Abstract: Contemplated systems and methods employ chimeric reference sequences that include a plurality of viral genome sequences to identify/quantify integration and co-amplification events. Most typically, the viral genome sequences are organized in the chimeric reference sequences as single chromosomes and the chimeric reference sequences are in BAM format.

Abstract: Systems and methods are presented that allow for selection of tumor neoepitopes that are filtered for various criteria. In particularly contemplated aspects, filtering includes a step in which the mutation leading to the neoepitope is ascertained as being located in a cancer driver gene.

Abstract: Contemplated compositions and methods are directed to cancer neoepitopes and uses of such neoepitopes, especially to generate synthetic antibodies against neoepitopes that may then be employed in the manufacture of a therapeutic agent. Preferred therapeutic agents will comprise a synthetic antibody against a neoepitope, and most preferably in combination with a cellular or non-cellular component for use as a diagnostic or therapeutic agent.

Abstract: Systems and methods are presented that provide for improved NK cell function. In preferred aspects, NK-92 cells express recombinant er/LSP-IL-15 to so render the NK-92 cells independent of exogenous cytokines and to provide extracellular immune stimulation.

Abstract: Pharmaceutical compositions comprising an IL-15 agonist or derivative thereof, such as nogapendekin alfa-inbakicept (NAI), are provided herein for enhancing immunity and for inhibiting viral infections. The IL-15 agonist or derivative thereof may be used to increase proliferative capacity and/or cytotoxicity of various immune competent cells, and especially NK and cytotoxic T cells in healthy individuals. The IL-15 agonist or derivative thereof may be used alone or in combination with one or more other therapeutic agents, such as in conjunction with a vaccine.

Abstract: Cancer immunotherapy is enhanced by co-expression of cancer associated or tumor-specific (neo)epitopes with co-stimulatory molecules and/or other immune activators. Where desired, treatment may be enhanced by administration of a immune checkpoint inhibitor.

Abstract: Systems and methods are presented that provide for improved NK cell function. In preferred aspects, NK-92 cells express recombinant er/LSP-IL-15 to so render the NK-92 cells independent of exogenous cytokines and to provide extracellular immune stimulation.

Abstract: Systems and methods are presented that allow for selection of tumor neoepitopes that are filtered for various criteria. In particularly contemplated aspects, filtering includes a step in which the mutation leading to the neoepitope is ascertained as being located in a cancer driver gene.

Abstract: Contemplated systems and methods employ chimeric reference sequences that include a plurality of viral genome sequences to identify/quantify integration and co-amplification events. Most typically, the viral genome sequences are organized in the chimeric reference sequences as single chromosomes and the chimeric reference sequences are in BAM format.

Abstract: Techniques are provided for determining classifications based on WSIs. A varied-size feature map is generated for each training WSI by generating a grid of patches for the training WSI, segmenting the training WSI into tissue and non-tissue areas, and converting patches comprising the tissue areas into tensors. Bounding boxes are generated based on the patches comprising tissue areas and segmented into feature map patches. A fixed-size feature map is generated based on a subset of the feature map patches. A classifier model is trained to process fixed-size feature maps corresponding to the training WSIs such that, for each fixed-size feature map, the classifier model is operable to assign a WSI-level tissue or cell morphology classification or regression based on the tensors. A classification engine is configured to use the trained classifier model to determine a WSI-level tissue or cell morphology classification or regression for a test WSI.

Abstract: Single cell analysis from tumor tissue comprising tumor cells and immune competent cells and from peripheral white blood cells are used to obtain an immunome signature, and to gain information about the TCR repertoire. Such information is then employed to generate recombinant and patient specific therapeutic cells, including T cells (including T effector memory, T memory stem, naïve T, T central memory, CD8+ T, and CD4+ T cells), NK cells (cord-blood derived or PBMC derived or NK92), NKT cells, and dendritic cells.

