Methods for diagnosing and monitoring the status of systemic lupus erythematosus

A method for predicting flare in a patient diagnosed with SLE comprising:

• analyzing expression in a sample from the patient to produce a gene expression profile
• wherein a first portion of the analysis comprises using the expression of at least one gene selected from each of at least two of the clusters 1 through 15 of Table 1 and at least one statistical method to produce a patient gene expression profile, and
• a second portion of the analysis comprises using expression of at least two interferon response genes and a linear algorithm to classify the patient as having type 1 SLE or type 2 SLE, wherein expression of the two or more interferon response genes correlates with the expression of IFI27 from about 0.5 to about 1.0 and from about −0.5 to about −1.0 as calculated using a Pearson correlation;
• and
• predicting flare by comparing the patient gene expression profile to at least one reference profile.