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: 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: Embodiments of the invention include methods of identifying microorganisms and/or diagnosing infections in subjects cause by microorganisms. Embodiments of the invention may also include further characterizing (e.g., determining the presence of one or more antibiotic resistance markers) the microorganisms and determining a strain identity of the microorganisms.

Abstract: Embodiments of the invention provide a method of treating cancer, the method comprising providing a subject having cancer cells, and contacting the cancer cells with a therapeutically effective amount of a G2/M checkpoint inhibitor. Embodiments of the invention also provide a method of treating cancer in a subject, the method comprising the steps of: (a) receiving a sample of the cancer cells from the subject; (b) determining if at least a portion of the sample of the cancer cells is LKB1 deficient; and (c) contacting the cancer cells with a therapeutically effective amount of a G2/M checkpoint inhibitor. Embodiments of the invention also provide a method of treating cancer in a subject, the method comprising contacting the cancer cells with a therapeutically effective amount of a Wee1 inhibitor and a therapeutically effective amount of a second pharmaceutical composition.

Abstract: The invention provides microRNA markers and methods for determining the risk a subject has for developing mild traumatic brain injuries (mTBI). In some aspects, the methods further include determine the fitness of a subject for participating in an activity with increased chances of receiving a head impact. Certain embodiments are directed to kits designed for these purposes.

Abstract: The present technology provides a method of determining whether a subject with cancer is likely to experience one or more metastases. The method may include determining a methylation level of at least one gene selected from the group consisting of BEND4, CDH4, C1QL3, ERG, GP5, GSC, HTR1B, LMX1B, MCF2L2, PENK, REC8, RUNX3, PAX5, PCDHIO, SP8, SP9, STAC2, ULBP1, UNC13A, VIM, VWC2 in a subject-derived sample and then comparing the subject-derived methylation level determined in step a) with a normal control level obtained from a normal sample. Thereafter, the method may include correlating an increase of said subject-derived methylation level as compared to the normal control level to a diagnosis the subject as likely to experience one or more metastases.

Abstract: Embodiments of the invention provide a method of treating cancer, the method comprising providing a subject having cancer cells, and contacting the cancer cells with a therapeutically effective amount of a G2/M checkpoint inhibitor. Embodiments of the invention also provide a method of treating cancer in a subject, the method comprising the steps of: (a) receiving a sample of the cancer cells from the subject; (b) determining if at least a portion of the sample of the cancer cells is LKB1 deficient; and (c) contacting the cancer cells with a therapeutically effective amount of a G2/M checkpoint inhibitor. Embodiments of the invention also provide a method of treating cancer in a subject, the method comprising contacting the cancer cells with a therapeutically effective amount of a Wee1 inhibitor and a therapeutically effective amount of a second pharmaceutical composition.

Abstract: The present invention relates to a method of creating a biomarker profile, the method comprising the steps of: obtaining a sample of biofluid from a subject, wherein the sample is stored on a sample collection apparatus; removing the sample from the sample collection apparatus; extracting nucleic acids from the sample; sequencing the extracted nucleic acids to generate sequence data; and analyzing the sequence data using a two-step analytical methodology to create the biomarker profile. The present invention athletic performance in a subject.

Abstract: The invention provides biomarkers and methods for determining the risk of a subject for developing mild traumatic brain injuries (mTBI). In some aspects, the methods of the invention also determine the fitness of a subject for participating in an activity with increased chances of receiving a head impact. Some embodiments of the invention are directed to kits for determining the risk of a subject for developing mTBI or the fitness of a subject for participating in an activity with increased chances of receiving a head impact.

Abstract: The present invention provides method of classifying a subject into a necrotizing meningoencephalitis (NME) disease risk group. The method may include assessing the presence of one or more marker (e.g., SNPs or risk loci) in a sample from the subject. For example, detection of the presence of one or more markers that are associated with an increased risk of NME can indicate that the subject should be classified into a risk group.

Abstract: The present invention comprises methods of treating an infection using a pharmaceutical composition comprising an active ingredient selected from Table 1. In some aspects, the infection can be caused by one or more pathogens, including fungal pathogens. For example, the infection may be Valley Fever.

