Abstract: The invention relates to methods, kits and uses thereof for detecting gene mutations. The method comprises the step of: providing a mixture of nucleic acid molecules comprising both a genomic DNA and a RNA molecule derived from said genomic DNA, performing a reverse transcription reaction with a reverse transcriptase to provide cDNA molecules from said RNA molecule in said mixture; and performing PCR using both said genomic DNA and said cDNA molecules as templates. This method can simultaneously detect a trace amount of a mutation in both DNA and RNA from a whole blood sample using a small amount of sample. At the same time, by adjusting the reaction system, the detection limit of a mutant in a background of wild-type molecules can reach 0.01% or lower.

Abstract: This disclosure provides methods and compositions for sample processing, particularly for sequencing applications. Included within this disclosure are bead compositions, such as diverse libraries of beads attached to large numbers of oligonucleotides containing barcodes. Often, the beads provides herein are degradable. For example, they may contain disulfide bonds that are susceptible to reducing agents. The methods provided herein include methods of making libraries of barcoded beads as well as methods of combining the beads with a sample, such as by using a microfluidic device.

Abstract: Disclosed are methods for nucleic acid amplification wherein nucleic acid templates, beads, and amplification reaction solution are emulsified and the nucleic acid templates are amplified to provide clonal copies of the nucleic acid templates attached to the beads. Also disclosed are kits and apparatuses for performing the methods of the invention.

Abstract: The invention provides methods, devices, compositions and kits for diagnosing or predicting transplant status or outcome in a subject who has received a transplant.

Abstract: The present invention provides a method for determining a survival rate and prognosis state and providing care for a patient having esophageal carcinoma, comprising: (a) providing a tissue sample from the patient; (b) measuring an expression level of a plurality of target genes comprising peptidase inhibitor 3 (PI3) and CD14 in the tissue sample from the patient using reagents specific for a gene product of the plurality of target genes that are selected from the group consisting of probes, primers, antibodies, and antibody fragments, wherein the expression level is measured by RNA expression or protein expression; (c) comparing the expression level of the plurality of target genes to a predetermined threshold indicative of a survival rate and prognosis state for the patient; and (d) providing care for the patient when the survival rate and prognosis state is worse, wherein the care is advising the patent to reduce the time between return visit or to add adjuvant chemotherapy after surgery.

Abstract: Described herein are methods and compositions that provide highly efficient nucleic acid amplification. In some embodiments, this allows a greater than 2-fold increase of amplification product for each amplification cycle and therefore increased sensitivity and speed over conventional PCR.

Abstract: Provided herein are methods and apparatus for the identification of pathogenic and non-pathogenic microorganisms in food and environmental samples. The disclosure solves existing challenges encountered in identifying food borne pathogens, including pathogens of the Salmonella, Campylobacter, Listeria, and Escherichia genera in a timely and efficient manner. The disclosure also provides methods for differentiating a transient versus a resident pathogen, correlating presence of non-pathogenic with pathogenic microorganisms, distinguishing live versus dead microorganisms by sequencing.

Abstract: A method and system are disclosed for detecting microbial pathogens in a sample suspected of containing the pathogens. The method includes combining loop-mediated isothermal amplification (LAMP) reagents and a polymer gel, such as a hydrogel, together with the sample to form a mixture. The gel polymerizes over a short time to immobilize the viral particles within the mixture. If target DNA/RNA are present in the sample, amplicons are produced. The target microorganisms are detected by visually detecting the presence or absence of the amplicons. The target microorganism concentrations may be determined based on the number of fluorescent amplicon dots after the reaction using a smartphone or a fluorescent microscope. The method may be employed for rapidly and inexpensively quantifying microbial pathogens in environmental water samples with high sensitivity.

Abstract: Kits and methods for detecting a target polynucleotide sequence are disclosed. The kits and methods described herein allow for the detection of a target polynucleotide sequence that lacks a missing base selected from adenine, cytosine, guanine, thymine, uracil, and combinations thereof, using rolling circle amplification and a padlock probe polynucleotide sequence that lacks the base complementary to the base missing in the target polynucleotide sequence. The kits and methods may be used to detect any target polynucleotide sequence, such as DNA or RNA from a bacterial, fungal, or viral pathogen.

