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: The present invention relates to compounds of formulas III and V that are useful as pharmaceutical agents, particularly as autophagy inhibitors.

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.

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 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 LKB 1 deficient; and (c) contacting the cancer cells with a therapeutically effective amount of a G2/M checkpoint inhibitor.

Abstract: The invention 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: The present invention is directed to a method of detecting a genomic rearrangement in a nucleic acid sample with Long Insert Whole Genome Sequencing (LI-WGS). The method may include obtaining a nucleic acid sample and then fragmenting the nucleic acid sample (e.g., via sonication). In particular, the fragmenting may result in the production of a plurality of inserts. Thereafter, the method comprises purifying the plurality of inserts using magnetic beads and then amplifying the purified plurality of inserts. In addition, the method further comprises sequencing the purified and amplified plurality of inserts. In some aspects, the plurality of inserts have a length of between about 800 and about 1,100 base pairs.

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 present invention relates to processes for characterizing and screening for the existence or predisposition to X-linked disorders associated with changes in X-chromosome inactivation. The present invention also relates to processes of reducing a disease phenotype associated with an X-linked disorder in a female subject.

Abstract: Methods of tests that assess the expression of DPC4 (SMAD4) to identify subjects with pancreatic cancer that are likely or unlikely to respond to treatment with BTK inhibitors; methods of treating subjects based on identification of the subjects as likely to respond to treatment with BTK inhibitors; therapeutic targets for cancers, particularly cancers with inactivated DPC4 gene or protein; methods of screening of new therapeutic agents using the target; pharmaceutical composition comprising BTK inhibitors, such as PCI-32765 or derivatives thereof, for cancer treatment; and kits that facilitate the performance of the methods are disclosed.

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: The invention relates to the identification of genetic signatures and expression profiles that are a part of the Base Excision Repair (BER) pathway, a major DNA repair pathway that modifies base lesions. In one embodiment, the present invention provides a method of determining responsiveness of treatment by BER inhibitors for malignant glioma by determining the presence of a low level of expression of Apex 1, a low level of expression of Apex 2, and a high level of expression of MPG.

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.