Abstract: Disclosed is a method of detecting and quantifying genomic and gene expression alterations using RNA in a biological sample. The disclosed method may include determining presence or absence of the genomic alteration and/or determining presence or absence of the gene expression and/or quantifying the level of the gene expression, by performing variant calling of the sequence alignment obtained from the disclosed method. Variant calling may comprise the steps of identifying differences between a consensus read and a reference genome based on the sequence alignment from the disclosed method; and determining the read count of sequence alignments comprising genomic alteration. The genomic alteration may be an insertion (such as a duplication), a deletion, a single nucleotide variant, or combinations thereof. Also disclosed is a kit for detecting and quantifying genomic and gene expression alterations using RNA in a biological sample.

Abstract: A reagent solution includes water, a nucleotide, and tris(2-carboxyethyl)phosphine in a range of 0.5 ?M to 1000 ?M. The reagent solution can further include a non-ionic surfactant in an amount of 0.001% to 1% or a biocidal agent in an amount of 0.001% to 1%. The reagent solution can include salts, such as sodium chloride or magnesium sulfate.

Abstract: The present invention relates to the use of the editing profile of PDE8A pre-mRNA as a specific bio marker of ADARs activities in evolved primate, particularly in Human tissues. The present invention also relates to an in vitro method for predicting in Human an alteration of the mechanism of the ADARs catalysed pre-mRNA editing of target genes, by analysing the PDE8A pre-mRNA editing profile in a peripheral tissue sample containing cells expressing said PDE8A pre-mRNA, such as blood sample. The present invention is also directed to an in vitro method for the screening of potential therapeutic compound and to predict and assess therapeutic efficacy and/or efficiency or to diagnose potential severe brain or peripheral drug side effects implementing said PDE8A pre-mRNA editing profile as specific biomarker.

Abstract: The present disclosure relates to a composition for improving molecular barcoding efficiency and a use thereof, and provided are a method for preparing a DNA library, a molecular barcoding method for nucleic acid sequencing, and a composition for preparing a DNA library. According to the method and composition, by using a barcode sequence arranged to include the position of a first nucleotide in an adapter on the basis of a terminal region of the adapter ligated with a DNA fragment, molecular barcoding switching can be reduced and the accuracy of nucleic acid sequencing can be improved.

Abstract: Described and featured herein are isolated oligonucleotides containing, from 5? to 3?, a nicking enzyme recognition sequence, at least 9 nucleotides that specifically bind a target nucleic acid molecule, and 2? modified nucleotides. The isolated oligonucleotides may be used in compositions and methods for quantifying detection of a target oligonucleotide in a sample in real time. These methods are compatible with target oligonucleotides amplified using a Nicking and Extension Amplification Reaction (NEAR) reaction.

Abstract: The present disclosure provides compositions and methods that employ the compositions for conducting pairwise sequencing and for generating concatemer template molecules for pairwise sequencing. The concatemers can be generated using a rolling circle amplification reaction which is conducted either on-support, or conducted in-solution and then distributed onto a support. The rolling circle amplification reaction generates concatemers containing tandem copies of a sequence of interest and at least one universal adaptor sequence. An increase in the number of tandem copies in a given concatemer increases the number of sites along the concatemer for hybridizing to multiple sequencing primers which serve as multiple initiation sites for polymerase-catalyzed sequencing reactions. When the sequencing reaction employs detectably labeled nucleotides and/or detectably labeled multivalent molecules (e.g.

Abstract: A method of sample analysis is provided. In certain embodiments, the method involves: a) amplifying a product from a sample that comprises both wild type copies of a genomic locus and mutant copies of the genomic locus that have a point mutation relative to said wild type copies of the genomic locus, to produce an amplified sample, where: i. the amplifying is done using a first primer and a second primer; and ii. the first primer comprises a 3? terminal nucleotide that base pairs with the point mutation and also comprises a nucleotide sequence that is fully complementary to a sequence in the locus with the exception of a single base mismatch within 6 bases of the 3? terminal nucleotide; and b) detecting the presence of said product in said amplified sample using a flap assay that employs an invasive oligonucleotide. A kit for performing the method is also provided.

Abstract: Provided herein are methods for determining a location of a protein in a biological sample including: disposing the sample onto an array comprising a plurality of capture probes, where a first and second capture probe include a first and second spatial barcode, respectively, and a capture domain. The second capture probe is not covered by the sample and is contacted with a solution comprising TdT and one or more dideoxynucleotides, where a dideoxynucleotide is incorporated into the second capture domain. Analyte capture agents comprising an analyte binding moiety that binds protein and an oligonucleotide including an analyte capture sequence and an analyte binding moiety barcode are contacted with the sample. The analyte capture sequence hybridizes to the first capture domain, and the sequence of the first spatial barcode and the analyte binding moiety barcode, or complements thereof, are used to determine the location of the protein in the biological sample.

Abstract: Methods, devices, and kits are provided for performing PCR in <20 seconds per cycle, with improved efficiency and yield.

Abstract: A PCR reaction vessel includes: a substrate; a channel formed on the substrate; a pair of filters, a first filter and a second filter, provided at respective ends of the channel; a pair of air communication ports, a first air communication port and a second air communication port, that communicate with the channel through the first filter and the second filter; a thermal cycle region formed between the first filter and the second filter in the channel; a branch point formed between the first filter and the second filter in the channel; a branched channel whose one end is connected to the branch point; and a sample introduction port formed at the other end of the branched channel.

