A method for detecting different analytes includes mixing different analytes with sensing probes, wherein at least some of the sensing probes are specific to respective ones of the analytes. The analytes respectively are captured by the sensing probes that are specific to those analytes. Fluorophores respectively are coupled to sensing probes that captured respective analytes. The sensing probes are mixed with beads, wherein the beads are specific to respective ones of the sensing probes, and wherein the beads include different codes identifying the analytes to which those sensing probes are specific. The sensing probes respectively are coupled to beads that are specific to those sensing probes. The beads are identified that are coupled to the sensing probes that captured analytes using at least fluorescence from the fluorophores coupled to those sensing probes. The analytes that are captured are identified.

The invention discloses a method and a system to detect a target nucleic acid sequence in a sample using padlock probe-based rolling circle amplification and nuclease protection. Padlock probe-based rolling circle amplification and nuclease protection may be used in combination with other detection assays to detect target nucleic acid sequences in a sample.

The invention discloses a method and a system to detect a target nucleic acid sequence in a sample using padlock probe-based rolling circle amplification and nuclease protection. Padlock probe-based rolling circle amplification and nuclease protection may be used in combination with other detection assays to detect target nucleic acid sequences in a sample.

The present disclosure relates to a mutant cell-free DNA isolation kit and a mutant cell-free DNA analysis method using a CRISPR-Cas system and an exonuclease.

The present disclosure relates to a mutant cell-free DNA isolation kit and a mutant cell-free DNA analysis method using a CRISPR-Cas system and an exonuclease.

The present invention relates to a method for the highly specific, targeted capture of regions of human genomes and transcriptomes from the blood, i.e. from cell free circulating DNA, exosomes, microRNA, circulating tumor cells, or total blood cells, to allow for the highly sensitive detection of mutation, expression, copy number, translocation, alternative splicing, and methylation changes using combined nuclease, ligation, polymerase, and massively parallel sequencing reactions. The method generates a collection of different circular chimeric single-stranded nucleic acid constructs, suitable for sequencing on multiple platforms. In some embodiments, each construct of the collection comprised a first single stranded segment of original genomic DNA from a host organism and a second single stranded synthetic nucleic acid segment that is linked to the first single stranded segment and comprises a nucleotide sequence that is exogenous to the host organism. These chimeric constructs are suitable for identifying and enumerating mutations, copy changes, translocations, and methylation changes. In other embodiments, input mRNA, lncRNA, or miRNA is used to generate circular DNA products that reflect the presence and copy number of specific mRNA's, lncRNA's splice-site variants, translocations, and miRNA.

The present invention relates to a method for the highly specific, targeted capture of regions of human genomes and transcriptomes from the blood, i.e. from cell free circulating DNA, exosomes, microRNA, circulating tumor cells, or total blood cells, to allow for the highly sensitive detection of mutation, expression, copy number, translocation, alternative splicing, and methylation changes using combined nuclease, ligation, polymerase, and massively parallel sequencing reactions. The method generates a collection of different circular chimeric single-stranded nucleic acid constructs, suitable for sequencing on multiple platforms. In some embodiments, each construct of the collection comprised a first single stranded segment of original genomic DNA from a host organism and a second single stranded synthetic nucleic acid segment that is linked to the first single stranded segment and comprises a nucleotide sequence that is exogenous to the host organism. These chimeric constructs are suitable for identifying and enumerating mutations, copy changes, translocations, and methylation changes. In other embodiments, input mRNA, lncRNA, or miRNA is used to generate circular DNA products that reflect the presence and copy number of specific mRNA's, lncRNA's splice-site variants, translocations, and miRNA.

The present invention relates to a method of isolating a nucleic acid target region from a population of nucleic acid molecules, said method comprising the steps of a) contacting said population of nucleic acid molecules with a Class 2 Type V Cas protein-gRNA complex, wherein the gRNA comprises a guide segment that is complementary to a first site adjacent to said target region, thereby forming a Class 2 Type V Cas protein-gRNA-nucleic acid complex, b) contacting the population of nucleic acid molecules comprising said Class 2 Type V Cas protein-gRNA-nucleic acid complex with at least one enzyme having single-strand 3′ to 5′ exonuclease activity, thereby forming a 5′ single-stranded overhang in said first site, c) removing the Class 2 Type V Cas protein-gRNA complex from the population of step b), d) contacting the population of step c) with an oligonucleotide probe, said probe comprising a sequence that is at least partially complementary to said overhang, thereby forming a duplex between said probe and said overhang, and e) isolating said duplex from the population of nucleic acid molecules of step d), thereby isolating said nucleic acid target region.

The present invention relates to a method of isolating a nucleic acid target region from a population of nucleic acid molecules, said method comprising the steps of a) contacting said population of nucleic acid molecules with a Class 2 Type V Cas protein-gRNA complex, wherein the gRNA comprises a guide segment that is complementary to a first site adjacent to said target region, thereby forming a Class 2 Type V Cas protein-gRNA-nucleic acid complex, b) contacting the population of nucleic acid molecules comprising said Class 2 Type V Cas protein-gRNA-nucleic acid complex with at least one enzyme having single-strand 3′ to 5′ exonuclease activity, thereby forming a 5′ single-stranded overhang in said first site, c) removing the Class 2 Type V Cas protein-gRNA complex from the population of step b), d) contacting the population of step c) with an oligonucleotide probe, said probe comprising a sequence that is at least partially complementary to said overhang, thereby forming a duplex between said probe and said overhang, and e) isolating said duplex from the population of nucleic acid molecules of step d), thereby isolating said nucleic acid target region.

The present invention relates to a method for a non-specific amplification of a natural short-fragment nucleic acid, comprising the following steps: (1) performing end repair on the natural short-fragment nucleic acid to obtain an end-repaired nucleic acid; (2) connecting the end-repaired nucleic acid to a double-stranded linker to obtain a ligation product, in which each strand of the double-stranded linker contains only three bases; (3) performing PCR amplification on the ligation product using a PCR primer labeled with deoxyuridine to obtain a PCR product, in which the PCR primer is completely or partially complementary to a strand of the double-stranded linker and contains only three bases; and (4) digesting the PCR product by using an enzyme having a deoxyuridine cleavage function, followed by digesting the PCR product by using an enzyme with both 5′.fwdarw.3′ polymerase activity and 3′.fwdarw.5′ exonuclease activity in the presence of a deoxynucleotide solution to obtain a non-specific amplification product of the natural short-fragment nucleic acid. The deoxynucleotide solution only contains the complementary base of the base lacking in the primer. The present invention also relates to a kit for implementing the aforementioned method.