Abstract: The present invention relates to compositions and methods for the use of polymerase chain reaction (PCR) as a reporter assay for rapid and simultaneous bacterial identification and phenotype testing for antimicrobial susceptibility (AST). The current invention uses a strategy that has shown the ability for multiplexing and for handling polymicrobial samples for antimicrobial susceptibility testing.

Abstract: The present disclosure relates to nucleic acid extraction and purification methods and devices to accomplish the same.

Abstract: Disclosed herein in are methods and systems for determining genetic variants (e.g., copy number variation) in a polynucleotide sample. A method for determining copy number variations includes tagging double-stranded polynucleotides with duplex tags, sequencing polynucleotides from the sample and estimating total number of polynucleotides mapping to selected genetic loci. The estimate of total number of polynucleotides can involve estimating the number of double-stranded polynucleotides in the original sample for which no sequence reads are generated. This number can be generated using the number of polynucleotides for which reads for both complementary strands are detected and reads for which only one of the two complementary strands is detected.

Abstract: The present invention relates generally to methods and kits for detecting one or more biomarkers, such as an Epidermal Growth Factor Receptor (EGFR) mutation, e.g., T790M mutation, L858R mutation, one or more exon19 insertions and/or one or more exon19 deletions in the EGFR gene, in a biological sample to aid in diagnosis, prognosis, monitoring, or therapy selection for a disease such as, for example, cancer. The methods and kits are useful in aiding in diagnosis, prognosis, monitoring, or therapy selection for lung cancer, e.g., non-small cell lung cancer (NSCLC).

Abstract: Embodiments of a method and/or system can include generating a set of target-associated molecules (e.g., spike-in molecules) associated with one or more biological targets; generating one or more spike-in mixtures based on processing the set of target-associated molecules with one or more samples including the one or more biological targets; performing one or more Sanger sequencing operations on the one or more spike-in mixtures; determining one or more abundance metrics based on chromatogram-related outputs from the one or more Sanger sequencing operations; and/or facilitating characterization of one or more medical conditions based on the one or more abundance metrics.

Abstract: The present disclosure provides nucleic acid-based nanoswitch catenanes and methods of use. A nanoswitch catenane may include a single-stranded nucleic acid comprising a first and second terminal domain linked to each other to form a host ring by one of a first, second or third switchable bridges, wherein the first switchable bridge is formed in the presence of a reaction agent through the reaction of two cognate functional groups, each linked to a terminal domain of the single-stranded nucleic acid, wherein the second switchable bridge is formed in the presence of a biomolecule of interest through binding of the bio-molecule of interest to two cognate antibodies, each linked to a terminal domain of the single stranded nucleic acid, and wherein the third switchable bridge is a link between two cognate functional groups that breaks in the presence of a dissociation agent. A nanoswitch catenane may also include a circular nucleic acid guest ring catenated with the host ring.

Abstract: Medical systems for detecting a genetic variation in a polynucleotide analyte in a sample. A fluorophore is attached to a first primer, a quencher is attached to a second primer, and the first primer and the second primer are specific for the polynucleotide analyte. The primers are configured to amplify the polynucleotide analyte having the genetic variation and a corresponding polynucleotide analyte lacking the generic variation. There is a detectable difference between a change in signal generated by the fluorophore and quencher, and measured by a sensor of the medical system, when using the first and second primers to amplify the polynucleotide analyte with the genetic variation, and a change in signal generated by the fluorophore and quencher, and measured by the sensor of the medical system, when using the first and second primers to amplify the corresponding polynucleotide analyte lacking the genetic variation.

Abstract: Disclosed herein are systems, methods, and compositions useful for profiling T cell receptor (TCR) and B cell receptor (BCR) repertoire using next-generation sequencing (NGS) methods. In certain embodiments, the methods include enriching a sample for TCR/BCR RNA sequences, and determining the TCR/BCR profile of a subject using five different oligonucleotide pools. Also disclosed herein are systems and methods for diagnosing, treating, or predicting infection, disease, medical conditions, therapeutic outcome, or therapeutic efficacy based on the TCR/BCR profile data from a subject in need thereof.

Abstract: This invention relates to methods, compositions and kits for extending a polynucleotide and for preparing sequencing library of polynucleotides involving generating modified target polynucleotide on an adaptor template oligonucleotide and tagging one or two strands of a target sequence. The sequencing library is suitable for massive parallel sequencing and comprises a plurality of double-stranded nucleic acid molecules.

Abstract: Disclosed are a set of genes for bladder cancer detection and their use. The set of genes includes the following 32 genes: CA9 gene, CDK1 gene, CTSE gene, DMBT1 gene, ERBB2 gene, HOXA13 gene, IGF2 gene, CXCR2 gene, MAGEA3 gene, MDK gene, MMP1 gene, MMP12 gene, RBP2 gene, CCL18 gene, SNAI2 gene, VEGFA gene, MFAP5 gene, SGK2 gene, WFDC2 gene, POSTN gene, NPFFR2 gene, ANXA10 gene, CTAG2 gene, ZDHHC2 gene, KRT20 gene, PPP1R14D gene, FGD3 gene, AHNAK2 gene, SEMA3D gene, ZNF707 gene, LOC100652931 gene, and LINC00565 gene. After clinical validation, the kit provided by the present invention is used to detect bladder cancer with a high accuracy rate and objective interpretation of results. Meanwhile, as a non-invasive detection, the compliance of patients is greatly improved comparing with the existing cystoscopy, which has an important clinical significance for the early detection and postoperative monitoring of bladder cancer.

