171 results about "DNA sequencing" patented technology

Methods and systems for analysis of image data generated from various reference points. Particularly, the methods and systems provided are useful for real time analysis of image and sequence data generated during DNA sequencing methodologies.

The invention belongs to the technical field of biomedical engineering, and particularly relates to a single-base resolution laminated two-dimensional material nanopore structure, a DNA sequencing device and a DNA sequencing method. The two-dimensional material nanopore structure comprises an insulating layer and conducting layers arranged on the upper side and the lower side of the insulating layer, through nanopores are formed in the insulating layer and the conducting layers, and the pore diameter of the nanopores is 2-5 nm; the insulating layer and the conductive layer are made of two-dimensional materials. The conductive layers on the two sides serve as upper and lower electrodes, and a power supply is connected between the upper and lower electrodes to form a phase conductive path which is provided with a longitudinal current detection element. A plurality of groups of two-dimensional material nanopore structures are stacked, and meanwhile, a plurality of groups of base pair signals are obtained. According to the invention, the advantages of small thickness, high physical strength and the like of the two-dimensional material nanopore are kept by using a few layers of two-dimensional material films, the vibration of the films is reduced by increasing the number of layers and improving the mechanical strength, so that the signal-to-noise ratio is improved, and the spatial resolution of the nanopore sensor is improved by designing the upper electrode and the lower electrode.

The invention discloses a biomarker combination for predicting calendar age, a model and application of the biomarker combination. 57 kinds of DNA methylated CpG sites screened from many elderly subjects are creatively introduced, through multiple detection and large-scale parallel DNA sequencing, operation is easy, the result is highly repeatable, and the age prediction model constructed based on the method is good in stability and accuracy and high in sensitivity and has good application prospects. Calendar age can be predicted from trace blood samples associated with forensic cases.

Provided herein are modified Archaeal family B polymerases derived from species of the Archaeal microorganism Pyrococcus that exhibit improved incorporation of nucleotide analogues utilized in DNA sequencing.

Disclosed herein are systems, methods, and compositions for identifying subjects likely to respond to an immune oncology therapy. The disclosed methods may include applying one or more model components to a machine learning algorithm. The one or more model components are derived from RNA and / or DNA sequencing from a subject and may include a checkpoint related gene signature, an immune exhaustion signature, a immune oncology signature, a tumor mutational burden, or a granulocytic myeloid derived suppressor cell signature.

The present disclosure provides flow cell devices, systems, and methods for facilitating and performing DNA sequencing analysis with reduced system complexity and cost, significant cost of goods (COGS) savings and reduced contamination levels.

Methods and systems for analysis of image data generated from various reference points. Particularly, the methods and systems provided are useful for real time analysis of image and sequence data generated during DNA sequencing methodologies.

This invention provides a process for sequencing single-stranded DNA by employing a nanopore and modified nucleotides.

The invention relates to the technical field of polymerase, and provides a high-fidelity Pfu DNA polymerase mutant and a preparation method and application thereof.The mutant at least comprises one mutation of the following sites on the basis of wild-type Pfu DNA polymerase with the amino acid sequence shown as SEQ ID NO: 1: V82A, G211R, E383K, R594K and W616V. A plurality of mutant Pfu DNA polymerases with good enzyme activity and high fidelity are obtained by performing mutation modification on amino acids at multiple sites (V82A, G211R, E383K, R594K and W616V) of wild Pfu DNA, and mutants with five sites protruding all have the best enzyme activity and the highest fidelity and are suitable for a DNA sequencing technology, an NGS library building technology and the like.

The invention discloses an intelligent compression system and method for sequencing data, and relates to the field of intelligent compression, and the method comprises the steps: firstly obtaining a plurality of short gene sequences containing ID, Base and Quality data, and then carrying out compression processing on the to-be-stored DNA sequencing data. A short gene sequence to be compressed is matched with a spliced sequence, and if all Base data are successfully matched, direct compression is carried out; and if partial matching exists, splitting into a matched sequence and an unmatched sequence, and respectively compressing the matched sequence and the unmatched sequence. And for an unmatched sequence, further segmenting the unmatched sequence into a sub-sequence set, obtaining a refined subset based on sequence selection guided by population feature distribution, and finally carrying out compression coding on the refined subset. According to the method, the compression ratio is effectively improved, particularly when unmatched sequences are processed, redundant information is reduced through fine screening, the overall storage efficiency and the data retrieval speed are improved, and the effective mining capacity for long-range redundancy is further enhanced.

