to a display information regarding the calculated levels of analytes.