Abstract: In some aspects, the present disclosure provides methods for identifying sequence variants in a nucleic acid sample. In some embodiments, a method comprises identifying sequence differences between sequencing reads and a reference sequence, and calling a sequence difference that occurs in at least two different circular polynucleotides, such as two circular polynucleotides having different junctions, as the sequence variant. In some aspects, the present disclosure provides compositions and systems useful in the described methods.

Abstract: The present invention provides a method for detecting multiple target nucleic acids, the method making it possible to amplify a plurality of genes using one reaction vessel containing therein one type of reaction solution and further using a single label. Computation is performed in accordance with the following formulas for every specific cycle and/or every cycle during amplification reaction using a kit for detecting the multiple target nucleic acids. (Formula 1): f1[n]=fhyb.1[n]/fden.1[n], (Formula 1?): f2[n]=fhyb.2[n]/fden.2[n], (Formula 2): Fr[n]=(a?f2 [n])/(a?f1 [n]).fhyb.1[n]: Fluorescence intensity value in elongation step of first target nucleic acid detecting step. The same hereinafter.

Abstract: Provided herein are methods identifying protein-protein interactions in a single cell context. In some cases, the methods may be used to measure the abundance of protein-protein interactions in a single cell context. In some cases, the methods may be used to map relationships (e.g., spatial relationships) between proteins in a single cell context. Generally, the methods employ the use of proximity probes coupled with splint oligonucleotides to link information about the relationship of proteins within a single cell context, which may then be read in a downstream process (e.g., a sequencing reaction).

Abstract: The present application provides methods for detecting a target nucleic acid molecule in a sample comprising contacting said sample with a ligatable probe comprising one or more parts and allowing said probe to hybridise to the target nucleic acid molecule, ligating any probe which has hybridised to the target nucleic acid molecule, amplifying the ligated probe, and detecting the amplification product, thereby to detect the target nucleic acid molecule, wherein said probes comprise at least one ribonucleotide at or near to a ligation site and/or wherein the probe or a probe part comprises an additional sequence 5? to a target-specific binding site which is not hybridised to the target nucleic acid molecule upon hybridisation of the probe to the target nucleic acid molecule and forms a 5? flap containing one or more nucleotides at its 3? end that is cleaved prior to ligation, and methods of synthesising a DNA molecule with Phi29 DNA polymerase using a template nucleic acid molecule comprising at least one ribo

Abstract: Compositions and methods for treating type II diabetes in a subject. A viral vector is provided which includes a nucleic acid molecule comprising a sequence encoding a propeptide and the active portion of GLP-1, wherein, when expressed, the N-terminal amino acid of GLP-1 immediately follows the C-terminal amino acid of the propeptide. In desired embodiments, the subject is a cat or dog.

Abstract: A sequence of polymer units in a polymer (3), eg. DNA, is estimated from at least one series of measurements related to the polymer, eg. ion current as a function of translocation through a nanopore (1), wherein the value of each measurement is dependent on a k-mer being a group of k polymer units (4). A probabilistic model, especially a hidden Markov model (HMM), is provided, comprising, for a set of possible k-mers: transition weightings representing the chances of transitions from origin k-mers to destination k-mers; and emission weightings in respect of each k-mer that represent the chances of observing given values of measurements for that k-mer. The series of measurements is analysed using an analytical technique, eg. Viterbi decoding, that refers to the model and estimates at least one estimated sequence of polymer units in the polymer based on the likelihood predicted by the model of the series of measurements being produced by sequences of polymer units.

Abstract: A method for detecting an AFB1 content using fluorescence analysis based on optical sectioning is provided, which relates to the field of biological detection technologies. The method includes steps for detecting the AFB1 content by using a fluorescence probe combination, which includes fluorescence probes aptamer and PC-strand. The nucleotide sequence of the aptamer is shown as SEQ ID NO: 1, and a FAM group is labeled at a 3? end of the nucleotide sequence shown as SEQ ID NO: 1. The nucleotide sequence of the PC-strand is shown as SEQ ID NO: 2, a TAMRA group is labeled at a 5? end of the nucleotide sequence shown as SEQ ID NO: 2, and a PC group is labeled between 10th bp and 11th bp of the nucleotide sequence shown as SEQ ID NO: 2. The method can achieve photosensitive detection of AFB1, with high detection sensitivity and strong specificity.