Abstract: Provided herein are optimized methods for performing multiplexed detection of a plurality of sequence variations. Also provided are methods for performing multiplexed amplification of target nucleic acid.

Abstract: The present invention provides methods, compositions, mixtures and kits utilizing 5-Chloro-2-methyl-4-isothiazolin-3-one in sequencing reactions, and in particular, sequencing reactions where deoxynucleoside triphosphates comprising a 3?-O position capped by a disulfide-based 3?-terminator group are used. In one embodiment, the deoxynucleoside triphosphates comprise a 3?-O position capped by a group comprising methylenedisulfide as a cleavable protecting group and a detectable label reversibly connected to the nucleobase of said deoxynucleoside. In addition, thiol-containing compounds and scavengers of thio-containing compounds are described. Such compounds provide new possibilities for future sequencing technologies, including but not limited to Sequencing by Synthesis.

Abstract: Methods and devices are provided for the identification and/or quantification of microbes. In particular, the methods comprise: (a) extracting DNA from a microbial sample; (b) performing 16S ribosomal RNA gene-targeted sequencing to obtain DNA sequences; and (c) analyzing the DNA sequences to identify the species of the one or more microbes.

Abstract: The present disclosure provides methods and compositions for tracking nucleic acid fragment origin by target-specific barcode tagging when original nucleic acid targets break into small fragments. Nucleic acid targets are captured in vitro on a solid support with clonally localized nucleic acid barcode templates. Many nucleic acid targets canbe processed simultaneously in a massively parallel fashion without partition. These nucleic acid target tracking methods can be used for a variety of applications in both whole genome sequencing and targeted sequencing in order to accurately identify genomic variants, haplotype phasing and assembly, for example.

Abstract: A method of tracking proximity relationships is disclosed, comprising: (a) introducing a body into a solution of bio-molecule(s), said body comprising at least two capture probes, wherein each capture probe comprises a barcode and a capture domain, and at least one capture probe is a releasable capture probe, connected to the body via at least one cleavable linker; (b) allowing at least two capture probes to bind to their respective target bio-molecule(s) via their respective capture domains; and (c) releasing the at least one releasable capture probe from the body by cleaving its at least one cleavable linker.

Abstract: Methods are provided herein for identifying rare and/or unknown DNA sequences by next-generation sequencing approaches. Isolated double-stranded (ds), single-stranded (ss), or ds/ss DNA is fragmented and the fragments are polished, phosphorylated, and tailed, as necessary. Fragmentation can be enzymatic or mechanical. A universal adapter sequence is ligated to each fragment, wherein the adapter can have a top strand without a 5? phosphate, a 3? with an —H in place of the —OH, and/or a 3? extra base complementary to any base added to the polished fragments. The ligatamers may then serve as templates for amplification using a forward primer complementary to the adapter sequence and a reverse primer targeted to the fragment sequence. Compositions produced by these methods and kits adapted for performing these methods are also described herein.

Abstract: One or more nanoparticles, each of which is conjugated with at least one oligonucleotide, are used to multiply nucleic acids. One or more of the oligonucleotides has at least one primer sequence and an additional segment extending from the end of the primer sequence proximal to the nanoparticle in the direction of the nanoparticle, and the additional segment has at least one abasic modification. The disclosed method for multiplying nucleic acids has a multiplication step and a test step for determining the concentration of the products of the multiplication reaction. The test step begins after the multiplication step ends, and in the test step, either at least one part of the sample is supplied with substances or no substances are supplied. In a method for multiplying nucleic acids, nanoparticles transfer heat into their surroundings in a reaction volume upon being excited.

Abstract: A method for the analysis of minimal residual disease is provided. In some embodiments, the method comprises obtaining multiple pairs of primers designed to amplify sequences that contain a plurality of sequence variations that have been previously identified in a patient's tumor. Amplicons are then obtained through a targeted multiplex amplification that amplifies those sequences from cell-free DNA isolated from a plasma sample. The amplicons are sequenced and two or more of the sequence variations are detected from sequence reads, wherein the detecting comprises comparing a quantity of sequence reads containing a sequence variation against a threshold value. A score is then calculated for the patient sample based on the combined allele frequencies of the detected two or more sequence variations, wherein the score indicates the presence of minimal residual disease.

Abstract: The invention provides compositions and methods for sequencing nucleic acids and other applications. In sequencing by synthesis, unlabeled reversible terminators are incorporated by a polymerase in each cycle, then labeled after incorporation by binding to the reversible terminator a directly or indirectly labeled antibody or other affinity reagent.

Abstract: Provided herein are fluorescently-labeled nucleotide conjugates for nucleic acid analysis. Also provided are reagents used for forming binding complexes between a fluorescently-labeled nucleotide conjugate and a target nucleic acid sequence in the presence of one or more reagents disclosed herein. Binding complexes can be detected in the presence of the one or more reagents. For example, the one or more reagents may contain a photobleaching reducing agent configured to reduce photobleaching resulting from use of the fluorescently-labeled nucleotide conjugate to form the binding complex in a nucleic acid analysis. Such nucleic acid analysis may be used to identify sites of nucleobase binding or incorporation between the target nucleic acid sequence and one or more nucleotide moieties of the fluorescently-labeled nucleotide conjugate in a nucleic acid sequence reaction.