The present application relates to detection of changes in the number of nucleotides in short homopolymeric nucleic acid repeats, in particular in short homopolymeric microsatellites, for example for the purpose of diagnosing microsatellite instability (MSI) and/or mismatch repair (MMR-) deficiency in tumors. Accordingly, methods are provided for detecting changes in the number of nucleotides present in short homopolymeric nucleotide repeat sequences as well as kits and cartridges for automated detection of said changes.

The present application relates to detection of changes in the number of nucleotides in short homopolymeric nucleic acid repeats, in particular in short homopolymeric microsatellites, for example for the purpose of diagnosing microsatellite instability (MSI) and/or mismatch repair (MMR-) deficiency in tumors. Accordingly, methods are provided for detecting changes in the number of nucleotides present in short homopolymeric nucleotide repeat sequences as well as kits and cartridges for automated detection of said changes.

Methods and materials are provided for detecting nucleic acid sequence differences including single nucleotide mutations or polymorphisms, one or more nucleotide insertions, and one or more nucleotide deletions in single molecule target members present in a test population of nucleic acid fragments. Heteroduplexes are formed between members of the test nucleic acid population and their corresponding complements provided in a pool of mismatch cleavage probes. Mismatched base pairs in the heteroduplexes are specifically cleaved and cleaved probe fragments are electronically detected to signal the present of the target members in the test population.

Methods and materials are provided for detecting nucleic acid sequence differences including single nucleotide mutations or polymorphisms, one or more nucleotide insertions, and one or more nucleotide deletions in single molecule target members present in a test population of nucleic acid fragments. Heteroduplexes are formed between members of the test nucleic acid population and their corresponding complements provided in a pool of mismatch cleavage probes. Mismatched base pairs in the heteroduplexes are specifically cleaved and cleaved probe fragments are electronically detected to signal the present of the target members in the test population.

Disclosed herein include systems, methods, compositions, and kits for labeling nucleic acid targets in a sample. In some embodiments, nucleic acid targets (e.g., mRNAs) are initially barcoded on the 3′ end and are subsequently barcoded on the 5′ end following a template switching reaction and intermolecular and/or intramolecular hybridization and extension. 5′- and/or 3′-barcoded nucleic acid targets can serve as templates for amplification reactions and/or random priming and extension reactions to generate a sequencing library. The method can comprise generating a full-length sequence of the nucleic acid target by aligning a plurality of sequencing reads. Immune repertoire profiling methods are also provided in some embodiments.

The present invention relates to a promer that has a structure of X-Y-Z and that has a detectable marker attached to both ends or the inside thereof and also that is used as a primer and a probe during real-time detection of nucleic acid or protein, and to a method for real-time detection of nucleic acid, having amplifying a nucleic acid to be detected using the promer, and then measuring the amount of fragments of the promer cleaved, or to a method for real-time detection of protein. The method for detection of nucleic acid or protein according to the present invention uses a small amount of oligos compared to a conventional detection method, does not require a separate probe for real-time detection, and thus can achieve real-time detection of the nucleic acid or protein to be detected in a cost-effective and simple manner. Furthermore, mutations in the Y region can be detected through amplification after cleavage of the Y region of the promer, and multiplex detection of nucleic acids or proteins larger than the number of fluorescent labels attached to the promer is possible. Thus, the present invention can be effectively used for diagnosis of various diseases and for prognostic diagnosis.

The present invention relates to a promer that has a structure of X-Y-Z and that has a detectable marker attached to both ends or the inside thereof and also that is used as a primer and a probe during real-time detection of nucleic acid or protein, and to a method for real-time detection of nucleic acid, having amplifying a nucleic acid to be detected using the promer, and then measuring the amount of fragments of the promer cleaved, or to a method for real-time detection of protein. The method for detection of nucleic acid or protein according to the present invention uses a small amount of oligos compared to a conventional detection method, does not require a separate probe for real-time detection, and thus can achieve real-time detection of the nucleic acid or protein to be detected in a cost-effective and simple manner. Furthermore, mutations in the Y region can be detected through amplification after cleavage of the Y region of the promer, and multiplex detection of nucleic acids or proteins larger than the number of fluorescent labels attached to the promer is possible. Thus, the present invention can be effectively used for diagnosis of various diseases and for prognostic diagnosis.

Diaryl-azo derivatives are efficient fluorescence quenchers as well as nucleic acid duplex-stabilizing agents and are useful in oligonucleotide conjugates and probes. The oligonucleotide-quencher conjugates may be used in detection methods for nucleic acid targets.

Diaryl-azo derivatives are efficient fluorescence quenchers as well as nucleic acid duplex-stabilizing agents and are useful in oligonucleotide conjugates and probes. The oligonucleotide-quencher conjugates may be used in detection methods for nucleic acid targets.

Disclosed herein include systems, methods, kits, and compositions for labeling nuclear target-associated DNA in a cell. Some embodiments provide digestion compositions comprising a DNA digestion enzyme and a binding reagent capable of specifically binding to the nuclear target. Some embodiments provide conjugates comprising a transposome and a binding reagent capable of specifically binding to a nuclear target. The transposome can comprise a transposase (e.g., Tn5 transposase), a first adaptor having a first 5 overhang, and a second adaptor having a second 5 overhang. The methods can comprise contacting a permeabilized cell comprising a nuclear target associated with dsDNA, such as genomic DNA (gDNA), with the compositions provided herein to generate a plurality of nuclear target-associated dsDNA fragments (e.g., nuclear target-associated gDNA fragments) each comprising the one or two single-stranded overhangs.