Abstract: The invention provides methods to noninvasively profile the tumor or the tumor microenvironment using a body fluid sample such as a blood draw. Methods of the disclosure use a liquid biopsy analysis to profile immune cell abundance and diversity in the tumor microenvironment and to predict a patient's response to therapy, particularly to immunotherapy. Specifically, methods of the disclosure are useful to predict immunotherapy toxicity (and treatment toxicity more generally) from cell-free DNA methylation cell state analysis.

Abstract: Among the various aspects of the present disclosure is the provision of treatments, monitoring treatment or progression, or methods for detecting utDNA in a subject having or suspected of having a urinary tract-associated cancer.

Abstract: The present invention provides methods of diagnosing diseases and other pathologies by obtaining fluid from a thoracic duct or right lymphatic duct of a subject and detecting one or more biomarkers indicative of a disease or pathology in the collected fluid.

Abstract: The present invention provides methods for using waste effluent biofluids in cell culture assays as all or part of the cell culture microenvironment. Methods of the invention contemplate that biofluids typically regarded as waste may be used in cell-based assays to achieve a cell culture microenvironment that provides a novel understanding of cellular response.

Abstract: Low-pass whole genome sequencing, as well as targeted hybrid-capture next-generation sequencing, were performed to detect both small mutations and genome-wide copy number alterations to more precisely detect MRD after physician's-choice neoadjuvant chemotherapy. A machine learning model using both cell-free DNA and pre-treatment clinical characteristics is disclosed. With this method, it was possible to significantly predict both progression-free and overall survival.

Abstract: Systems and methods for the selection of a treatment for pancreatic adenocarcinoma (PDAC) in a patient in need based on single-cell RNA sequencing data obtained from a tumor biopsy sample obtained prior to treatment are disclosed. Also disclosed are systems and methods for predicting a clinical outcome of a pancreatic adenocarcinoma (PDAC) patient based on the single-cell RNA sequencing data.

Abstract: The present invention provides methods for using surgical drainage waste fluid as a means for diagnosing disease, assessing disease progression, predicting metastatic disease, assessing cancer metastasis, disease staging, molecular staging, and assessing metastatic disease. During surgery, suction is used to drain fluids such as blood, tissue fluids, and other bodily fluids away from the surgery site. The suction drainage fluid waste, also called drain fluid, is removed from the patient during the surgical procedure. Because surgical drain fluid is typically viewed as something that is not useful, it is disregarded and thrown away during the surgery. Instead, the invention provides that drain fluid, which is mostly lymphatic fluid and interstitial fluid, is diagnostically rich and contains important information for assessing, diagnosing, and treating disease. The methods of the invention use this waste fluid for the valuable data it contains.

Abstract: The present invention relates to novel surgical drains and associated methods and systems. Specifically, the present invention includes a surgical drain with at least two ports. A first port drains lymphatic fluid from a subject for collection and analysis. The second port functions to introduce a therapeutic into the subject.

Abstract: The invention related to diagnostic methods for identifying indicia of cancer in fluid collected from a lymphatic channel.

Abstract: The present invention relates to novel surgical drains and associated methods and systems. Specifically, the present invention includes a surgical drain with at least two ports. A first port drains lymphatic fluid from a subject for collection and analysis. The second port functions to introduce a therapeutic into the subject.

Abstract: The invention related to diagnostic methods for identifying indicia of cancer in fluid collected from a lymphatic channel.

Abstract: The present invention provides methods for testing surgical fluid for biomarkers of disease, including cancer.

Abstract: The present invention provides methods for using surgical drainage waste fluid as a means for diagnosing disease, assessing disease progression, predicting metastatic disease, assessing cancer metastasis, disease staging, molecular staging, and assessing metastatic disease. During surgery, suction is used to drain fluids such as blood, tissue fluids, and other bodily fluids away from the surgery site. The suction drainage fluid waste, also called drain fluid, is removed from the patient during the surgical procedure. Because surgical drain fluid is typically viewed as something that is not useful, it is disregarded and thrown away during the surgery. Instead, the invention provides that drain fluid, which is mostly lymphatic fluid and interstitial fluid, is diagnostically rich and contains important information for assessing, diagnosing, and treating disease. The methods of the invention use this waste fluid for the valuable data it contains.

Abstract: Disclosed here in are methods and kits for identifying a prostate cancer treatment for a subject. The methods include obtaining a fluid sample from the subject, the fluid sample comprising noncellular DNA (ncDNA) from the subject, transforming the ncDNA into a plurality of genomic variations to determine if the ncDNA contains castration-resistant structural variations including at least one of a genomic alteration in AR encoding an androgen receptor and a genomic alteration of an AR enhancer; and identifying the prostate cancer treatment for the subject based on the plurality of genomic variations.

Abstract: A method for detecting at least one surgery-related condition within a surgical site of a subject following a surgery is disclosed. The method includes providing at least one modular nucleic acid assay, obtaining a surgical drainage sample from the surgical site of the subject, isolating a nucleic acid-containing portion from the sample, and detecting and quantifying at least a portion of the amount of nucleic acids within the nucleic acid-containing portion using the at least one nucleic acid assay to produce at least one assay result. At least one assay result may be provided to a practitioner and used to select at least one additional treatment. The modular nucleic acid assays may be used in any combination with a single surgical drainage sample to assess minimal residual cancer, local immune environment, infection, transplant organ rejection, and/or free flap failure.

Abstract: A method for detecting at least one systemic condition and at least one locoproximal condition within a surgical site of a subject following a surgery is disclosed. The method includes obtaining a surgical drainage fluid sample from the surgical site and a blood sample from the subject, isolating analyte-containing portions from the surgical drainage fluid sample and the blood sample, and detecting and quantifying at least a portion of the analytes within the analyte-containing portions to produce at least one assay result, wherein the at least one assay result is indicative of the at least one systemic condition and the at least one locoproximal condition within a surgical site of a subject. At least one assay result may be provided to a practitioner and used to select at least one additional treatment.

Abstract: Among the various aspects of the present disclosure is the provision of methods for detecting cancer in Neurofibromatosis Type 1 (NF1) patients.

Abstract: The present disclosure relates to regulation of macrophage activation by delivering of miRNAs, for example miR-125b or anti-miR-125b, to macrophages. For example, in some embodiments, macrophage activation can be elevated or reduced by administering miR-125b or anti-miR-125b oligonucleotides. Also disclosed are methods for promoting T cell activation and method for treating various disorders such as tumor and autoimmune diseases.

Abstract: The present disclosure relates to regulation of macrophage activation by delivering of miRNAs, for example miR-125b or anti-miR-125b, to macrophages. For example, in some embodiments, macrophage activation can be elevated or reduced by administering miR-125b or anti-miR-125b oligonucleotides. Also disclosed are methods for promoting T cell activation and method for treating various disorders such as tumor and autoimmune diseases.