Abstract: The present invention provides a method of diagnosing a breast cancer central nervous system (CNS) metastasis in a subject, comprising determining the expression level of at least one biomarker in a subject-derived brain or breast tissue comparing the subject-derived expression level with a normal control level obtained from normal brain or breast cells; and correlating an increase or decrease of the subject-derived expression level as compared to the normal control level to a diagnosis of a breast cancer CNS metastasis. The present invention also provides a method for the treatment of a breast cancer CNS metastasis in a subject comprising administering to the subject an inhibitor of an overexpressed gene associated with CNS metastasis.

Abstract: The present invention provides a method of determining integrity and/or quantity of cell free DNA (cfDNA) in a bio logical sample comprising amplifying target sequences with at least a first primer/probe set and at least a second primer probe/set, amplifying the target sequences of differing lengths, and monitoring for detection of the labels of the oligonucleotide probes, and determining the integrity and/or quantity of the cfDNA based on the level of detection of the label of the oligonucleotide probe from the first primer/probe set compared to the level detection of the label of the oligonucleotide probe from the second primer/probe set. The present invention also provides methods for generating a library with the cfDNA for sequencing and analysis.

Abstract: Among other aspects provided herein is a method describing the use of Single Nucleotide Polymorphism (SNP) genotyping microarrays to resolve whether genetic material (such as genomic DNA) derived from a particular individual is present in a genetic material mixture (such as a complex genomic DNA mixture) is disclosed. Furthermore, it is demonstrated that the identification of the presence of genetic material (such as genomic DNA) of specific individuals within a series of complex genomic mixtures is possible.

Abstract: The technology encompasses methods of treating a patient with cancer, such as glioblastoma. The methods may include the administration of one or more pharmaceutical compositions that are capable of inhibiting TROY to treat the patient with cancer.

Abstract: Methods for the production of lipids and biofuels with a culture of Candidatus Microthrix spp. grown on a medium such as wastewater or sewage sludge are provided. The Candidatus Microthrix spp. may be cultured with additional microorganisms that contribute to the accumulation of lipids from the growth medium such as Zoog!oea spp., Rhizobacter spp., Blautia spp., Hydrolatea spp., ODI genera incertae sedis. Further discloses are transformed organisms comprising genes isolated from Candidatus Microthrix parvicella, as well as methods and processes for producing lipids, fatty acids, or biofuels in vitro using the protein products of the isolated genes.

Abstract: Some embodiments of the invention include a method of preparing a sample for sequencing that includes receiving a sample and amplifying at least one marker within the sample. In some embodiments, amplification of the first marker may include mixing the sample with a first oligonucleotide that comprises a first universal tail sequence and a second oligonucleotide that comprises a second universal tail sequence. In some aspects of the invention, the first universal tail sequence and the second universal tail sequence are different sequences.

Abstract: Embodiments of the invention provide methods of creating clinical models for different forms of metastatic cancer. The methods may include obtaining samples from subjects with metastatic cancer, determining an allelic status of one or more markers in the samples (e.g., creating a molecular profile of the subject's cancer), and using model organisms with subject-derived xenografts for treatment selection.

Abstract: Embodiments of the invention provide a method of treating cancer, the method comprising providing a subject having cancer cells, and contacting the cancer cells with a therapeutically effective amount of a G2/M checkpoint inhibitor. Embodiments of the invention also provide a method of treating cancer in a subject, the method comprising the steps of: (a) receiving a sample of the cancer cells from the subject; (b) determining if at least a portion of the sample of the cancer cells is LKB1 deficient; and (c) contacting the cancer cells with a therapeutically effective amount of a G2/M checkpoint inhibitor. Embodiments of the invention also provide a method of treating cancer in a subject, the method comprising contacting the cancer cells with a therapeutically effective amount of a Wee1 inhibitor and a therapeutically effective amount of a second pharmaceutical composition.

Abstract: The present invention provides a method of detecting a heteroresistant population of a pathogen in a sample, the method comprising: a) providing a sample comprising a population of a pathogen; b) extracting nucleic acids from the sample; c) amplifying a target locus of the genome of the pathogen in the extracted nucleic acids, wherein the target locus comprises at least one minor variant associated with drug resistance in the pathogen; d) consecutively sequencing both overlapping nucleic acid strands from a single DNA molecule amplified from the target locus on a Next Generation Sequencing (NGS) platform; e) applying an alignment algorithm to sequencing data from the overlapping nucleic acid strands; and f) performing an analysis of the aligned sequencing data to detect the at least one minor variant and heteroresistant population of the pathogen.