Abstract: The invention provides compositions and methods for identifying autism and autism spectrum disorders in humans. The invention also includes compositions and methods for identifying unique gene expression profiles in children with regressive autism spectrum disorder (ASD) and ileocolitis.

Abstract: A method for estimating a risk for a subject suffering from encapsulating peritoneal sclerosis is provided, including measuring an expression level of at least one microRNA from a sample of the subject, and the microRNA is selected from miR-17, miR-100, miR-155, miR-202, miR-422a, and miR-483; comparing the expression level of the microRNA in the sample to that of a same miRNA of a control, when the expression level of miRNA in the sample is lower than that of the control, the subject is estimated having the risk of encapsulating peritoneal sclerosis. A kit for estimating a risk for a subject suffering from encapsulating peritoneal sclerosis is also provided, including at least one agent for identifying the at least one microRNA as above mentioned from the sample of the subject.

Abstract: Methods are disclosed for identifying antibacterial compounds which inhibit propagation of selected spectrum bacteria, which bacteria use specific tRNA to code for Ala, Met, Ser, or Leu that other bacteria do not use. In one embodiment, the selected spectrum bacteria use GCA to code for Ala, whereas other bacteria use a different codon to code for alanine. The methods involve determining whether putative inhibitors promote or inhibit complex formation between the tRNA and a bacterial ribosome, or between the tRNA and an aminoacyl synthetase. Compounds which promote or inhibit complex formation can disrupt protein production, which bacteria need to propagate. The identified antibacterial compounds can selectively inhibit bacterial propagation. By limiting their effects to the selected spectrum bacteria, these compounds can treat or prevent specific bacterial infections without disrupting the normal bacterial flora, the patients' microbiome, or causing antibacterial resistance.

Abstract: A method for determining a patient's responsiveness to a therapy comprising administration of type I interferon in order to make the decision to treat a patient with type I interferon and use of a SNP rs9984273 (C/T) in IFNAR2 as a marker for determining a patient's responsiveness to said therapy.

Abstract: The present invention relates generally to a method of monitoring pharmacodynamic responses mediated by in vivo administration of glucocorticoids. More specifically, the present invention relates to a method of using a change in gene signature as a pharmacodynamic marker of glucocorticoid exposure.

Abstract: The present disclosure provides a method for diagnosing a head and neck cancer in a subject. The method comprises the steps of: a) measuring an expression level of miR-125b or miR-342 and miR-125b in a sample from the subject; b) measuring an expression level of a normalizing miR in the sample and normalizing the measured expression level of miR-125b or miR-342 and miR-125b using the measured expression level of the normalizing miR; and c) diagnosing a head and neck cancer in a subject having a normalized measured expression level of miR-125b elevated relative to a reference expression level of miR-125b or having a ratio of normalized measured expression level of miR-342 to normalized measured expression level of miR-125b reduced relative to a reference ratio of expression level of miR-342 to expression level of miR-125b. Uses and kits associated with the herein disclosed methods are also disclosed.

Abstract: Provided herein, among other things, is a method of treating a cancer patient without the need for a tissue biopsy. In some embodiments, the method may comprise (a) performing or having performed a sequencing assay on cell-free DNA (cfDNA) from a sample of blood from the patient to determine if the cell-free DNA comprises actionable and/or non-actionable sequence variations in one or more target genes, and (b) treating the patient using the following method: i. administering a therapy that is targeted to an actionable sequence variation if the patient is identified as having the actionable sequence variation, and ii. administering a non-targeted therapy in the absence of any follow-up genetic testing on DNA extracted from a tissue biopsy if one or more non-actionable sequence variations and no actionable sequence variations are identified.

Abstract: This disclosure relates to new assay methods for analysis of RNA, e.g., from circulating tumor cells (CTCs), tumor-specific exosomes, or tumor-specific cell-free RNA, in a subject's blood sample to determine an expression level of one or more lineage markers in the blood sample, wherein the expression level of a specific one or more lineage markers is predictive of progression-free survival and overall survival for a specific anti-cancer treatment regimen in that subject.

Abstract: The invention relates to an in vitro method of determining a subjects risk of liver dysfunction, specifically after partial liver resection, said method comprising the steps of providing a sample from said subject, determining in said sample the expression level of at least one miRNA, selected from the group consisting of miR-151a, miR-192 and miR-122, and comparing these expression level(s) with at least one reference expression level, or identifying the ratios of the expression levels of miR-15 la to miR-192 and/or of miR-122 to miR-151a and comparing said expression level ratios with reference expression level ratios, and classifying the sample from the outcome of the comparison into one of at least two classes, wherein each class is one of the at least two categories “high-risk” and “low-risk”.