The invention discloses a sub-nano two-dimensional heterojunction nanopore preparation method based on HIM pore preforming and STEM closed-loop control, and belongs to the technical field of micro-nano manufacturing and MEMS. HIM is utilized to form a 1-3 nm primary pore in a two-dimensional heterojunction film, and then level convergence of the pore diameter is achieved in the STEM through HAADF image intensity threshold monitoring and PID self-adaptive control; and the nano titanium dioxide is stably controlled in a range of 0.5-0.9 nm. The prepared hole has the characteristics that mu belongs to [0.50, 0.90] nm, sigma is smaller than or equal to 0.10 nm, RMS is smaller than or equal to 0.30 nm, the drift rate is smaller than or equal to 0.02 nm.h <-1 > and the like, the repeatability of the hole preparation process is high, the edge is smooth and stable, and the method is suitable for DNA sequencing, ion screening and environmental combined pollutant detection.

The present disclosure relates to predicting genomic instability status in biological samples using machine learning techniques with comprehensive genomic and immune profiling (CGIP) data. Particularly, aspects are directed towards performing a genomic instability test on a biological sample. Then, multi-omics data for the subject are obtained by DNA sequencing and RNA sequencing assays, including genomic alteration data for a first set of genes and expression data for a second set of immune genes. The multi-omics data are input into a machine learning model having a tree-based architecture, which is configured to analyze features by traversing paths from root nodes to terminal nodes in each tree based on values generated from the data. The model predicts a genomic instability status, which is then provided via a user interface notification or as part of a testing report.

The invention discloses a compression and decompression method for DNA sequencing data, and belongs to the technical field of biological information. The technical problems that in the prior art, when third-generation sequencing data are compressed, flexibility is poor, and the compression rate is low are solved. According to the compression method for the DNA sequencing data, global compression or block compression can be dynamically selected before compression, different compression methods are adopted for different types of data, and the flexibility of the compression method is improved; when the base sequence is compressed, the adopted self-indexing structure is a lossless compression method, the initial positions of all the sequences can be compressed and restored by using smaller data volume, and the compression rate is improved. Due to the fact that a special design is adopted in a run length coding structure, a character part is removed, an obtained run length segment is shorter, lossless compression of the position and the sequence is guaranteed, and meanwhile a better compression effect is provided. The method is mainly used for compression and decompression of DNA sequencing data.

The invention belongs to the technical field of biological medicine, and discloses a cancer risk prediction and personalized vaccine preparation system and method based on single sample DNA sequencing, and the system comprises: a, a microsampling module; b, a multi-omics analysis engine; the engine synchronously executes the following operations: identifying a cfDNA terminal motif mode through a convolutional neural network; the presentation probability of the HLA-II type molecules is predicted on the basis of a Transform architecture; quantifying tumor mutation load (TMB) and microsatellite instability (MSI); c, a vaccine synthesis device; the device comprises: a programmable microfluidic mRNA synthesis chip; a self-assembly unit of lipid nanoparticles (LNP); and d, a closed-loop feedback system: monitoring the IFN-gamma through a wearable device to dynamically adjust the vaccine dosage. According to the invention, the early canceration detection rate can be improved, the antigen prediction accuracy is improved, the timeliness demand of early cancer intervention is met, and the adverse reaction rate is reduced.

Described herein are variants of alpha-hemolysin having at least one mutation, such as a mutation to a positive charge. In certain examples, the mutation is selected from V149K, E287R, H35G, T109K, P151K, K147N, E111N, M113A, or combinations thereof in the mature, wild-type alpha-hemolysin amino acid sequence. The α-hemolysin variants may also include a substitution at H144A and / or a series of glycine residues spanning residues 127 to 131 of the mature, wild-type alpha hemolysin. Also provided are nanopore assemblies including the alpha-hemolysin variants, the assembly having a decreased time-to-thread. The decreased time-to-thread, for example, increases DNA sequencing efficiency and accuracy.

Methods and systems for analysis of image data generated from various reference points. Particularly, the methods and systems provided are useful for real time analysis of image and sequence data generated during DNA sequencing methodologies.

Provided herein are modified Archaeal family B polymerases derived from the Archaeal microorganism Pyrococcus abyssi that exhibit improved incorporation of nucleotide analogues utilized in DNA sequencing.