Abstract: Methods of analyzing DNA molecules in a cell sample are provided. The DNA molecules have DNA binding moiety signatures which are defined by at least two non-identical DNA binding moieties. Kits for analyzing the DNA are also provided.

Abstract: The present disclosure provides compositions, methods and kits for Omega amplification technologies. In addition, the present disclosure provides compositions, methods and kits for universal FQ probe and for G-quadruplex detection methods for use in isothermal amplification technologies.

Abstract: A method of predicting the variation of porcine intramuscular fat profile. The method includes detecting a BRCA1 gene and/or a JAML gene, or an expression product thereof. The disclosure also provides a method of selecting and breeding pigs. The method includes detecting a BRCA1 gene and/or a JAML gene, or an expression product thereof.

Abstract: A method of sequencing a nucleic acid comprising the steps of (1) generating a stream of single nucleoside triphosphates; (2) producing at least one substantially double-stranded primary oligonucleotide used probe comprising (a) a first single-stranded oligonucleotide including a first restriction endonuclease nicking-site, a single nucleotide capture site, and oligonucleotide flanking regions juxtaposed either side of the capture site and (b) second and third single-stranded oligonucleotides; (3) nicking the first oligonucleotide strand of the used primary probe; (4) separating the first oligonucleotide components; (5) producing at least one substantially double-stranded secondary used probe by reacting with a corresponding secondary probe comprising (c) a complementary fourth oligonucleotide and optionally (d) a single-stranded fifth oligonucleotide; (6) nicking the fourth oligonucleotide strand of the used secondary probe to create separate fourth oligonucleotide components having fluorophores and a single

Abstract: Methods, compositions, and kits are provided for quantification of genome editing.

Abstract: A method for spatially tagging nucleic acids of a biological specimen, including steps of (a) providing a solid support comprising different nucleic acid probes that are randomly located on the solid support, wherein the different nucleic acid probes each includes a barcode sequence that differs from the barcode sequence of other randomly located probes on the solid support; (b) performing a nucleic acid detection reaction on the solid support to locate the barcode sequences on the solid support; (c) contacting a biological specimen with the solid support that has the randomly located probes; (d) hybridizing the randomly located probes to target nucleic acids from portions of the biological specimen; and (e) modifying the randomly located probes that are hybridized to the target nucleic acids, thereby producing modified probes that include the barcode sequences and a target specific modification, thereby spatially tagging the nucleic acids of the biological specimen.

Abstract: Methods of detecting multiple nucleic acid targets in single cells through indirect capture of labels to the nucleic acids are provided. Methods of assaying the relative levels of nucleic acid targets through normalization to levels of reference nucleic acids are also provided. Methods of detecting individual cells, particularly rare cells from large heterogeneous cell populations, through detection of nucleic acids are described. Related compositions, systems, and kits are also provided.

Abstract: Provided herein, in some embodiments, are methods, compositions and kits for controlling nucleation and assembly of molecular nanostructures, microstructures and macrostructures.

Abstract: Methods and compositions for the amplification of nucleic acids and generation of concatemers are disclosed. Amplification methods provided herein may be performed under isothermal conditions. Methods and compositions may include reagents such as nucleic acid polymerases and primers.

Abstract: The present invention provides nucleic acid probes for detection of a target nucleic acid molecule by an RCA reaction in the presence of the target nucleic acid molecule, comprising a first circular template strand which is capable of acting as a template for RCA, and which is protected from RCA in the absence of the target nucleic acid molecule by at least a second protector strand which comprises a region of complementarity to the first template strand and is hybridised thereto to form a double-stranded circular structure containing the first template strand inside the protector strand(s), wherein at least one of the second and/or any further protector strands comprises a target binding site, such that upon binding of the probe to the target nucleic acid molecule the probe is able to undergo a strand displacement reaction which allows RCA of the first template strand, and kits containing the same. Methods of detecting target analytes using such probes are also provided.

Abstract: A composition and a method for improving sensitivity and specificity of detection of nucleic acids, use dCas9 and gRNA, which binds to a target nucleic acid sequence, in amplification of nucleic acids including DNAs, RNAs, and the like increases efficiency in amplification of nucleic acids and thereby can ultimately improve sensitivity and specificity of a target diagnosis on the basis of a functional difference between Cas9 and dCas9.

