Abstract: The present invention relates autoantibody biomarkers, kits, and methods for increasing the accuracy of a cancer or autoimmune screening of a subject suspected of having cancer or an autoimmune condition.

Abstract: Described herein are biosensor microarrays comprising detector polypeptide monolayers substantially free of contaminants. Also provided are methods for generation of such biosensor microarrays by capture of polypeptides by arrays comprising capture moieties and associated sensors.

Abstract: Provided herein are compositions comprising coordinated sets of unique DNA barcodes and methods for using the same for multiplex detection and measurement of multiple target molecules in multiple samples using a single next-generation sequencing reaction. In particular, methods are provided in which unique DNA barcodes linked to affinity reagents are contacted to a sample to bind antigens if present in said sample, and then a PCR-based amplification reaction adds barcoded index sequences that contain universal sequencing adaptors as well as unique barcode sequences and amplifies affinity reagent-bound targets for DNA sequencing.

Abstract: Provided herein are methods and systems for sensitive and multiplexed in situ analysis of samples such as biological samples using cleavable hapten linked targeting agents and cleavable detectably-labeled hapten-binding agents. In particular, provided herein are methods for multiplexed single-cell in situ biomolecule profiling in samples, including fixed or fresh tissues, and also allows the investigation of the different cell compositions and their spatial organizations in intact tissues through consecutive cycles of probe hybridization, fluorescence imaging, and signal removal.

Abstract: Methods and compositions for multiplexed protein-protein interaction profiling (e.g., immunoprofiling), based on nucleic acid tagging of polypeptides (e.g., by RNA display) are described. In some embodiments the described compositions and methods utilize a library of prey polypeptide targets linked to prey RNAs encoding them, and a population of bait polypeptides, e.g., a mixture of antibodies, that bind to one or more of the prey polypeptide targets and are used to isolate and identify the bound prey polypeptide targets by amplification of their associated prey RNAs and sequencing of the corresponding cDNAs. In other embodiments the prey polypeptide targets are linked to DNA Bar Codes, which serve as unique identifiers of the tagged polypeptide.

Abstract: The present invention provides reagents and methods for breast cancer detection.

Abstract: The present disclosure provides for characterization of normal flora and identifying biomarkers in the gut of healthy, neurotypical subjects. Aspect of the disclosure provide for the characterization of the gut microbiome in ADS subjects, characterized by reduced richness and significant loss of the ‘Prevotella-like enterotype’ compared to neurotypical subjects. The relative abundance of genera Prevotella, Coprococcus, Prevotellaceae and Veillonellaceae are significantly lower in autistic children than in neurotypical children. Further, Prevotella, is one of the three main classifiers for the human enterotypes, along with Bacteroides and Ruminococcus. These three core genera are among main contributors in the principle component analysis. ‘Prevotella-like enterotype’ was absent in the autistic group, while neurotypical samples showed an even distribution among the three enterotypes.

Abstract: The present invention provides reagents and methods for breast cancer detection.

Abstract: Cancer patients make antibodies to tumor-derived proteins that are potential biomarkers for early detection. Twenty-eight antigens have been identified as potential biomarkers for the early detection of basal-like breast cancer (Tables 1, 2). Also, a 13-AAb classifier has been developed that differentiate patients with BLBC from healthy controls with 33% sensitivity at 98% specificity (Table 3).

Abstract: Provided herein are methods for multiplexed in situ analysis of biomolecules in a tissue. In particular, provided herein are methods for multiplexed single-cell in situ protein and nucleic acid profiling in fixed or fresh tissues, and also allows the investigation of the different cell compositions and their spatial organizations in intact tissues through consecutive cycles of probe hybridization, fluorescence imaging, and signal removal.

Abstract: Type 1 diabetes (T1D) patients make antibodies to self-proteins that are potential biomarkers for early detection and risk prediction. We have identified seventeen antigens as biomarkers for early diagnosis and risk prediction of T1D, including the antigens MLH1, MTIF3, PPIL2, NUP50, TOX4, FIGN, C9orf142, ZNF280D, HES1, QRFPR, CTRC, SNX6, SYTL4, ELA2A, IGRP, PAX6, and HMGN3.

