Abstract: Methods are provided for treating lung cancer, and more particularly for treating pulmonary adenocarcinoma in a canine subject. The method may comprise assaying a biological sample from the canine subject, such as a tumor sample or a plasma sample, for a mutation in the HER2 gene. The mutation may include HER2 V659E, HER2 A664T, or HER2 K676E. If one or more of the mutations is present in the biological sample, the methods further include treating the canine subject by administering a therapeutically effective amount of an inhibitor of HER2. For example, a HER2 V659E may indicate increase sensitivity to a HER2 inhibitor. The HER2 inhibitor may include a small molecule HER2 inhibitor, such as trastuzumab, neratinib, lapatinib, erlotinib, and pertuzumab.

Abstract: The invention provides a tagged sequencing library and methods for tagging low abundance target sequences and generating a sequencing library for detecting low abundance target sequences.

Abstract: Methods are provided to classify and identify features in mass spectral data using neural network algorithms. A convolutional neural network (CNN) was trained to identify amino acids from an unknown protein sample. The CNN was trained using known peptide sequences to predict amino acid presence, diversity, and frequency, peptide length, subsequences of amino acids classified by features include aliphatic/aromatic, hydrophobic/hydrophilic, positive/negative charge, and combinations thereof. Mass spectra data of a sample unknown to the trained CNN was discretized into a one-dimensional vector and input into the CNN. The CNN models can potentially be integrated to determine the complete peptide sequence from a spectrum, thereby improving the yield of identifiable protein sequences from mass spec analysis.

Abstract: Methods, kits, and oligonucleotides used in the detection of the coronavirus strain, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), are disclosed. In some aspects, the oligonucleotides are primers or probes used in the described methods or kits. The oligonucleotide consists of 40 or less nucleotides and has a nucleotide sequence that consists essentially of, or is a variant of, the nucleotide sequence of: SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, or SEQ ID NO:10.

Abstract: The present disclosure includes a multiplexed peptide assay to generate an epitope-resolved view of antibody reactivity across all human coronaviruses (CoVs). PepSeq accurately classifies SARS-CoV-2 exposure status and reveals epitopes across the Spike and Nucleocapsid proteins. Two of these represent recurrent reactivities to conserved, functionally-important sites in the S2 subunit of Spike, regions that we show are also targeted for the endemic CoVs in pre-pandemic controls. At one of these sites, we demonstrate that the SARS-CoV-2 response strongly and recurrently cross-reacts with the endemic virus hCoV-OC43. The disclosed epitope-resolved analysis reveals new CoV targets for the development of diagnostics, vaccines and therapeutics, including a site that may have broad neutralizing potential.

Abstract: Various embodiments provide compositions and methods for detecting cancers containing an NRG1 fusion event and treating a patient with a therapeutic agent that is targeted to the NRG1 fusion. Exemplary compositions for treating cancers containing the NRG1 fusion may comprise therapeutic agents inhibiting Epidermal Growth Factor Receptor and/or ERBB2 such as cetuximab, panitumumab, Sym004, MM-151, mAb 806, mAb 528, MEHD794A, gefitinib, erlotinib, lapatinib, afatinib, PD153035, AG1478, trastuzumab, and pertuzumab. In some embodiments, the therapeutic agent may be a combination of trastuzumab, and pertuzumab.

Abstract: The invention provides a method for validating patient-specific oligos using spike-in sequences.

Abstract: Methods are provided for diagnosing and treating idiopathic pulmonary fibrosis (IPF) in humans and canine idiopathic pulmonary fibrosis (CIPF) in canines. The methods include detecting expression of genes found to indicate a predisposition, a risk, or a presence of IPF: SDHAF2, CPSF7, and MUC5B. One variant, rs22669389, corresponding to position 54992254 on canine (CanFam3.1) chromosome 18, was identified at a suggestive level of significance to be associated with CIPF. The methods further comprise performing whole genome sequencing (WGS) of DNA in the sample to confirm detection of a variant indicating a predisposition, a risk, or a diagnosis of IPF or CIPF. The method further includes treating a subject for IPF or CIPF, based on the diagnosis of IPF or CIPF.

Abstract: This invention is in the field of medicinal chemistry. In particular, the invention relates to a new class of small-molecules having a benzimidazole or imidazopyridine structure which function as inhibitors of DYRK1A protein, and their use as therapeutics for the treatment of Alzheimer's disease, Down syndrome, glioblastoma, autoimmune diseases, inflammatory disorders (e.g., airway inflammation), and other diseases.

Abstract: Embodiments of the invention provide a method of detecting one or more strains of Klebsiella pneumoniae. The method may include forming a plurality of mixtures for nucleic amplification. The method can include amplification of specific sequences within the K. pneumonia genome that can provide definitive information to distinguish between one or more types or strains of K. pneumonia.