Abstract: Provided are methods of producing product nucleic acids involving the use of oligonucleotides that are modified by the application of a stimulus. Aspects of such methods may include producing product nucleic acids using de-activatable oligonucleotides that are deactivated by a de-activating stimulus, as well as methods that may include producing product nucleic acids using activatable oligonucleotides that are activated by an activating stimulus and de-activatable oligonucleotides that are deactivated by a de-activating stimulus. Also provided are kits, compositions and devices that include de-activatable oligonucleotides or activatable and de-activatable oligonucleotides, e.g., for use in performing the methods as described herein.

Abstract: The present disclosure provides compositions, methods, and systems for preparing nucleic acid samples for sequencing, including attaching adapters to a template nucleic acid molecule having a first and second strands; attaching the template nucleic acid molecule to a support; detaching the first and second strands from each other; generating a reverse complement copy of the second strand using a primer coupled to the support; generating amplified copies of the first strand and the reverse complement copy of the second strand using primers coupled to the support; and identifying the sequences of the first strand and the reverse complement copy of the second strand. Further provided herein are methods of error correction by preserving both strands of a template nucleic acid molecule during amplification.

Abstract: Provided are synthetic strands for nucleic acid sequencing. In some embodiments, the strands include a plurality of rotatable solid supports. The plurality of rotatable solid supports comprises solid supports each comprising on its surface a first moiety that binds to adenine (A), a second moiety that binds to cytosine (C), a third moiety that binds to guanine (G), a fourth moiety that binds to thymine (T), uracil (U), or both (T/U). Each of such solid supports further comprises on its surface a position marker that indicates the rotational position of the solid support, where the first, second, third, and fourth moieties are spaced about the circumference of the solid support. The solid supports enable hybridization of the synthetic strand to a nucleic acid. Also provided are methods of using the synthetic strands, as well as related compositions, kits, and nucleic acid sequencing systems.

Abstract: The present invention discloses a method of detecting the presence of mutated genes, mRNAs or microRNAs in a subject. The method comprises the following steps: (1) Provide a body fluid sample containing cells, circulating tumor cells (CTCs), and/or extracellular vesicles (EVs); and use an analyzer having overhang molecular beacons to measure fluorescence signals generated by interactions between the body fluid sample and the overhang molecular beacons, so as to detect the presence of the mutated genes, mRNAs or microRNA. Furthermore, a biochip comprising a gold coating substrate and tethered lipoplex nanoparticles encapsulating the overhang molecular beacons is also provided in the invention.

Abstract: The disclosure relates to in vitro cultures of human hepatocytes, and in particular co-cultures systems including human hepatocytes, non-parenchymal cells, and human endothelial cells, and the use of the co-cultures in developing and screening drugs.

Abstract: A method of treating bladder cancer comprising diagnosing bladder cancer in a human, measuring the human's level of CDKN2A expression, and then instilling into the human an agent which induces interferon expression.

Abstract: The present disclosure relates, according to some embodiments, to compositions and analysis of RNA (e.g., dephosphorylated oligoribonucleotides) including, for example, natural and/or synthetic RNAs. A composition may comprise, for example, an endoribonuclease having an amino acid sequence that (i) corresponds to an amino acid sequence of a first species (e.g., Homo sapiens, Escherichia coli, Aspergillus oryzae, Momordica charantia, Pyrococcus furiosus, Cucumis sativus, and Sus scrofa) or (ii) is a non-naturally occurring sequence; and/or an RNA end repair enzyme having an amino acid sequence that (i) corresponds to an amino acid sequence of a species other than the first species (e.g., a bacterial species or a bacteriophage species) or (ii) is a non-naturally occurring sequence.

Abstract: Provided herein, in some embodiments, are molecular authentication methods, systems, and compositions.

Abstract: Provided herein is a method for barcoding, comprising: (a) obtaining multiple populations of cells or cell organelles in a plurality of first volumes, wherein: i. within each first volume the cells or cell organelles comprise nucleic acid molecules that are associated with a first subcode of a set of first subcodes, and ii. in different first volumes the nucleic acid molecules are associated with different first subcodes of the set of first subcodes, (b) pooling the cells or cell organelles, (c) separating the pooled cells or cell organelles into a plurality of second volumes, and (d) associating the nucleic acid molecules with a set of second subcodes in the second volumes, wherein a plurality of the second volumes each receive a different second subcode. This method produces at least some nucleic acid molecules that comprise a first subcode and a second subcode.

