Cryopreserved specimens are incubated with cytokines (e.g., interleukins), growth factors (e.g., sargramostim or filgrastim), and chemotherapeutic agent (e.g., cytarabine, etoposide) and other modulators. Cells are then fixed, permeabilized, and stained with antibodies that recognize extracellular markers (for example, surface phenotypic markers such as clusters of differentiation, drug transporters, and receptors) in conjunction with intracellular activation-state-specific epitopes of designated signaling molecules. Subsequently, cell are analyzed by phospho-flow cytometry (FC) in a random manner (without knowledge of clinical variables and outcomes) to a training set (complete pre-specified FC) versus a testing set. Cells are also analyzed by proteomic assays. Results are then compared with individual patient scores, including predicted clinical outcomes.