The invention belongs to the technical field of plant molecular biology, and discloses a PCR amplification primer suitable for molecular identification of amorphophallus konjac and amorphophallus albus hybrids, the PCR amplification primer comprises a ZJ20 primer, and the sequence of the ZJ20 primer is F: CAGACCATAATCAGCATG; r is GTCTCCACT GCCGTACCTT, and R is GTCTCCACT The molecular identification method comprises the following steps: step 1, extracting genome DNA of a to-be-detected konjak sample, carrying out amplification by using the PCR primer, then carrying out first-generation DNA sequencing, and if a hybrid genotype A / T is observed at three positions of 170-180bp, 190bp-200bp and 210bp-220bp, determining that a hybrid first filial generation of amorphophallus konjac and amorphophallus albus is obtained, and a reaction system for PCR amplification in the step 2 is as follows: the reaction total volume is 25 microliters, and the reaction time is 30 minutes; a reagent contained in the step 3 is as follows: 12.5 mu L of a 2 * PCR Mix premixed solution, 0.3 mu M of R and F primers and 30 ng of a sample genome DNA solution, finally, sterile ultrapure water is used for complementing the deficient volume, and the amplification process of the PCR reaction in the step 3 is as follows: pre-denaturation at 95 DEG C is performed for 5 minutes, then denaturation at 95 DEG C is performed for 45 seconds, annealing at 56 DEG C is performed for 45 seconds, extension at 72 DEG C is performed for 45 seconds, and 35 amplification cycles are performed in total.

Example systems and methods for de novo sequencing of DNA or DNA-like sequences using Viterbi-like correlation analysis are described. A sequencing system receives the read data for multiple copies of a DNA strand from a sequence reader, such as a nanopore reader. The sequencing system generates a convolutional matrix based on one copy and a reference matrix based on another copy and uses them to generate a correlation matrix. A most likely path through the correlation matrix is determined to identify and correct errors between the two copies.

Described are DNA sequencing systems and methods. Systems and methods may establish a link between read sequences when the sequences are within a threshold distance. The read sequences that are mapped and aligned with high confidence may be used to determine the location of the nearby linked read sequences that would otherwise be difficult to place. The systems and methods may identify structural variants in the polynucleotide by analyzing sequence reads located within a threshold distance to the anchor sequence reads on the flowcell to determine sequence reads linked to the anchor sequence reads.

Fluorescence imaging systems and methods of are described herein that enable imaging of sequencing samples with a light source of a single color and a single image sensor. The optical systems herein provides higher signal efficiency, simpler optical filter design, and lower costs for DNA sequencing analysis and other imaging applications.

The present disclosure provides flow cell devices, systems, and methods for facilitating and performing DNA sequencing analysis with reduced system complexity and cost, significant cost of goods saving, and reduced contamination level. The sequencing systems described herein permit processing of multiple flow cells simultaneously, such that sequencing and imaging steps, or multiple sequencing methods, can be performed in parallel using a single sequencing system.

The present application relates to the technical field of fluorescent dyes, in particular to an asymmetric pentamethine cyanine compound. The compound comprises a structure as shown in formula I. The compound provided by the present application has good water solubility, near-infrared absorption, high fluorescence quantum yield and good molar absorption coefficient, and can be used in nucleic acid labeling, DNA sequencing, cell imaging, protein labeling or specific recognition of amino acids.

The invention discloses a method for adding name information to a protein or a strain or a cell and enabling a name to be never decayed and application. The method comprises the following steps: creating a name for the protein or the strain or the cell; representing each character in the name of the protein or strain or cell with a specific DNA sequence fragment; connecting the DNA sequence fragments in series to form a tandem DNA sequence; fusing the tandem DNA sequence with name information and the DNA sequence of the protein into a fusion gene; constructing the fusion gene into an expression vector, and transforming the vector into a host strain or cell; and checking the expression condition of the fusion protein in the strain or the cell. According to the invention, tandem DNA or fusion protein with names or strains or cells containing name information can be obtained. The name information of the fusion protein can be read through DNA sequencing or indirectly verified through expression of the fusion protein. The method has the advantages that a name can be added to the protein or the strain or the cell, and the protein or the strain or the cell with the proprietary intellectual property right can be obviously proved compared with a common DNA information storage technology. Besides, the protein, the strain and the cell are named and DNA with name information is added, so that the protein, the strain and the cell are personified, and the protein, the strain and the cell with names are more interesting. And the name can be never decayed along with passage of strains and cells.

The invention discloses a method for improving backfat thickness of Sichuan consumption cattle, which is characterized in that the genotype of SNP (Single Nucleotide Polymorphism) of COL8A1 gene of Sichuan consumption cattle is detected, the SNP is located at the 44071475th site of the first chromosome of an AR-UCD2.0 version cattle genome NC037328.1: 44071475, the backfat thickness of a TT genotype individual is obviously lower than that of a CT or CC genotype individual, and the TT genotype is a dominant genotype. The genetic polymorphism of the COL8A1 gene of the Sichuan yak and the correlation between the COL8A1 gene and the meat quality character are found through a DNA sequencing technology and a PCR method in molecular biology, the backfat thickness character of the Sichuan yak can be evaluated through the genetic polymorphism, molecular breeding of the backfat thickness character of the Sichuan yak is carried out, and the backfat thickness of the Sichuan yak is improved. The invention provides a theoretical basis for marker-assisted breeding for improving meat quality of yaks and establishment of dominant high-quality groups.

