Abstract: Provided herein are compositions and methods for accurate and scalable Primary Template-Directed Amplification (PTA) nucleic acid amplification and sequencing methods, and their applications for research, diagnostics, and treatment.

Abstract: The present disclosure discloses a method for detecting single strand breaks (SSBs) in DNA based on the following steps. First, DNA of interest is fragmented with a method that generates 3? ends that cannot be tailed. Second, the available 3? ends of the fragmented DNA corresponding to the pre-existing breaks are tailed. Third, SSBs are captured and their positions are identified genome-wide based on the following steps: (1) the tailed fragments are linearly amplified using a chimeric 5?-DNA-RNA-3? primer; (2) the products of primer extension are tailed at the 3? ends; (3) the desired products are amplified by PCR with oligonucleotides containing Illumina® adaptor sequences complementary to both tails and subjected to next-generation sequencing (NGS); 4) finally, positions of SSBs are revealed through the analysis of sequencing results.

Abstract: Devices, containers, and methods are provided for performing biological analysis in a closed environment. Illustrative biological analyses include high density nucleic acid amplification and detection and immuno-PCR.

Abstract: A primer set for detecting telomerase activity, the primer set including a first primer set or a second primer set. The first primer set includes: an upstream primer selected from MTS; and a downstream primer selected from the group consisting of ACX-M4, Beacon ACX62-2C, and Beacon ACX62-10. The second primer set includes: an upstream primer selected from STS or CTS; and a downstream primer selected from the group consisting of ACX, CXT, ACX-M4, Beacon ACX62-2C, or Beacon ACX62-10. The sequences of the primers ACX, CXT, ACX-M4, Beacon ACX62-2C, Beacon ACX62-10, STS, CTS and MTS are shown as SEQ ID NOs: 1 to 8, respectively.

Abstract: A minimal-copy-ratio of templates is a problem in detecting early stage cancer where minimal copies of somatic cancer-specific mutations are targeted in the presence of large copies of wildtype genome DNA, commonly a 1/10,000 or even less minimal-copy-ratios between the mutant target and wildtype control templates. To overcome this problem, delayed pyrophosphorolysis activated polymerization (delayed-PAP) was developed which can delay product accumulation of the wildtype control to a much later time or cycle, such as by 15 cycles or by 30,000 folds. In the multiplex format, delayed-PAP is particularly useful to amplify not only the wildtype control but also mutant target templates accurately and consistently in the minimal-copy-ratio situation.

Abstract: A portable genome sequencing and genotyping device includes a sample processing module, a sequencing module, an analyzing module, and a communication module. The sample processing module is configured to process a sample so as to generate at least one DNA segment of the sample. The sequencing module is connected to the sample processing module, and is configured to generate a number of base sequences corresponding to the at least one DNA segment. The analyzing module is coupled to the sequencing module, and is configured to generate a genotyping analysis result based on the base sequences. The communication module is configured to receive the genotyping analysis result and transmit the genotyping analysis result to a user terminal.

Abstract: Provided herein are methods, compositions, and kits for removing a portion of a sequence in a member of a nucleic acid library.

Abstract: Disclosed in the present invention are a digital nucleic acid amplification testing method and an integrated detection system based on CRISPR-Cas technology. The integrated detection system comprises an integrated reaction chip, a temperature control module, a light source and an optical signal detector. The method comprises: uniformly dividing a nucleic acid amplification reagent into amplification micro-droplets, then mixing the amplification micro-droplets after digital nucleic acid amplification with detection micro-droplets containing CRISPR-Cas detection reagent to perform a CRISPR reaction, and when the reaction is finished, detecting an optical signal to realize high-specificity testing of a target object, and the concentration or copy number of nucleic acid molecules in a sample to be tested is also obtained, and high-sensitivity absolute quantitative testing of a target object is realized.

Abstract: Disclosed herein is a method which includes extracting genomic deoxyribonucleic acid (DNA) at locations at or near cancer hotspots from a subject, modifying Tier-1 5hmC on the DNA to a modified 5hmC, detecting and identifying the presence or absence of the modified 5hmC, quantifying the detected and identified modified 5hmC; and providing a report comprising a score, wherein the score is indicative of the presence of cancer.

