Abstract: Provided herein are methods of preparing cell-free DNA (cfDNA) for sequencing such that variant allele frequencies are maintained. Also provided are sequencing libraries prepared according to such methods. In addition, methods are provided for analyzing sequencing reads to determine variant allele frequencies. These methods may be used for diagnosing and/or evaluating cancer patients.

Abstract: Methods are provided for treating cancer patients who have elevated expression of FOXC2. In certain aspects, patients having elevated FOXC2 are treated with an anti-cancer therapy in conjunction with a p38 MAPK inhibitor. Methods of identifying cancer patients to be treated with p38 MAPK inhibitors are also provided. Further provided herein are methods for treating and/or preventing breast cancer metastasis by the administration of a p38 MAPK inhibitor. In certain aspects, patients are treated with an anti-cancer therapy in conjunction with a p38 MAPK inhibitor. In addition, methods are provided for the treatment of BCR-ABL positive cancers, such as acute lymphoblastic leukemia, by the administration of a p38 MAPK inhibitor and/or a glucocorticoid inhibitor in combination with a tyrosine kinase inhibitor.