Abstract: 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.

Abstract: The invention generally relates to methods for maintaining the integrity and identification of a nucleic acid template in a multiplex sequencing reaction. In certain embodiments, methods of the invention involve obtaining a template nucleic acid, incorporating a pair of sequence identifiers into the template, and sequencing the template.

Abstract: A method of detecting the length of an individual telomere is provided. In one embodiment, the method includes contacting genomic DNA with a guide RNA having a portion complementary to a telomere repeat sequence in the genomic DNA and with Cas9 nickase to produce a single-strand break in the genomic DNA at the telomere repeat sequence. The nicked DNA is contacted with a polymerase and fluorescently labeled nucleotide, wherein the fluorescently labeled nucleotide is incorporated into the nicked DNA at the telomere repeat sequence. The genomic DNA is contacted with a second nicking endonuclease which is specific for a sequence motif in the genomic DNA thereby producing a second nick in the genomic DNA at the motif sequence. The nicked DNA is contacted with a polymerase and second fluorescently labeled nucleotide of different color, wherein the second fluorescently labeled nucleotide is incorporated into the nicked DNA at the motif sequence location.

Abstract: A method for testing a sample for the presence of one or more targets comprises multiplexed catalyzed reporter deposition (CARD) is provided.

Abstract: Disclosed herein are method for separating, amplifying, or detecting a nucleic acid from a sample may comprise contacting a sample lysate with a plurality of buoyant, inorganic, nucleic-acid-capture microspheres. The nucleic-acid-capture microspheres may comprise unicellular hollow microspheres having a diameter between 5 and 300 ?m and/or a true particle density between 0.05 and 0.60 grams/cm3. The microspheres may comprise hollow soda-lime-borosilicate microspheres. In some embodiments, the microspheres comprises hollow soda-lime-borosilicate microspheres surrounded by an amorphous silica shell. Also disclosed are kits for performing the methods.

Abstract: The present disclosure describes oligonucleotide-tethered nucleotides, methods of making them, and methods of using them. The oligonucleotide-tethered nucleotides comprise, in some embodiments, a nucleotide linked to an oligonucleotide of from about 3 to about 100 nucleotides in length. These oligonucleotide-tethered nucleotides can be used to label a plurality of different types of nucleic acids in a plurality of different situations with a known oligonucleotide, which can serve as a barcode in some embodiments. The resulting oligonucleotide-labeled nucleic acids oligonucleotides can be used in a variety of nucleic acid sequencing methods.

Abstract: The present invention is directed to methods, compositions and systems for capturing and analyzing sequence information contained in targeted regions of a genome. Such targeted regions may include exomes, partial exomes, introns, combinations of exonic and intronic regions, genes, panels of genes, and any other subsets of a whole genome that may be of interest.

Abstract: A method for testing target nucleic acid includes the steps from (1) through (5) below: (1) mixing a specimen containing target nucleic acid with positive control nucleic acid to obtain a specimen mixture of the specimen and the positive control nucleic acid; (2) mixing the specimen mixture with a PCR buffer solution containing a surfactant to obtain a buffer solution mixture; (3) adding a portion of the buffer mixture to a solid composition for PCR control containing DNA polymerase, positive control nucleic acid, and PCR reaction control nucleic acid; (4) adding a portion of the buffer mixture to a solid composition for PCR reaction containing DNA polymerase and one or more kinds of PCR primer pair; and (5) detecting a PCR product generated as a result of the steps (3) and (4).

Abstract: The improved Tm mapping method using imperfect-match linear long quenching probes can accurately distinguish among and identify microorganisms at least at the genus level and often at the species level even in a real-time PCR instrument having measurement errors of Tm values between PCR tubes within ±0.5° C. Therefore, the Tm mapping method can be performed in almost all real-time PCR instruments and can identify unspecified infection-causing pathogenic microorganisms in about 4 hours after sample collection.

Abstract: This invention relates to methods and compositions for assessing an amount of total cell-free DNA, such as from a transplant subject. The methods and composition provided herein can be used to determine risk of complications following transplantation, including infection, cardiac arrest, and death, in a subject.

Abstract: The present invention provides methods, compositions and kits for detecting duplicate sequencing reads. In some embodiments, the duplicate sequencing reads are removed.