Abstract: Disclosed herein are methods, compositions, and devices for use in the early detection of cancer. The methods include preparing cell-free nucleic acid molecules from a subject for sequencing, sequencing a panel of regions in the cell-free nucleic acid molecules, and detecting one or more markers that are indicative of a cancer.

Abstract: The invention is directed to compositions and methods for collecting, transporting, and storing, without refrigeration, biological materials, which may comprise samples of biological, clinical, forensic, and/or environmental origin. These compositions preserve the viability of the collected organisms and/or the RNA/DNA and proteins in the sample composition mixture and permit the long-term storage of samples. Compositions are compatible with subsequent manipulation of the sample, including propagation and culture of the collected microorganisms, or isolation, purification, detection, and characterization of proteins, nucleic acids, and other macromolecules.

Abstract: Disclosed herein are methods, compositions, and devices for use in the early detection of cancer. The methods include preparing cell-free nucleic acid molecules from a subject for sequencing, sequencing a panel of regions in the cell-free nucleic acid molecules, and detecting one or more markers that are indicative of a cancer.

Abstract: Disclosed herein, inter alia, are substrates, kits, and efficient methods of preparing and sequencing two or more regions of a double-stranded polynucleotide.

Abstract: Described herein are devices, systems, and methods for trapping single-cell lysates in sealed, microwells capable of printing RNA on glass or capturing RNA on beads. These provide efficient, inexpensive manipulation of RNA from individual cells suitable for single-cell transcriptomics on a large scale. Also described are dual barcode capture beads and merged barcode capture beads.

Abstract: The present invention relates to a microfluidic system including a temperature controller and a thermoplastic microfluidic chip that enables rapid PCR in a PCR chamber of the microfluidic chip. Thermal control of the PCR chamber is achieved by applying voltage to heater electrodes patterned directly onto one layer of the microfluidic chip. The temperature controller adjusts the voltage applied to the heater electrodes by changing temperature controller parameters selected to minimize duration of each PCR cycle. Furthermore, simple operation of the microfluidic chip is provided through using an integrated passive capillary valve, requiring minimum operator intervention and eliminating the need for fluidic interfacing, pumping, or metering during chip loading.

Abstract: Methods of detecting the absence or presence of a micro-organism in a sample comprising: contacting the sample with a nucleic acid molecule which acts as a substrate for nucleic acid modifying activity of the micro-organism in the sample, incubating the thus contacted sample under conditions suitable for nucleic acid modifying activity; and specifically determining the absence or presence of a modified nucleic acid molecule resulting from the action of the nucleic acid modifying activity on the substrate nucleic acid molecule to indicate the absence or presence of the micro-organism. Corresponding kits are also provided.

Abstract: Provided herein are compositions and methods of use thereof for screening a plurality of uniquely identifiable therapeutic moiety in vivo by identifying one or more reporters indicative of a cell state.

Abstract: The present invention provides a method for sequencing a nucleic acid using an immersion reaction protocol. The immersion reaction protocol comprises sequentially immersing a solid support having nucleic acid molecules immobilized thereon in different reaction containers to realize nucleic acid sequencing.

Abstract: Disclosed is a method for sequencing a nucleotide sequence of a target nucleic acid. The method comprises: providing a pool of amplicons, wherein the pool of amplicons is prepared by attaching a unique identifier to the target nucleic acid, and amplifying by PCR the target nucleic acid to which the unique identifier is attached; and sequencing the amplicons comprising the unique identifier and the target nucleic acid. In the method, a nucleotide sequence of the unique identifier comprises both a random nucleotide (N) and a predetermined nucleotide.

Abstract: The present invention discloses a Polymerase Chain Reaction (PCR) apparatus for real-time detecting of one or more fluorescent signals. According to the apparatus, the PCR is performed by controlling heating and cooling intervals of a reagent container receiving space. With the aid of an added specific probe and fluorescent material, as well as a light source and a spectrometer, a generated fluorescent signal is detected. Meanwhile, the apparatus is also pre-loaded with an algorithm configured to analyze and quantify the fluorescent signal in a real-time manner.