Abstract: Compositions and methods are described for standardizing the DNA amplification efficiencies of a highly heterogeneous set of oligonucleotide primers as may typically be used to amplify a heterogeneous set of DNA templates that contains rearranged lymphoid cell DNA encoding T cell receptors (TCR) or immunoglobulins (IG). The presently disclosed embodiments are useful to overcome undesirable bias in the utilization of a subset of amplification primers, which leads to imprecision in multiplexed high throughput sequencing of amplification products to quantify unique TCR or Ig encoding genomes in a sample. Provided is a template composition comprising a diverse plurality of template oligonucleotides in substantially equimolar amounts, for use as a calibration standard for amplification primer sets. Also provided are methods for identifying and correcting biased primer efficiency during amplification.

Abstract: An in vitro process for the production of closed linear deoxyribonucleic acid (DNA) comprises (a) contacting a DNA template comprising at least one protelomerase target sequence with at least one DNA polymerase in the presence of one or more primers under conditions promoting amplification of the template; and (b) contacting amplified DNA produced in (a) with at least one protelomerase under conditions promoting production of closed linear DNA. A kit provides components necessary in the process.

Abstract: The invention relates to methods for labelling individual nucleic acid molecules present in a sample, comprising contacting the nucleic acid molecules with an adaptor or mixture of adaptors, wherein the adaptor or adaptors comprise one or more universal nucleotide bases and a ligation moiety at their 3? end, and ligating an adaptor to the nucleic acid of interest, wherein the adaptor is ligated to the nucleic acid molecules at the 3? end of the adaptor. A random tag is then generated in situ by conducting an extension reaction over the ligated adaptor. Methods of the invention may be used to detect genetic alterations or variants in any nucleic acid with high specificity and high sensitivity, including mutations in nucleic acids such as ctDNA, cfDNA, and in viral, microbiome and plant nucleic acids. Methods of the invention may also be used in detection and correction of errors introduced into nucleic acids during processing.

Abstract: An object of the present invention is to provide a method for accurately and quantitatively discriminating and detecting a wide variety of gene mutations, or particularly, single base substitutions or point mutations. In an ASP for analyzing gene mutations, or particularly, single base substitutions or point mutations, when a non-nucleotide component is added to the 5? end of at least one of the ASP and a primer paired therewith before amplification by PCR and amplification products thereof are separated by ion-exchange chromatography, even the amplification products having the same length can be separated and detected.

Abstract: A non-invasive method for organ transplant rejection prediction is described, involving measurement of the ratio between donor-specific nucleic acid sequences and recipient-specific nucleic acid sequences in a biological sample obtained from an organ transplant recipient. In specific implementations, the method includes analyzing a biological sample (e.g., blood) obtained from an organ transplant recipient to measure the ratio between donor-derived marker sequences and recipient-derived marker sequences, having three or more markers selected from the markers listed in Tables 1 to 10, and thereby predicting organ transplant rejection based on the ratio. Using next-generation sequencing (NGS) or digital base amplification in the disclosed method enables its application to minute amounts of a sample. The method is rapid, inexpensive, enables rapid data analysis, is applicable irrespective of organ type and race(s) of the donor and recipient, and can detect the probability of sequencing error.

Abstract: A target polynucleotide is expanded. In respect of each nucleotide in the target polynucleotide, the target polynucleotide comprises clock nucleotides and at least one signal nucleotide in a predetermined order. The clock nucleotides have a predetermined sequence common to each nucleotide in the target polynucleotide. The at least one signal nucleotide is characteristic of the identity of the respective nucleotide in the target polynucleotide. During translocation of the expanded polynucleotide through a nanopore, electrical measurements dependent on the polynucleotide within the pore are made, to derive an analysis signal. Clock signals derived from the clock nucleotides are identified. Relative to the positions of the identified clock signals, nucleotide signals derived from the least one signal nucleotide are derived to analyse the target polynucleotide.

