Methods for identifying, diagnosing, and predicting survival of lymphomas

A method for predicting survival in a diffuse large B cell lymphoma (DLBCL) subject comprising the steps of:

• a) isolating gene expression product from a biopsy sample from a subject;
• b) obtaining gene expression data for a set of genes in said biopsy sample, wherein the gene expression data includes expression levels of BMP6, proliferation gene expression signature genes, germinal center B cell gene expression signature genes, MHC class II gene expression signature genes, and lymph node gene expression signature genes;
• c) determining an average gene expression level of genes in the proliferation gene expression signature to obtain a proliferation gene expression signature value;
• d) determining an average gene expression level of genes in the germinal center B cell gene expression signature to obtain a germinal center B cell gene expression signature value;
• e) determining an average gene expression level of genes in the MHC class II gene expression signature to obtain an MHC class II gene expression signature value;
• f) determining an average gene expression level of genes in the lymph node gene expression signature to obtain a lymph node gene expression signature value;
• g) measuring the expression level of BMP6 to obtain a BMP6 expression value;
• h) determining a survival predictor score corresponding to:
• [0.241*(proliferation gene expression signature value)]+[0.310*(BMP6 expression value)]−[0.290*(germinal center B cell gene expression signature value)]−[0.311*(MHC class II gene expression signature value)]−[0.249*(lymph node gene expression signature value)], wherein a higher survival predictor score is associated with worse survival;
• i) analyzing said sample for a gain or amplification in the 3p11-p12 region of chromosome 3, wherein a gain or amplification in said region is associated with worse survival.