Abstract: The present invention provides a primer composition for analyzing intestinal flora, a detection kit composed thereof, and an application of the same. The present invention employs two-step amplification to obtain a sequencing library, and the primer composition comprises a random base.

Abstract: Provided herein are compositions, systems and methods for tagging molecular events, reactions, species, etc., but without the need for complex, highly diverse libraries of tagging molecules. Provided are tagging moieties that can have a smaller number, a few, or even a single original “tagging” structure that may be transformed or transformable, in situ, into a collection of larger numbers of unique tagging or “barcode” moieties.

Abstract: A method in which a microorganism operational taxonomic unit (OTU) in a sample is defined based on a DNA sequence of a system generation information gene of microorganism in the sample. In the method, qualified sequence segments are obtained by means of processing and reading of an original sequence; the segments are sorted according to a relative abundance value of each segment; and only the qualified sequences with the high abundance values are used to obtain the temporary OTU. The qualified sequences with the low abundance values are reallocated; and the qualified sequence can be distributed to the proper temporary OTU respectively when a sequence similarity degree between the qualified sequence and an OTU sequence reaches at least 97%. The present disclosure also provides a sequence-assisted microorganism separation method.

Abstract: Disclosed herein include systems, methods, compositions, and kits for PCR normalization. In some embodiments, after barcoding copies of a higher abundance target (e.g., a cDNA species), the barcoded copies are amplified using a pair of forward primers comprising one or more mismatches and a reverse primer. The amplified copies can be further linearly amplified using a forward primer comprising the sequence of one of the pair of forward primers, and a reverse primer.

Abstract: Disclosed are methods and systems for determining the three-dimensional structure of chromatin in eukaryotic cells. More specifically, disclosed are methods and systems for obtaining chromatin structural information by surface immobilization that includes tethering crosslinked protein:DNA complexes and/or ligated DNA complexes to media such as beads, gels, and or matrices during the conformation capture assay.

Abstract: The disclosure relates generally to molecular diagnostic devices configured to amplifying a single nucleotide polymorphism (SNP) locus and discriminate between two or more allelic variants of the SNP, indicating presence or absence of a target allele. In some embodiments, the molecular diagnostic devices are capable of detecting, at point-of-care, SNPs associated with resistance or susceptibility to antibiotic treatment of organism infections. In other aspects, the disclosure provides methods of treatment for disease or disorders (e.g. organism infections) where treatment is guided by presence or absence of an allele at a SNP locus as determined by such molecular diagnostic devices.

Abstract: The invention provides a method and kit for preventing inhibition of a thermal cycling reaction by protein coagulation in a sample.

Abstract: The present disclosure relates to methods for treating glioblastoma in a subject in need thereof using gene signatures in exosomal RNA derived from the subject. The gene signatures comprise: at least one of FAM229B, ZNF35, CTD-2647L4.4, CABP5, CYP20A1, CEP126, DTX2P1-UPK3BP1-PMS2P11, RP11-507K12.1, KRBA2, CALD1, LRFN1, RP2, SLC2A13, CDKL3, SLC8A3, ANTXR2, TIGD5, AC074289.1 RP11-932O9.7; at least one of tRNA-Lys-CTT-2-2, tRNA-Pro-AGG-2-7, LAMTOR2, RAD51AP1, DENND2A, A1BG, THSD1, CSF1, RP11-332M2.1, ZNF717, ZNF860, ORC6, Clorf50, PSPH, HIST1H4C, CYP2U1, THAP8, TMEM192, NAA20; or at least one of CREBBP, CXCR2 and S100A9. The treatment methods comprise measuring the expression level of at least one of the aforementioned genes in exosomal RNA from a subject and administering to the subject a glioblastoma treatment based on the expression level(s).

Abstract: The invention is a novel method of making and using a library such as a sequencing library of single stranded circular nucleic acid templates via splint ligation. In particular, disclosed are methods of making circular target nucleic acid molecules and libraries of such molecules for downstream analysis such as nucleic acid sequencing. The method comprises the steps of adding universal sequences to nucleic acid molecules, rendering single-stranded these nucleic acid molecules with universal sequences on their ends by contacting with a probe complementary to at least a portion of the universal sequences, and allowing the hybridized probe to enable circularization and formation of single-stranded circular (sscDNA) molecules.

Abstract: The invention relates to a method for the duplication of nucleic acids by means of a polymerase chain reaction, in the case of which a cycle consisting of the steps of denaturing, annealing and elongation is repeatedly performed. In one embodiment, in at least one passage of the cycle, the quotient of the duration of effect tA and the reaction volume Vr irradiated by the energy source is less than 1 seconds per microliter. In another embodiment, in at least one passage of the cycle, the ratio of the duration of effect (tA) and the duration of the PCR cycle (tc) is less than 20%. In certain embodiments, the yield (g) of nucleic acids at the end of at least one of the passages of the cycle is less than 80% of the nucleic acids present at the start of the passage.