Abstract: qRT-PCR primers capable of detecting EML4-ALK gene variant based on circulating tumor cells at a more sensitive detection limit than a conventional method. Also disclosed is a lung cancer patient screening method which is capable of detecting EML4-ALK gene variant using circulating tumor cells even in a lung cancer patient on whom ALK-FISH testing has been difficult to perform, due to difficulty in collecting a solid lung cancer tissue sample, and is able to determine whether an anticancer drug targeting the EML4-ALK gene variant may be applied to the lung cancer patient.

Abstract: The present disclosure provides methods and materials for determining if antibiotic resistant H. pylori is present in a sample. The methods may comprise obtaining a threshold level of H. pylori DNA from the sample, amplifying a region of the H. pylori DNA to generate multiple copies of the region of the H. pylori DNA, sequencing the multiple copies of the region of the H. pylori DNA, comparing sequences of multiple copies of the region of the H. pylori DNA to a reference sequence, identifying the presence of a mutation in multiple copies of the region of the H. pylori DNA, and determining a number of the multiple copies of the region of the H. pylori DNA with the mutation, wherein antibiotic resistant H. pylori is present in the sample when the number of the multiple copies of the region of the H. pylori DNA with the mutation is above a predetermined amount.

Abstract: Methods of isolating cell free RNA from individual's bodily fluid and reliably obtain cell free RNA data are presented, preferably by use of high-stability portions and/or use of targeted small amplicons on the cell free RNA.

Abstract: Provided herein is a method for detecting the presence of clade variants in the COVID-19 virus in a human sample and/or an environmental sample. Samples are processed to obtain total RNA. The RNA is used as a template in a combined reverse transcription and amplification reaction to obtain fluorescent COVID-19 virus amplicons. These amplicons are hybridized on a microarray with nucleic acid probes having sequences that discriminate among the various clade variants. The microarray is imaged to detect the clade variant and each clade variant is distinguished from others by generating an intensity distribution profile from the image, which is unique to each of the clade variants.

Abstract: Methods, kits, and compositions for evaluating the quality of nucleic acids within a biological sample for analysis in a molecular assay are provided.

Abstract: The invention relates to a method for synthesising long nucleic acids, including at least one cycle of elongating initial fragments of nucleic acids, including a) a phase comprising the enzymatic addition of nucleotides to said fragments, b) a phase comprising the purification of the fragments having a correct sequence, c) an optional phase of enzymatic amplification, each cycle being performed in a reaction medium which is compatible with enzymatic addition and amplification, such as an aqueous medium, the synthesis method also comprising, at the end of all the elongation cycles, a last step of final amplification. The invention also relates to the use of the method for the production of genes, or sequences of synthetic nucleic acids, DNA or RNA. The invention further relates to a kit for implementing said method.

Abstract: The present disclosure relates to methods of enzymatic treatment of double-stranded PCR amplified products for eliminating or minimizing primer-dimers in multiplex PCR reactions and for the efficient ligation of adapters. The present disclosure relates to methods and compositions that allow more efficient highly multiplex target amplification compared to conventional methods, compositions and kits by minimizing laboratory steps, eliminating primer-dimers and increasing the efficiency of adapter ligation. The disclosed methods use multiple target-specific primers for specific and selective amplification of targets in a subject's genome. The disclosed methods can be used for numerous downstream procedures and analysis, including DNA sequencing.

Abstract: The present invention provides apparatus and methods for enriching components or cells from a sample and conducting genetic analysis, such as SNP genotyping to provide diagnostic results for fetal disorders or conditions.

Abstract: A portable nucleic acid extraction kit includes a portable nucleic acid extraction apparatus, at least one lysis buffer, at least one binding buffer, at least one washing buffer, at least one elution buffer, and at least three kit sample tubes. The portable nucleic acid extraction apparatus includes a handle, a rod, a tip, and may include a nucleic acid binding medium. The method of using the portable nucleic acid extraction apparatus includes, treating a biological sample having a nucleic acid, binding the nucleic acid in the treated biological sample to the tip of the portable nucleic acid extraction apparatus, incubating the tip of the portable nucleic acid extraction apparatus bound with the nucleic acid, washing the tip of the portable nucleic acid apparatus bound with the nucleic acid, eluting the bound nucleic acid, and analyzing the eluted nucleic acid.