Abstract: Massively parallel sequencing of cell-free, maternal plasma DNA was recently demonstrated to be a safe and effective screening method for fetal chromosomal aneuploidies. Here, we report an improved sequencing method achieving significantly increased throughput and decreased cost by replacing laborious sequencing library preparation steps with PCR employing a single primer pair. Using this approach, samples containing as little as 4% trisomy 21 DNA could be readily distinguished from euploid samples.

Abstract: Provided are a PCR primer pair and an application thereof. The PCR primer pair comprises a first primer and a second primer, wherein the first primer comprises a first specific sequence, a first random sequence, and a first universal sequence, the first specific sequence is located at the 3? end of the first primer, the first random sequence is located at the 5? end of the first primer, and the first universal sequence is located between the first specific sequence and the first random sequence; the second primer comprises a second specific sequence, a second random sequence, and a second universal sequence, the second specific sequence is located at the 3? end of the second primer, the second random sequence is located at the 5? end of the second primer, and the second universal sequence is located between the second specific sequence and the second random sequence, wherein the first random sequence and the second random sequence are inversely complementary.

Abstract: The present disclosure provides a pharmaceutical composition comprising a Bcl-2/Bcl-xL inhibitor, a chemotherapeutic agent, and a pharmaceutically acceptable carrier. The present disclosure also provides a method of treating cancer, comprising administering to a subject in need thereof a therapeutically effective amount of a Bcl-2/Bcl-xL inhibitor and a therapeutically effective amount of a chemotherapeutic agent. The present disclosure also provides use of a combination of a Bcl-2/Bcl-xL inhibitor and a chemotherapeutic agent in the manufacture of an anti-tumor medicament. In the present disclosure, a significantly enhanced anti-tumor effect can be achieved by administration of a Bcl-2/Bcl-xL inhibitor in combination with a chemotherapeutic agent.

Abstract: Provided is a gene amplification apparatus. The gene amplification apparatus includes a supply roller, a roll-type film chip which has a plurality of polymerase chain reaction (PCR) chambers, with which PCR samples are filled, and is wound around the supply roller, a heating roller configured to rotate after being pressed against the film chip and then induce a PCR, a plurality of heating blocks which are disposed on a circumferential surface of the heating roller at preset intervals and brought into contact with the film chip, and a discarding roller configured to discard the film chip which passes the heating roller and on which the PCR is performed.

Abstract: The present invention relates to a system for performing assays on a solid phase to measure the level of analyte in a sample. Such a system may perform immunoassays using electrochemiluminescence (ECL) including a counterbalanced orbital shaking apparatus for assay consumables. The counterbalanced orbital shaking apparatus also incubates the assay consumables, and has a cooling system to maintain a preset temperature within the shaking apparatus.

Abstract: Disclosed is a method for amplifying RNA and/or DNA from immune cell populations and using the amplified products to produce an immune response profile and evaluate the possible correlation between a normal or abnormal immune response and the development of a disease such as an autoimmune disease, cancer, diabetes, or heart disease.

Abstract: Methods of characterizing a test subject's risk of having or developing cardiovascular disease are provided. The methods include using an analytic device to determine levels of choline-related trimethylamine-containing compounds such as trimethylamine N-oxide, choline, or betaine in a biological sample obtained from the subject and comparing the levels of the choline-related trimethylamine-containing compound in the subject's biological sample to a control value. The test subject's risk of having cardiovascular disease is then characterized as higher if the levels of the choline-related trimethylamine-containing compound are higher than the control value. Also provided are methods of identifying a subject at risk of experiencing a complication of atherosclerotic cardiovascular disease, and methods of evaluating the efficacy of a cardiovascular therapeutic agent in a subject with cardiovascular disease using levels of choline-related trimethylamine-containing compounds.