Abstract: Provided herein are methods and apparatus for the identification of pathogenic and non-pathogenic microorganisms in food and environmental samples. The disclosure solves existing challenges encountered in identifying food borne pathogens, including pathogens of the Salmonella, Campylobacter, Listeria, and Escherichia genera in a timely and efficient manner. The disclosure also provides methods for differentiating a transient versus a resident pathogen, correlating presence of non-pathogenic with pathogenic microorganisms, distinguishing live versus dead microorganisms by sequencing.

Abstract: The invention relates to a new method of characterising a target polynucleotide using a pore. The method involves controlling the formation of secondary structure by the target polynucleotide after the polynucleotide has moved through the pore.

Abstract: A gene sequencing chip, a sequencing method thereof and a gene sequencing device are provided. The gene sequencing chip includes: a first substrate having a first surface; at least one recessed portion recessed from the first surface into the first substrate; a graphene oxide layer located at a bottom of the recessed portion; and a first electrode and a second electrode which are electrically connected with the graphene oxide layer. The recessed portion is configured to receive a sample to be tested, and the first electrode and the second electrode are configured to detect a resistance of the graphene oxide layer.

Abstract: The present disclosure provides methods for determining the ploidy status of a chromosome in a gestating fetus from genotypic data measured from a mixed sample of DNA comprising DNA from both the mother of the fetus and from the fetus, and optionally from genotypic data from the mother and father. The ploidy state is determined by using a joint distribution model to create a plurality of expected allele distributions for different possible fetal ploidy states given the parental genotypic data, and comparing the expected allelic distributions to the pattern of measured allelic distributions measured in the mixed sample, and choosing the ploidy state whose expected allelic distribution pattern most closely matches the observed allelic distribution pattern. The mixed sample of DNA may be preferentially enriched at a plurality of polymorphic loci in a way that minimizes the allelic bias, for example using massively multiplexed targeted PCR.

Abstract: The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing. Such polynucleotide processing may be useful for a variety of applications, including polynucleotide sequencing.

Abstract: The present invention relates to a method for the detection of the presence or absence of at least one nucleic acid sequence specific for the sex of chicken using polymerase chain reaction in a high-throughput manner, a kit for conducting the method of the present invention and a pair of oligonucleotides.

Abstract: The present invention relates to novel methods for the prevention, treatment and diagnosis of Alzheimer's disease. In addition, the invention relates to methods for assessing an individual's susceptibility or pre-disposition to Alzheimer's disease. The methods of the present invention involve the use of therapeutic targets and diagnostic and/or predictive markers within the mTOR signalling pathway. The methods also involve screening subjects for genetic polymorphisms associated with rapamycin-sensitive genes.

Abstract: The invention provides methods for simultaneously amplifying multiple nucleic acid regions of interest in one reaction volume as well as methods for selecting a library of primers for use in such amplification methods. The invention also provides library of primers with desirable characteristics, such as minimal formation of amplified primer dimers or other non-target amplicons.

Abstract: The present invention relates to prognosing, diagnosing and treating an aggressive form of Crohn's disease characterized by rapid progression to complication and/or surgery from the time of diagnosis. In one embodiment, the prognosis, diagnosis and treatment is based upon the presence of one or more genetic risk factors.

Abstract: Methods and compositions are provided for the molecular subtyping of lung cancer samples. Specifically, a method of assessing whether a patient's adenocarcinoma lung cancer subtype is terminal respiratory unit (TRU), proximal inflammatory (PI), or proximal proliferative (PP) is provided herein. The method entails detecting the levels of the classifier biomarkers of Table 1-Table 6 or a subset thereof at the nucleic acid level, in a lung cancer sample obtained from the patient. Based in part on the levels of the classifier biomarkers, the lung cancer sample is classified as a TRU, PI, or PP sample.

Abstract: Described herein is a mutation that confers resistance to the treatment with a BTK inhibitor. Described herein is a modified PLC?2 polypeptide that is modified at amino acid position 742, 845, or 1140 and the modified PLC?2 polypeptide exhibits decreased inhibition (e.g., resistance) to a covalent and/or irreversible BTK inhibitor. Described herein are diagnostic methods for detecting the modified polypeptide and nucleic acid encoding the modified polypeptide and applications of the methods thereof. Described herein are compositions, combinations, and kits containing the modified polypeptide and methods of using the modified polypeptide. Also described herein are methods of using the modified polypeptide as screening agents for the identification and design of inhibitors of PLC?2.

