Abstract: A method of detecting the efficacy of a cytotoxic treatment for cancer in a patient is disclosed that includes comparing first and second tumor signals detected from first and second biofluids samples using ultra-low-pass whole genome sequencing (ULP-WGS) to obtain a tumor signal increase, and determining an efficacy of the cytotoxic treatment based on the tumor signal increase. The first and second biofluid samples are obtained from the patient prior to and after initiation of the cytotoxic treatment, respectively. A tumor signal increase exceeding a threshold level is indicative of the efficacy of the cytotoxic treatment.

Abstract: Methods and systems for detecting cell states in a biological sample are disclosed. Methods and systems for predicting a therapeutic response, a severe immune-related adverse event (irAE), a symptomatic irAE, and an irAE grade of a subject to be administered an immunotherapy treatment based on cell states detected from a single biological sample from the subject are also disclosed.

Abstract: Methods are disclosed for predicting a likelihood of developing a severe immune-related adverse event (irAE) associated with the administration of an immunotherapy in a melanoma patient based on abundances of activated CD4 memory T cells and/or diversities of T cell receptors (TCR) within a peripheral blood sample obtained from the patient.

Abstract: Among the various aspects of the present disclosure is the provision of compositions and methods for treating cancer and sensitizing cancer or tumors to treatments. An aspect of the present disclosure provides for a method of preventing treatment resistance in non-HPV-associated cancer comprising administering a pharmaceutical composition comprising HPV-associated DNA (e.g., HPV-associated exosomes). Another aspect of the present disclosure provides for a method of increasing response to cancer treatment, optionally, surgery, radiation therapy, and chemotherapy in a subject having, suspected of having, being treated for, having previously been treated for, or diagnosed with cancer comprising administering a pharmaceutical composition comprising HPV-associated DNA (e.g., HPV-associated exosomes).

Abstract: The present disclosure encompasses methods to detect. quantify. and/or analyze various surgical drain fluid (SDF) exosomal biomarkers and the uses thereof to inform diagnosis of diseases. select patients for further diagnostic testing, and guide treatment decisions.

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

Abstract: Among the various aspects of the present disclosure is the provision of methods and systems for detecting cell states in a biological sample. An aspect of the present disclosure provides for a method of determining cell type or cell states. In some embodiments, the method comprises providing or having been provided a sample comprising DNA or RNA and generating a methylation profile for the DNA or RNA in the sample or providing or having been provided a methylation profile of the DNA or RNA in the sample.

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

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 invention provides methods for using effluent obtained from medical procedures resulting in stomas or percutaneous drains or ports to assess diagnostic biomarkers indicative of disease. Identified biomarkers are used to inform surgical success and/or to assess and monitor efficacy of treatment.

Abstract: A surgical drainage system is disclosed that includes an assay device operatively coupled to a surgical drainage tube. The drainage tube is configured for implantation within a surgical bed of a subject to drain surgical drain fluid out of the surgical bed. The assay device is configured to detect at least one analyte within the drainage fluid. The at least one analyte is indicative of a surgical bed condition.

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