Abstract: A terminal device according to an embodiment includes an accepting unit, a secret value generating unit, a response data generating unit, and an output unit. The accepting unit accepts an inquiry about genome data of each user. The secret value generating unit generates a secret value by applying a one-way function to the genome data. The response data generating unit generates response data to the inquiry on the basis of the secret value generated by the secret value generating unit and contents of the inquiry. The output unit outputs the response data generated by the response data generating unit.

Abstract: As cell-free DNA from brain and spinal cord tumors cannot usually be detected in the blood, we assessed the cerebrospinal fluid (CSF) that bathes the CNS for tumor DNA, here termed CSF-tDNA. The results suggest that CSF-tDNA could be useful for the management of patients with primary tumors of the brain or spinal cord.

Abstract: This document relates to methods and materials for detecting premalignant and malignant neoplasms. For example, methods and materials for determining whether or not a stool sample from a mammal contains nucleic acid markers or polypeptide markers of a neoplasm are provided.

Abstract: The present disclosure provides variant OmpG polypeptides, compositions comprising the OmpG variant polypeptides, and methods for using the variant OmpG polypeptides as nanopores for determining the sequence of single stranded nucleic acids. The variant OmpG nanopores reduce the ionic current noise versus the parental OmpG polypeptide from which they are derived and thereby enable sequencing of polynucleotides with single nucleotide resolution. The reduced ionic current noise also provides for the use of these OmpG nanopore variants in other single molecule sensing applications, e.g., protein sequencing.

Abstract: The present disclosure relates to methods to deconvolute a mixture sample of genetic material from different origins or sources. The disclosed methods can be used in various applications, including, the non-invasive determination of a fetal genome, a fetal -ome (e.g. exome). or other targeted fetal locus from cell-free nucleic acids in maternal plasma or other body fluids; the determination of cancer-associated mutations from cell-free nucleic acids in a body fluid sample that contains a mixture of nucleic acids from normal cells and tumor cells; and quantification of donor cell contamination using a body fluid from a transplantation recipient to monitor and/or predict the outcome of a transplantation procedure.

Abstract: The present disclosure provides devices, methods and systems for analyte detection and/or monitoring, e.g., the continuous and/or semi-continuous monitoring of in-vivo analyte concentrations in real time. Generally, the devices, methods and systems of the present disclosure make use of signaling probes; methods or devices for reducing interferent-based fouling of the signaling probes, non-specific binding to the signaling probes and/or occlusion of a sensor surface; and methods and/or devices for providing an adjusted signal based on a detected signal from the signaling probes. Compositions including conformation switching signaling probes are also provided.

Abstract: Cross-contamination of a test sample used to determine cancer is identified using gene sequencing data. Each test sample includes a number of test sequences that may include a single nucleotide polymorphism (SNP) that can be indicative of cancer. The test sequences are be filtered to remove or negate at least some of the SNPs from the test sequences. Negating the test sequences allows more test sequences to be simultaneously analyzed to determine cross-contamination. Cross-contamination is determined by modeling the variant allele frequency for the test sequences as a function of minor allele frequency, contamination level, and background noise. In some cases, the variant allele frequency is based on a probability function including the minor allele frequency. Cross-contamination of the test sample is determined if the determined contamination level is above a threshold and statistically significant.

Abstract: Engineered nucleases are promising tools for genome manipulation and determining off-target cleavage sites of these enzymes is of great interest. This disclosure provides in vitro selection methods that interrogate 1011 DNA sequences for their ability to be cleaved by active nucleases, e.g., ZFNs and TALENs. The method revealed hundreds of thousands of DNA sequences that can be cleaved in vitro by two ZFNs, CCR5-224 and VF2468, which target the endogenous human CCR5 and VEGF-A genes, respectively. Analysis of the identified sites in cultured human cells revealed CCR5-224-induced mutagenesis at nine off-target loci. This disclosure provides an energy compensation model of ZFN specificity in which excess binding energy contributes to off-target ZFN cleavage. It was also observed that TALENs can achieve cleavage specificity similar to or higher than that observed in ZFNs.

