Abstract: Disclosed herein are methods, non-transitory computer readable media, systems, and kits for performing an intra-individual analysis for determining presence or absence of a health condition in an individual. Specifically, the intra-individual analysis involves combining sequence information from target nucleic acids with sequence information from reference nucleic acids obtained from the individual. The target nucleic acids include signatures that may be informative for determining presence or absence of the health condition and the reference nucleic acids include baseline biological signatures of the individual. By combining sequence information from the target nucleic acids and the reference nucleic acids, the resulting generated signal is more informative for determining presence or absence of the health condition in comparison to sequence information of the target nucleic acids alone.

Abstract: The invention relates generally to immortalized libraries, also referred to as archived reference samples, and their use in diagnostic methods.

Abstract: Disclosed herein are methods, non-transitory computer readable media, systems, and kits for performing a multiple tiered analysis for identifying individuals with a health condition for monitoring, treating, and/or enrolling the individuals in a clinical trial. Specifically, the multiple tiered analysis involves a first screen, which eliminates a large proportion of individuals who are identified as not at risk for a health condition, and a subsequent second analysis which detects presence of a health condition in the remaining individuals. The second analysis includes an intra-individual analysis, which involves combining sequence information from target nucleic acids and reference nucleic acids obtained from the individual. The target nucleic acids include signatures that may be informative for determining presence or absence of the health condition and the reference nucleic acids include baseline biological signatures of the individual.

Abstract: Disclosed herein are methods, non-transitory computer readable media, systems, and kits for performing a multiple tiered analysis for identifying individuals with a health condition for monitoring, treating, and/or enrolling the individuals in a clinical trial. Specifically, the multiple tiered analysis involves a first screen, which eliminates a large proportion of individuals who are identified as not at risk for a health condition, and a subsequent second analysis which detects presence of a health condition in the remaining individuals. The second analysis includes an intra-individual analysis, which involves combining sequence information from target nucleic acids and reference nucleic acids obtained from the individual. The target nucleic acids include signatures that may be informative for determining presence or absence of the health condition and the reference nucleic acids include baseline biological signatures of the individual.

Abstract: The disclosure provides methods and compositions that employ gene editing systems to enable cells to express guide RNAs. Gene editing systems specifically target fusions in tumor DNA to introduce a coding sequence that is expressed by tumor cells as a guide RNA that targets known repetitive elements in the human genome in tumor cells. The CRISPR-like systems are expressed in the tumor cells and cleave the tumor DNA at the known repetitive elements thereby inducing tumor cell death.

Abstract: The disclosure provides methods and compositions that employ gene editing for the treatment of cancer. Gene editing systems specifically target tumor DNA to introduce an expression cassette with a coding sequence that is expressed by tumor cells as a neoantigen that mark the tumor cells for cell death.

Abstract: The invention provides methods of selectively protecting nucleic acids of interest in a sample from damage that occurs during preparative procedures. The methods include binding proteins to ends and to one or more internal regions of a segment of the nucleic acid of interest so that damage to exposed regions of the segment does not lead to degradation of the entire segment.

Abstract: The invention provides methods of detecting genetic features that only require a single successful interrogation. A sample that includes nucleic acid may have a first set of adaptors ligated to free ends in a manner that is not target specific. Then, a reagent such as a Cas endonuclease is used to cut nucleic acid molecules that contain a target of interest, leaving a cut end. A second adaptor type is attached to the cut end(s) and provides a primer binding site. A primer bound to the second adaptor site is extended through the target of interest and through a strand of the first adaptor. This extension yields a template polynucleotide that includes the primer, the copy of the target, and the copy of the first adaptor.

Abstract: Disclosed herein are methods, non-transitory computer readable media, systems, and kits for performing a multiple tiered analysis for identifying individuals with a health condition for monitoring, treating, and/or enrolling the individuals in a clinical trial. Specifically, the multiple tiered analysis involves a first screen, which eliminates a large proportion of individuals who are identified as not at risk for a health condition, and a subsequent second analysis which detects presence of a health condition in the remaining individuals. The second analysis includes an intra-individual analysis, which involves combining sequence information from target nucleic acids and reference nucleic acids obtained from the individual. The target nucleic acids include signatures that may be informative for determining presence or absence of the health condition and the reference nucleic acids include baseline biological signatures of the individual.