Abstract: The present invention refers to the field of cancer and, in particular, to an in vitro method for the diagnosis of lung cancer by determining in a biological sample, taken from a subject, the methylation level of particular genes. It further relates to biomarkers and kits useful for said method.

Abstract: Aspects of the invention relate to detecting single nucleotide polymorphisms for CD33 and determining whether a subject is likely to respond to treatment with agents that selectively bind to CD33 based on the genotype of the subject for one or more CD33 single nucleotide polymorphisms.

Abstract: New methods for treating patents for urothelial cancer (UC) include combining selected phenotypic variables with levels of genotypic expression into a metric, the “G+P INDEX.” The G+P INDEX combines age, sex, smoking history, presence of hematuria, and frequency of hematuria with genotypic expression of the genetic markers, MDK, CDC2, HOXA13, IGFBP5, and optionally IL8Rb, then determining of the G+P INDEX value obtained for a patient is within one of three groups, either: (1) at High Risk of UC, (2) at Risk of UC, or (3) at Low Risk of UC. For groups 1 and 2, further clinical and laboratory work up or treatment is indicated, and patients in group 3 are monitored periodically to determine the need for further clinical workup. Using the G+P INDEX can save substantial time, effort, and funds by avoiding unnecessary medical diagnostic procedures for patients having or are at risk for developing UC.

Abstract: Disclosed are biomarkers, methods and assay for the identification of cancer patients who are predicted to benefit from the therapeutic administration of Wnt antagonist. The biomarkers include detection of RNF43 and ZNRF3 gene deletion, reduced RNF43 and ZNRF3 mRNA expression, reduced RNF43 and ZNRF3 protein expression, RNF43 and ZNRF3 inactivation mutation, phosphorylated LRP6, phophorylated Dishevelleds, and the expression of Frizzleds. These biomarkers can be associated with the better outcome for cancer patients treated with Wnt pathway inhibitors.

Abstract: The present invention relates to a biomarker composition for diagnosing radiation-resistant cancer comprising LRP-1 as an active ingredient and a method of diagnosing radiation-resistant cancer using the same, and identifies LRP-1 which a binding partner protein to which specific peptide sequences specifically targeting radiation-resistant colon cancer tissues are actually bound, and based on this, suggests the possibility of radiation therapy resistance factor for cancer.

Abstract: A method of classifying kidney tumors is provided. The method includes obtaining a sample from a subject, isolating DNA from the sample, determining the methylation status of the DNA, and comparing the methylation status of the DNA to one or more GO methylated biomarkers selected from the following: cg04877910, cg09667289, cg05274650, cg1 1473616, cg16935734, cg27534624, cg21851713, cg15867829, cg15679829, cg08884979, cg09538401, cg26811868, cg05367028, cg19816080, cg20108357, cg25504868, cg1 1201447, cg19922137, cg14706317, cg15902830, cg10794973, cg10777887, cg03290131, cg07851269, cg1 1264947, cg00279406, cg23140965, cg03574652, cg03265671, cg24864241, cg01572891, cg00193963, cg14329285, cg17819990, cg17298239, cg23856138, cg21049501, cg1 1808936, cg25170591, cg17983632, cg08141142, cg19848599, cg25799109, cg07093324, cg16223546, cg07604732, cg12149606, cg08949329, cg27166177, cg26177041, cg09885851, cg22876153, cg21386992, cg02309772, cg02833180, cg20007890, cg04972244, cg02666955 and cg12102682.

Abstract: It is intended to develop a therapeutic strategy for specifically targeting cancer cells having the functional suppression of PSS2. The present inventors have found that PSS1 and PSS2 are in a synthetic lethal relationship, and treatment inhibiting PSS1 serves as a promising approach for the treatment of cancer having the functional suppression of PSS2. It has also been revealed that this therapeutic strategy permits efficient treatment based on companion diagnostics because a PSS1 inhibitor can be administered to a subject selected by using the functional suppression of PSS2 as an index.