Abstract: A nucleic acid probe and a nucleic acid sequencing method for performing sequencing while ligating nucleic acids. The nucleic acid probe is a DNA sequencing probe, comprising a first moiety, a second moiety, a linker, and a detectable label. A base of the first moiety is A, T, U, C, or G, a base of the second moiety is a random base and/or a universal base, and 3 bases or more are present in the second moiety. The first moiety and the second moiety are ligated via the linker, the connection between the first moiety and the ligation can be cleaved, and the detectable label is ligated to the second moiety or the linker. The above probe, a combination formed therewith, or a sequencing method using the same can reduce the number or types of probes in nucleic acid sequencing, thereby reducing cost.

Abstract: An affinity reagent, having: (a) a retaining component such as a structured nucleic acid particle; and (b) one or both of (i) one or more label components attached to the retaining component, and (ii) one or more binding components attached to the retaining component.

Abstract: Provided herein are methods of detecting an analyte of interest to interrogate spatial gene expression in a sample using DNA templated ligation. For example, provided herein are methods for detecting an gDNA analyte in a biological sample where (i) the first RTL probe and second RTL probe hybridize to adjacent sequences on the gDNA analyte, (ii) enzyme-mediate cleavage of a 5? FLAP results in release of the 5? FLAP, and (iii) the sequence of the 5? FLAP is determined and used to detect the gDNA analyte in the biological sample.

Abstract: Biomarkers relevant to neurons in the brain, in particular at single cell levels, are identified by using olfactory neurons as the best surrogates from subjects so as to establish diagnosis, prognosis, and treatment of brain conditions.

Abstract: Provided are linkers suitable for preparing a conjugate of a nucleic acid and a peptide as a translation product thereof in a reconstituted cell-free translation system in genotype-phenotype mapping (display methods), said linkers comprising a single-stranded structure region having a side chain base pairing with the base at the 3?-end of an mRNA at one end and a peptidyl acceptor region containing an amino acid attached to an oligo RNA consisting of a nucleotide sequence of ACCA via an ester bond at the other end, characterized in that the ester bond is formed by using an artificial RNA catalyst. Also provided are display methods using [mRNA]-[linker]-[peptide] conjugates assembled via such linkers.

Abstract: The present invention provides a novel antisense oligonucleotide and a composition for preventing or treating glycogen storage disease type Ia. The present invention provides an antisense oligonucleotide which hybridizes with a pre-mRNA sequence derived from a region including at least one of a base at position 42911000, a base at position 42911004, and a base at position 42911005 in a base sequence of human chromosome 17 of GRCh38/hg38 and has activity to inhibit aberrant splicing of pre-mRNA of c.648G>T variant G6PC.

Abstract: An electrochemical sensor incorporates a ferrocenophane which is a compound with at least one bridging group covalently attached to and connecting the two cyclopentadiene rings associated with the same iron atom. This bridging group maybe tetramethylene. As compared to an equivalent sensor with ferrocene, the tolerance of elevated temperature is improved and so is the working life at ambient temperature.

Abstract: The present invention establishes a molecular therapy for glycogen storage disease type Ia. The present invention provides an oligonucleotide of 15-30 bases comprising a nucleotide sequence complementary to die cDNA of G6PC gene with c.648G>T mutation, wherein the oligonucleotide comprises a sequence complementary to a region comprising any site between the 82nd to the 92nd nucleotide from the 5? end of exon 5 of the G6PC gene with c.648C>T mutation, a pharmacologically acceptable salt or solvate thereof. Also provided is a pharmaceutical drug comprising the oligonucleotide, a pharmacologically acceptable salt or solvate thereof (e.g., therapeutic drug for glycogen storage disease type Ia).

Abstract: Methods for analyzing DNA-containing samples are provided. The methods can comprise isolating a single genomic equivalent of DNA from the DNA-containing sample to provide a single isolated DNA molecule. The single isolated DNA molecule can be subjected to amplification conditions in the presence of one or more sets of unique molecularly tagged primers to provide one or more amplicons. Any spurious allelic sequences generated during the amplification process are tagged with an identical molecular tag. The methods can also include a step of determining the sequence of the one or more amplicons, in which the majority sequence for each code is selected as the sequence of the single original encapsulated target. The DNA-containing sample can be a forensic sample (e.g., mixed contributor sample), a fetal genetic screening sample, or a biological cell.

Abstract: The present invention relates to small interfering RNA (siRNA) molecules against the HTT gene, adeno-associated viral (AAV) vectors encoding siRNA molecules and methods for treating Huntington's Disease (HD) using the siRNA molecules and AAV vectors.