Abstract: Systems and methods are presented that provide for improved NK cell function. In preferred aspects, NK-92 cells express recombinant er/LSP-IL-15 to so render the NK-92 cells independent of exogenous cytokines and to provide extracellular immune stimulation.

Abstract: Methods for targeting a tumor antigen for immunotherapy based on HLA allele type and the mutations present in the tumor antigen are presented. A patient's HLA allele type and a tumor antigen derived from a mutation in cancer driver gene can be matched with a majority allele type having a minimum affinity to the same tumor antigen or with those of a plurality of patients with a history of cancer treatment. Upon matching, a cancer treatment against the tumor antigen can be selected and administered to the patient to achieve a desired effect.

Abstract: Methods for targeting a tumor antigen for immunotherapy based on HLA allele type and the mutations present in the tumor antigen are presented. A patient's HLA allele type and a tumor antigen derived from a mutation in cancer driver gene can be matched with a majority allele type having a minimum affinity to the same tumor antigen or with those of a plurality of patients with a history of cancer treatment. Upon matching, a cancer treatment against the tumor antigen can be selected and administered to the patient to achieve a desired effect.

Abstract: Contemplated treatments and methods produce substantially increased quantities of memory T-cells and a persistent immune response by subcutaneous and/or subdermal co-administration of (1) a vector comprising a recombinant nucleic acid that encodes a cancer associated epitope, a cancer specific epitope, and/or a neoepitope, (2) an immune stimulating cytokine, and (3) a checkpoint inhibitor. Most typically, the co-administration is performed at substantially the same location, preferably within 1-21 days from each other, and the vector is an adenoviral expression vector, for example, included in a viral particle such as an AdV5 virus with a deletion of the E2b gene.

Abstract: A method for detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in a sample is provided. The method includes contacting at least two pairs of primers with a complementary deoxyribonucleic acid (cDNA) derived from SARS-CoV-2 ribonucleic acid (RNA) in the sample; amplifying a portion of the cDNA by quantitative loop-mediated isothermal amplification (qLAMP) in the presence of a marker that exhibits a detectable signal as the cDNA is amplified, wherein the portion of the cDNA comprises a portion of non-structural protein 3 (Nsp3)-gene cDNA, a portion of S-gene cDNA, a portion of a 3? end of N-gene cDNA, or combinations thereof; periodically measuring the detectable signal during the isothermally amplifying; and determining at least one of an amplification threshold breach or an amplification rate corresponding to levels of the detectable signal versus amplification time. Treatment methods, reaction mixtures, and assay kits are also provided.

Abstract: RNA from a biological fluid is stabilized during isolation and/or storage using DNA. In especially preferred aspects, the RNA is cfRNA and/or ctRNA, and the biological fluid is blood.

Abstract: Contemplated treatments and methods produce substantially increased quantities of memory T-cells and a persistent immune response by subcutaneous and/or subdermal co-administration of (1) a vector comprising a recombinant nucleic acid that encodes a cancer associated epitope, a cancer specific epitope, and/or a neoepitope, (2) an immune stimulating cytokine, and (3) a checkpoint inhibitor. Most typically, the co-administration is performed at substantially the same location, preferably within 1-21 days from each other, and the vector is an adenoviral expression vector, for example, included in a viral particle such as an AdV5 virus with a deletion of the E2b gene.

Abstract: Detection of under-expression of selected genes in NK cells is used to confirm a hypoxic tumor microenvironment that is ordinarily suppressive with respect to ADCC and cytotoxic cell killing of NK cells. Most notably, while hypoxia is known to upregulate HIF-1? and genes under the control of HIF-1?, hypoxia in a tumor microenvironment led to under-expression of selected genes, including HIF-1?. Thus, gene expression analysis of certain genes on NK cells can be used to detect conditions in a tumor that would indicate use of haNK cells.

Abstract: Cancer is treated using coordinated treatment regimens that uses various compounds and compositions that drive a tumor from the escape phase of cancer immunoediting to the elimination and equilibrium phase of cancer immunoediting.