Abstract: Methods and compositions disclosed herein generally relate to methods of identifying, validating, and measuring clinically relevant, quantifiable biomarkers of diagnostic and therapeutic responses for blood, vascular, cardiac, and respiratory tract dysfunction, particularly as those responses relate to septic shock in pediatric patients. In particular, the invention relates to identifying two or more biomarkers associated with septic shock in pediatric patients, obtaining a sample from a pediatric patient having at least one indication of septic shock, then quantifying from the sample an amount of two or more of said biomarkers, wherein the level of said biomarker correlates with a predicted outcome.

Abstract: Provided herein are methods and compositions for assessing the quality and potential of stem cells in a sample. Such methods and compositions are useful for helping to ensure the safety and quality of a population of stem cells before it is used in a subject.

Abstract: The present disclosure provides methods for determining whether a subject has sepsis, or is at risk of developing sepsis, and methods of treating the subject based on the determination. Also provided are methods for determining an increased risk of mortality in a subject with sepsis or suspected of having sepsis, and methods of treating the subject based on the determination. Systems useful for the same are also provided.

Abstract: Disclosed herein are methods of increasing the expression rate of epigenetic markers such as ELOVL2, KLF14, and PENK with administration of a therapeutic agent (e.g., vitamin C or its derivatives, analogs, metabolites, prodrugs, or pharmaceutically acceptable salts thereof). Also described herein are methods of modulating the methylation pattern of epigenetic markers such as ELOVL2, KLF14, and PENK with administration of a therapeutic agent (e.g., vitamin C or its derivatives, analogs, metabolites, prodrugs, or pharmaceutically acceptable salts thereof).

Abstract: Provided herein are methods for diagnosing cancer in a subject by determining the gene expression level of one or more genes in extracellular vesicles isolated from samples obtained from a subject.

Abstract: In accordance with the present invention, the single gene SERPINA1 has been identified as a significant predictor of survival in ER+ and ER+/HER2+ breast cancer patients. For example, patients with ER+/FIER2+ breast cancer generally have a worse outcome compared to ER+/FIER2? and ER?/FIER2+ patients. Currently there is no known predictive marker for the treatment C outcome of ER+ and ER+/FIER2+ breast cancers, thus the ability of SERPINA1 to predict the survival of this intrinsic subtype of breast cancer patients is valuable.

Abstract: Biomarkers predictive of responsiveness to integrin beta7 antagonists, including anti-beta7 integrin subunit antibodies, and methods of using such biomarkers are provided. In addition, methods of treating gastrointestinal inflammatory disorders such as inflammatory bowel diseases including ulcerative colitis and Crohn's disease are provided. Also provided are methods of using such predictive biomarkers for the treatment of inflammatory bowel diseases including ulcerative colitis and Crohn's disease.

Abstract: The present invention provides a method of detecting one or more Klebsiella species within a sample from a subject, the method comprising: subjecting DNA and/or RNA from the sample to a PCR amplification reaction using primer pairs targeting species-specific canonical single nucleotide polymorphisms (canSNPs); and analyzing amplification products resulting from the PCR amplification reaction to detect the one or more Klebsiella species. The present invention also provides a kit for detection of one or more Klebsiella species, Klebsiella clonal groups, AMR genes, and/or virulence genes, the kit comprising primer pairs targeting species-specific canSNPs, K. pneumoniae genes M1 and M2, clonal group-specific canSNPs, AMR genes, and/or virulence genes.

Abstract: The present subject matter provides, inter alia, a method of diagnosing invasive ductal cancer or detecting invasive ductal cancer risk in a subject who has ductal carcinoma in situ, a method of treating breast cancer in a subject detected to have invasive ductal cancer or determined to be at risk of invasive ductal cancer, compositions for detecting invasive presence or potential in ductal carcinoma in situ in a subject, and kits including reagents and composition for detecting invasive presence or potential in ductal carcinoma in situ in a subject.

Abstract: Methods and compositions are generally provided for treating metabolic disorders, e.g., obesity. One aspect discloses methods and compositions for obtaining a biological sample from the subject, evaluating the sample for the presence or absence of a genetic indicator, wherein the genetic indicator is selected from a single nucleotide polymorphism and a level of gene expression, and performing a first metabolic procedure if the genetic indicator is present, or performing an alternative second metabolic procedure if the genetic indicator is absent. One aspect discloses methods and compositions for obtaining a sample including deoxyribonucleic acids (DNA) from the subject, evaluating the DNA for an absence or presence of one or more genetic indicators and performing a first metabolic procedure or an alternative second metabolic procedure based on the absence or presence of the genetic indicator(s). Other aspects are also disclosed.

Abstract: The invention provides therapeutic compositions that present an artificial repertoire of mammalian pattern recognition receptor (PRR) agonists, so that the pattern of PRR agonists recapitulates a distinct portion of a PRR agonist signature of a mammalian pathogen. The artificial repertoire of PRR agonists may be formulated together in a therapeutic vehicle for combined presentation to an innate immune cell resident in a target tissue in a mammalian host, and the vehicle adapted to deliver the PRR agonists to the target tissue, so as to modulate an immune response.