Abstract: Methods, compositions and kits for screening for the presence of Epidermal Growth Factor Receptor variant 3 (EGFR(v3)) in a sample are disclosed. The method comprises obtaining a sample containing a plurality of cells; hybridizing a set of chromosomal probes to the sample, wherein the set comprises an EGFR(v3)-probe and a probe to chromosome 7 different from an EGFR(v3)-probe; and visualizing the hybridization pattern of the set of chromosomal probes in the plurality of cells of the sample, wherein the presence of at least one copy of chromosome 7 lacking a hybridization signal of the EGFR(v3)-probe in at least one cell is indicative of the presence of the EGFR(v3) in the sample. The methods, compositions and kits are suitable for diagnosing the therapeutic outcome for treating a patient having a cancer with an anti-EGFR therapeutic agent and for screening a sample for a predisposition for forming an EGFR-associated cancer.

Abstract: The invention relates to a method for in vitro diagnosis or prognosis of testicular cancer which comprises a step of detecting the presence or absence of at least one expression product from at least one nucleic acid sequence selected from the sequences identified in SEQ ID NOS: 1 to 6 or from the sequences which exhibit at least 99% identity with one of the sequences identified in SEQ ID NOS: 1 to 6, to isolated nucleic acid sequences and to the use thereof as a testicular cancer marker.

Abstract: A roller treatment process and a treatment device suitable for a total-amount steel slag treatment. The treatment process is: firstly, a slag tank (2) with the molten slag is tightly held by a slag tank tilting mechanism and moved to a slag inlet position, the slag tank (2) is tilted to pour the molten slag with good fluidity into a rotary roller device (5) through a feeding chute (51), so that a roller treatment is achieved; secondly, when the steel slag (3) without fluidity in the slag tank (2) cannot flow out, a slag removal machine (4) is used for pushing the high-viscosity slag or the solid slag into the roller device (5); and thirdly, the slag tank (2) is reversed by a large angle tilting to make the slag at the bottom of the tank drop into the roller device (5), so that the total-amount steel slag treatment of the same roller device (5) is achieved.

Abstract: An inoculant for manufacturing cast iron with lamellar, compacted or spheroidal graphite is disclosed. The inoculant has a particulate ferrosilicon alloy 40 and 80% by weight of silicon, 0.5 and 5% by weight of calcium and/or strontium and/or barium, 0 and 10% by weight of rare earths, 0 and 5% by weight of magnesium, less than 5% by weight of aluminium, 0 and 10% by weight of manganese and/or zirconium, and the balance being iron, wherein the inoculant additionally contains 0.1 to 10% by weight of particulate bismuth oxide particles and optionally 0.1 and 10% by weight of one or more particulate metal sulphides and/or one or more particulate iron oxides, where the particulate bismuth oxide is mixed or blended with the ferrosilicon particles, or is simultaneously added to cast iron together with the particulate ferrosilicon particles.

Abstract: This H section includes, as a chemical composition, C, Si, Mn, Nb, V, Ti, and N; in which the H section includes, as a metallographic structure, ferrite of 60 area % to less than 100 area %, an average grain size of this ferrite is 1 ?m to 30 ?m, a thickness of a flange is 20 mm to 140 mm, tensile yield stress is 385 MPa to 530 MPa, and Charpy absorbed energy at ?20° C. is 100 J or more.

Abstract: A method for manufacturing a high-strength cold-rolled steel sheet according to an embodiment includes the steps of: reheating a steel slab, which includes 0.10 wt % to 0.13 wt % carbon (C), 0.9 wt % to 1.1 wt % silicon (Si), 2.2 wt % to 2.3 wt % manganese (Mn), 0.35 wt % to 0.45 wt % chromium (Cr), 0.04 wt % to 0.07 wt % molybdenum (Mo), 0.02 wt % to 0.05 wt % antimony (Sb), and the remainder being iron (Fe) and inevitable impurities, at a temperature of 1150° C. to 1250° C.; hot-rolling the reheated slab in such a manner as to reach a finishing mill delivery temperature of 800° C. to 900° C.; cooling the hot-rolled slab to a temperature of 600° C. to 700° C. and coiling the cooled slab, thereby obtaining a hot-rolled steel sheet; pickling the hot-rolled steel sheet, followed by cold rolling; annealing the cold-rolled steel sheet in a two-phase region of ? and ? phases; and cooling the annealed steel sheet to the martensite temperature range, followed by overaging.