Abstract: The present disclosure provides for characterization of normal flora and identifying biomarkers in the gut of healthy, neurotypical subjects. Aspect of the disclosure provide for the characterization of the gut microbiome in ADS subjects, characterized by reduced richness and significant loss of the ‘Prevotella-like enterotype’ compared to neurotypical subjects. The relative abundance of genera Prevotella, Coprococcus, Prevotellaceae and Veillonellaceae are significantly lower in autistic children than in neurotypical children. Further, Prevotella, is one of the three main classifiers for the human enterotypes, along with Bacteriodes and Ruminococcus. These three core genera are among main contributors in the principle component analysis. ‘Prevotella-like enterotype’ was absent in the autistic group, while neurotypical samples showed an even distribution among the three enterotypes.

Abstract: Provided herein are methods, compositions, kits, and systems for diagnosing, predicting, and treating gastric cancer for a subject based on the presence and level of antibodies against particular H. pylori proteins in a biological sample obtained from the subject. In particular, provided herein are methods for identifying a subject having increased risk of developing gastric cancer, methods for detecting gastric cancer in a subject, methods for determining an H. pylori antibody signature comprising antibodies, contained in a biological sample from a subject, that specifically bind to immobilized H. pylori antigens, and kits comprising components and instructions for performing the methods of this disclosure.

Abstract: Cancer patients make antibodies to tumor-derived proteins that are potential biomarkers for early detection. Twenty-eight antigens have been identified as potential biomarkers for the early detection of basal-like breast cancer (Tables 1, 2). Also, a 13-AAb classifier has been developed that differentiate patients with BLBC from healthy controls with 33% sensitivity at 98% specificity (Table 3).

Abstract: Provided herein are methods, compositions, kits, and systems for detecting Epstein Barr virus infection (EBV) in gastric cancer (GC) patients. In particular, provided herein are methods, composition, kits, and systems for diagnosing and treating EBV-positive gastric cancer (EBV+ GC) in a biological sample of an individual based on the presence and level of antibodies against particular Epstein Barr virus proteins. EBV+ GC is a distinct subtype of gastric cancer and is associated with unique molecular profiles. Also provided herein are methods for providing more personalized therapy for each of these distinct cancer subtypes and methods for determining an Epstein Barr virus-positive gastric cancer antibody signature, and kits comprising components and protocols for performing the methods of this disclosure.

Abstract: Provided herein are methods for multiplexed in situ analysis of biomolecules in a tissue. In particular, provided herein are methods for multiplexed single-cell in situ protein and nucleic acid profiling in fixed or fresh tissues, that allows the investigation of the different cell compositions and their spatial organizations in intact tissues through consecutive cycles of probe hybridization, fluorescence imaging, and signal removal.

Abstract: Compositions and methods relating to a panel of antigen biomarkers for the early detection of ovarian cancer. The compositions and methods encompass antigen biomarkers coupled to a substrate, with the biomarkers being selected from the group consisting of one or more of ICAM3, CTAG2, p53, STYXL1, PVR, POMC, NUDT11, TRIM39, UHMK1, KSR1, and NXF3.

Abstract: Biomolecule arrays on a substrate are described which contain a plurality of biomolecules, such as coding nucleic acids and/or isolated polypeptides, at a plurality of discrete, isolated, locations. The arrays can be used, for example, in high throughput genomics and proteomics for specific uses including, but not limited molecular diagnostics for early detection, diagnosis, treatment, prognosis, monitoring clinical response, and protein crystallography.

Abstract: Disclosed is a method that combines high throughput and flexible nature of a cell-free protein microarray with the quantitative capability of surface plasmon resonance to detect >400 different protein interactions in <1 hour. A method of detecting interactions between a targeting agent and one or more proteins of interest is disclosed. The method includes producing a set of proteins of interest using a cell-free protein expression system; providing the set of proteins of interest on a protein microarray wherein each spot in the array comprises a protein of interest; contacting the protein microarray with a targeting agent that binds to one or more of the set of proteins of interest; and detecting the binding of the targeting agent to the set of proteins of interest using surface plasmon resonance imaging (SPRi), thereby detecting the targeting agent and one or more proteins of interest in the micro array.

Abstract: Described herein are biosensor microarrays comprising detector polypeptide monolayers substantially free of contaminants. Also provided are methods for generation of such biosensor microarrays by capture of polypeptides by arrays comprising capture moieties and associated sensors.