A disease prediction method, a model training method and apparatus, and a storage medium, the training method comprising: obtaining pre-training data and fine tuning data, the pre-training data comprising a plurality of DNA sequencing data, the fine tuning data comprising a plurality of DNA sequencing data and a type tag; pre-training a first generative model by using the pre-training data to obtain model pre-training parameters; performing fine tuning on the first generative model by using the fine tuning data to obtain model fine tuning parameters; and combining the model fine tuning parameters with the model pre-training parameters, and loading the combined parameters into the first generative model to obtain a trained disease prediction model.

The invention relates to the technical field of petroleum development, and discloses an inter-well connectivity calculation method based on a time step response relationship, which comprises the following steps: collecting and sequencing bacterial genome DNA of a water injection well and a producing well of an injection-production well, and determining corresponding strain types and bacterial abundance; the method comprises the following steps: constructing an impulse response model, respectively taking measured values of strain types and bacterial abundance of a water injection well and an oil production well as an input signal and an output signal in the impulse response model, introducing a Kalman filtering method to construct a response relationship based on time steps between the water injection well and the oil production well, and solving the response relationship by utilizing Laplace transformation, obtaining the strength of the response relation between the water injection well and the oil production well; representing the connectivity between the water injection well and the oil production well by utilizing the strength of the response relationship, and determining the connectivity between the water injection well and the oil production well; according to the method, the microorganism DNA sequencing result and the Kalman filtering calculation method are combined, and the dynamic change rule of the connectivity between the injection wells and the production wells is efficiently reflected in real time.

The present invention relates to a method for determining the sequence of a nucleic acid molecule. Specifically, the present invention provides a method comprising: i. Providing a nucleic acid molecule comprising a 5 '-region and a 3'-region wherein the 5 '-region and the 3'-region are covalently linked by a nucleotide sequence that can bind to a primer wherein the 5 '-region and the 3'-region are covalently linked by a nucleotide sequence that can bind to the primer, the base identity in one of the 5'region or the 3 'region and the base identity in the other region independently provide information about the base identity in the corresponding locus in the original nucleic acid molecule wherein the molecule further comprises: a linker located at the 5'end of the molecule; a linker located at the 3'end of the molecule; ii. Sequencing the molecule provided in step (i) using at least two different primers wherein the at least two different primers bind to at least three, preferably at least four, different regions of the nucleic acid molecule provided in (i), wherein: 1. At least one of the primers is capable of binding at least partially to at least a portion of the linker at the 5'end of said molecule for sequencing at least a portion of the 5 'region of the nucleic acid molecule provided in (i); 2. At least one of the primers is capable of at least partially binding to a nucleotide sequence region covalently linking the 5'region and the 3 'region of the nucleic acid molecule provided in (i) to sequence the 3' region of the nucleic acid molecule provided in (i); 3. At least one of the primers is capable of binding at least partially to at least a portion of the linker at the 3'end of the molecule to sequence at least a portion of the 3 'region of the nucleic acid molecule provided in (i); and / or 4. At least one of the primers is capable of at least partially binding to a region covalently linked to the 5'region and the 3 'region of the nucleic acid molecule provided in a to sequence the 5' region of the nucleic acid molecule provided in (i).

Next Generation DNA sequencing promises to revolutionize clinical medicine and basic research. However, while this technology has the capacity to generate hundreds of billions of nucleotides of DNA sequence in a single experiment, the error rate of approximately 1% results in hundreds of millions of sequencing mistakes. These scattered errors can be tolerated in some applications but become extremely problematic when “deep sequencing” genetically heterogeneous mixtures, such as tumors or mixed microbial populations. To overcome limitations in sequencing accuracy, a method Duplex Consensus Sequencing (DCS) is provided. This approach greatly reduces errors by independently tagging and sequencing each of the two strands of a DNA duplex. As the two strands are complementary, true mutations are found at the same position in both strands. In contrast, PCR or sequencing errors will result in errors in only one strand. This method uniquely capitalizes on the redundant information stored in double-stranded DNA, thus overcoming technical limitations of prior methods utilizing data from only one of the two strands.

There is a need for improved methods for determining the diagnosis and prognosis of patients with conditions, including autoimmune disease and cancer, especially lymphoid neoplasms, such as lymphomas and leukemias. Provided herein are methods for using DNA sequencing to identify personalized, or patient-specific biomarkers in patients with lymphoid neoplasms, autoimmune disease and other conditions. Identified biomarkers can be used to determine and / or monitor the disease state for a subject with an associated lymphoid disorder or autoimmune disease or other condition. In particular, the invention provides a sensitive method for monitoring lymphoid neoplasms that undergo clonal evolutions without the need to development alternative assays for the evolved or mutated clones serving as patient-specific biomarkers.