Abstract: Compositions and methods for quantitative detection of target nucleic acids, such as miRNAs are disclosed. The methods are especially advantageous for single-color multiplex detection of two or more targets simultaneously (e.g., in the same reaction). The methods can involve optional reverse transcription followed by amplification performed with universal primers, fluorophore-labeled detection probes, and quencher oligonucleotides for quenching fluorescence of any detection probe not bound to a target molecule. The methods employ differential stability of detection probe-quencher oligonucleotide complexes, and by extension, differential fluorescence at various temperatures to distinguish between different target molecules.

Abstract: The present disclosure provides methods for selectively tagging 5-methylcytosine in a DNA sample and using this approach for genome-wide profiling of 5-methylcytosine in a low input DNA sample such as circulating cell-free DNA.

Abstract: In a nanopore sensor, a nanopore disposed in a support structure has a nanopore diameter and nanopore resistance, RPore. A fluidic passage, disposed in fluidic connection between a first fluidic reservoir and the nanopore, has a cross-sectional extent, along at least a portion of the fluidic passage length, that is greater than the diameter of the nanopore and that is less than the fluidic passage length. The fluidic passage has a fluidic passage resistance, RFP, of at least about 10% of the nanopore resistance, RPore, and no more than about 10 times the nanopore resistance, RPore. The nanopore is disposed in fluidic connection between the fluidic passage and a second fluidic reservoir. At least one electrical transduction element is disposed at the fluidic passage and electrically connected to produce an indication of electrical potential local to the fluidic passage.

Abstract: Polynucleotides and vectors can be used for the expression of a transgene in cells, such as liver cells. The expression of the transgene from the polynucleotides and vectors can be useful in gene therapy. Various methods can be used for expressing the transgene from the polynucleotides and vectors in liver cells.

Abstract: A method of barcoding is provided. The method comprises performing a ligation assay on target nucleic acid molecules that are in or on cells or cell organelles to produce ligation products and adding cell-origination barcodes onto the ligation products or complements thereof by a split-pool barcoding process.

Abstract: A method for adding cell origination barcodes onto beads is provided. The method comprises: splitting a pool of beads into a plurality of reaction volumes, appending pre-made oligonucleotides onto the beads in the reaction volumes, wherein at least some of the reaction volumes each receive an oligonucleotide that contains a sequence that is different from the other oligonucleotides added to the reaction volumes, pooling the beads and repeating the splitting, appending and pooling steps one or more times to produce a pool of beads that comprise the cell origination barcodes. In the one or more repeats the oligonucleotides that are appended are added to previously appended oligonucleotides to form the cell origination barcodes.

Abstract: Determining relative relationships of people who share a common ancestor within at least a threshold number of generations includes: receiving recombinable deoxyribonucleic acid (DNA) sequence information of a first user and recombinable DNA sequence information of a plurality of users; processing, using one or more computer processors, the recombinable DNA sequence information of the plurality of users in parallel; determining, based at least in part on a result of processing the recombinable DNA information of the plurality of users in parallel, a predicted degree of relationship between the first user and a user among the plurality of users, the predicted degree of relative relationship corresponding to a number of generations within which the first user and the second user share a common ancestor.

Abstract: A kit for split-pool barcoding is provided. The kit comprises: a binding agent that binds to a target molecule that is in or on cells or cell organelles and at least two sets of assayable polymer subunit (APS) oligonucleotides. In the kit each set comprises at least 10 unique APS oligonucleotides, the APS oligonucleotides in a set each comprise a sequence that distinguishes the APS oligonucleotides from one another, and the APS oligonucleotides from different sets are configured to link together in an ordered fashion to form all or part of a cell or organelle origination barcode.

Abstract: A data storage medium is disclosed comprising a solid support matrix including an optional stabilising reagent or reagents in a dry form, for use as a support for artificially synthesised oligonucleotide sequences encoded with data. Preferably the matrix is fibrous (for example cellulose, or glass, fibres) formed into a support of sufficient strength to hold the oligonucleotide sequences. The stabilising reagents are preferably a combination of a weak base, and a chelating agent, optionally, uric acid or a urate salt, and optionally an anionic surfactant.