Abstract: Methods are provided for detecting non-human candidate DNA within a plasma sample from a human subject. A method of diagnosing and characterizing a bacterial infection may include the steps of obtaining a plasma sample from a subject suspected of having a bacterial infection, extracting cell-free DNA (cfDNA) from the plasma sample, performing whole genome sequencing on the cfDNA to obtain sequencing data, aligning the sequencing data with a human genome to identify human DNA and non-human DNA, removing the human DNA from the sequencing data, assigning the non-human DNA to a candidate pathogen DNA, selecting a subset of the non-human DNA based on a fragment length of the non-human DNA, and determining the presence of the candidate pathogen DNA within the subset of the non-human DNA.

Abstract: This invention is in the field of medicinal chemistry. In particular, the invention relates to a new class of small-molecules having a benzimidazole or imidazopyridine structure which function as inhibitors of DYRK1A protein, and their use as therapeutics for the treatment of Alzheimer's disease, Down syndrome, glioblastoma, autoimmune diseases, inflammatory disorders (e.g., airway inflammation), and other diseases.

Abstract: Methods are provided to classify and identify features in mass spectral data using neural network algorithms. A convolutional neural network (CNN) was trained to identify amino acids from an unknown protein sample. The CNN was trained using known peptide sequences to predict amino acid presence, diversity, and frequency, peptide length, subsequences of amino acids classified by features include aliphatic/aromatic, hydrophobic/hydrophilic, positive/negative charge, and combinations thereof. Mass spectra data of a sample unknown to the trained CNN was discretized into a one-dimensional vector and input into the CNN. The CNN models can potentially be integrated to determine the complete peptide sequence from a spectrum, thereby improving the yield of identifiable protein sequences from mass spec analysis.

Abstract: A method of detecting Enterovirus D68 is provided. The method may include adding to a mixture containing the sample from the subject, (a) a first forward primer comprising SEQ ID NO: 1, (b) a second forward primer comprising SEQ ID NO: 2, (c) a third forward primer comprising SEQ ID NO: 3, (d) a first reverse primer comprising SEQ ID NO: 4, and (e) a second reverse primer comprising SEQ ID NO: 5, subjecting the mixture to conditions that allow nucleic acid amplification, and detecting the presence or absence of Enterovirus D68 by analyzing the nucleic acid amplification products. The forward primers may include a first universal tail sequence and reverse primers may include a second universal tail sequence. The nucleic acid amplification products may be sequenced using next-generation sequencing.

Abstract: The disclosure includes methods of identifying a dog at risk of developing a an autoimmune disease or condition, for example a hypothyroid disease or condition, comprising testing whether the dog exhibits one or more selected single nucleotide polymorphisms (SNPs), together with diagnostic kits for carrying out such methods, methods of treatment or prophylaxis of such autoimmune disease or condition, e.g., comprising administering an effective amount of tea extract to a dog in need thereof, and a canine diet or supplement comprising tea extract, useful for treatment of prophylaxis of such autoimmune disease or condition, or for maintenance of thyroid health in a dog.

Abstract: Embodiments of the invention provide a method of genotyping a C. gattii sample, which can include forming a plurality of mixtures for nucleic amplification. The method can include amplification of specific sequences within the C. gattii genome that can provide definitive genotype information to distinguish between one or more types or subtypes of C. gattii.

Abstract: Methods of treating, and for selecting a chemotherapy regimen for treatment of cancer in a patient (FIG. 9). For example, a patient genetic sample from a bilary cancer such as cholangiocarcinoma is analyzed for a mutation in ERRFII and a chemotherapeutic agent is selected as a result of the analysis. If a mutation in ERRFII is present, treatment with an inhibitor of Epidermal Growth Factor Receptor (EGFR) is shown to have inhibitory effects on tumor growth. In this manner, the chemotherapy regimen is targeted to a given mutation in a patient's cancer.

Abstract: Methods are provided to detect and treat a fungal infection. The method may include the steps of obtaining a sample from a subject suspected of having a fungal infection, detecting an Uncharacterized Fungal Protein (CIMG_09001/CPSG_01366) in the sample, and determining the presence on the fungal infection if the Uncharacterized Fungal Protein is detected.

Abstract: The disclosure includes methods of identifying a dog at risk of developing a an autoimmune disease or condition, for example a hypothyroid disease or condition, comprising testing whether the dog exhibits one or more selected single nucleotide polymorphisms (SNPs), together with diagnostic kits for carrying out such methods, methods of treatment or prophylaxis of such autoimmune disease or condition, e.g., comprising administering an effective amount of tea extract to a dog in need thereof, and a canine diet or supplement comprising tea extract, useful for treatment of prophylaxis of such autoimmune disease or condition, or for maintenance of thyroid health in a dog.

Abstract: Embodiments of the invention provide a method of detecting one or more strains of Klebsiella pneumoniae. The method may include forming a plurality of mixtures for nucleic amplification. The method can include amplification of specific sequences within the K. pneumonia genome that can provide definitive information to distinguish between one or more types or strains of K. pneumonia.