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: The present invention concerns the use of biomarkers for acute lymphoblastic leukemia (ALL) to prognose or evaluate a patient with ALL who is Ph+. Methods and compositions are provided that concern these ALL biomarkers. In specific embodiments, methods for determining whether an ALL patient should be treated with standard chemotherapy are provided.

Abstract: Disclosed are methods for diagnosing cancer or dysplasia in a sample of tissue, involving testing cells of the sample to assess whether miR-196a expression in cells of the sample is greater than a reference, wherein a greater expression of miR-196a in cells of the sample compared to the reference is indicative of cancer or dysplasia. The cancer or dysplasia may be esophageal cancer or esophageal dysplasia. Also disclosed are method for diagnosing cancer or dysplasia in a sample of tissue, comprising testing cells of the sample to assess whether the expression of ANXA1, KRT5, SPRR2C, or S100A9 in cells of the sample is reduced compared to a reference control, wherein said reduced expression in cells of the sample compared to the reference control is indicative of cancer or dysplasia. Also disclosed are kits and methods involving kits for the diagnosis of cancer or dysplasia.

Abstract: The present invention generally regards gene expression profiling of esophageal cancers, including localized esophageal cancers. In particular, gene expression for a particular group of genes identifies individuals that are either going to be responsive to cancer therapy, for example chemotherapy and/or radiation, or that are not going to be responsive to cancer therapy. Exemplary genes having such expression profiles include, for example, PERP, S100A2, and SPRR3.