Abstract: The present disclosure describes a method of treating a sample comprising cells with a process of partial lysing. Cells are exposed to a process such as bead beating that lyses some cells in the mixture. The process generates a resultant sample mixture that is suitable for both cell morphology screening and genetic screening.

Abstract: Disclosed herein are methods, non-transitory computer readable media, systems, and kits for performing a multiple tiered analysis for identifying individuals with a health condition for monitoring, treating, and/or enrolling the individuals in a clinical trial. Specifically, the multiple tiered analysis involves a first screen, which eliminates a large proportion of individuals who are identified as not at risk for a health condition, and a subsequent second analysis which detects presence of a health condition in the remaining individuals. The second analysis includes an intra-individual analysis, which involves combining sequence information from target nucleic acids and reference nucleic acids obtained from the individual. The target nucleic acids include signatures that may be informative for determining presence or absence of the health condition and the reference nucleic acids include baseline biological signatures of the individual.

Abstract: Provided herein are methods of detecting nucleic acids. The nucleic acid of interest may be detected by using Cas endonuclease to degrade substantially all nucleic acid in a sample except for the nucleic acid of interest, leaving the nucleic acid of interest isolated and amenable to detection. In related methods, Cas endonuclease complexes are used to protect the nucleic acid of interest while unprotected nucleic acid is digested, e.g., by exonuclease, after which the isolated nucleic acid of interest is detected.

Abstract: The invention provides methods for diagnosing viral infections and determining a status of the infection, including transmissibility of the infection.

Abstract: The invention provided methods and devices for performing sequential, regulated multiplex reactions in a single tube without the addition or removal of contents from the tube.

Abstract: This disclosure provides methods and compositions for treating cancer. The invention relies on genome-editing tools to selectively target and kill cancer cells while minimizing deleterious effects to the subject. The genome-editing tools are designed to target and act on specific sequences identified in a genome of a tumor cell and absent from a genome of a healthy cell from the same patient. This specificity allows the genome-editing tool to target and kill cancer cells at the edge or border of a surgical site where a tumor was removed while leaving healthy cells unharmed.

Abstract: The disclosure provides methods and compositions that employ gene editing systems to enable cells to express guide RNAs. Gene editing systems specifically target fusions in tumor DNA to introduce a coding sequence that is expressed by tumor cells as a guide RNA that targets known repetitive elements in the human genome in tumor cells. The CRISPR-like systems are expressed in the tumor cells and cleave the tumor DNA at the known repetitive elements thereby inducing tumor cell death.

Abstract: Methods of detecting a mutation comprise introducing a Cas endonuclease complex to a nucleic acid sample, wherein guide RNA in the Cas endonuclease complex bind to a location of a suspected mutation. Unbound nucleic acid in the sample is degraded or separated from the bound complex, and presence of the mutation is detected by detecting bound Cas endonuclease complex. The Cas endonuclease complex comprises a Cas endonuclease and guide RNA. The guide RNA is designed to bind to the location of the suspected mutation. In some instances, the Cas endonuclease complex comprises a detectable label, such as a fluorescent label. Therefore, detecting presence of the mutation comprises detecting presence of the label. An exonuclease may be used to degrade or digest unbound nucleic acid and isolate the mutation. Methods include further analysis of the isolated mutation.

Abstract: The disclosure provides methods and compositions that employ gene editing for the treatment of cancer. Gene editing systems specifically target tumor DNA to introduce an expression cassette with a coding sequence that is expressed by tumor cells as a neoantigen that mark the tumor cells for cell death.

Abstract: The invention provides methods of detecting cancer in a subject. The methods of the invention entail monitoring accumulation of passenger fusions over time in a subject. An increase in the level of passenger fusions over time is indicative of the presence of cancer in the subject.

Abstract: The invention provides methods for determining the mutation burden of a tumor by assaying tumor DNA that is representative of genetic loci that are themselves representative of genetics of the tumor. The assayed tumor DNA may be itself agnostic as to loci, so long as it is representative of loci that are representative of tumor mutation burden. The invention provides for assays in which the tumor DNA being sequenced or tested can be something other than, and possibly less than, a full panel of oncogenes that is expected to stand for a tumor's mutational load.