234 results about "DNA sequencing" patented technology

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.

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 long-time inter-well injection and production connectivity discrimination method based on microorganism DNA sequencing in the technical field of oil-water well connectivity detection, which comprises the following steps of: sampling from a water injection well and a production well according to a set time interval and circulation time respectively, pretreating the sample, and then extracting DNA and sequencing DNA; based on the sequencing results of the water injection well produced fluid sample and the production well produced fluid sample, comparing and analyzing the difference of the two samples under the time scale so as to judge the injection-production connectivity; according to the method, sampling, sequencing and data analysis are carried out in a mode of screening and tracing strains and in a mode of endogenous tracing, main coordinate analysis is carried out on a sequencing result to reduce the dimension of a high-dimensional similarity matrix into a low-dimensional space, the decoupling difficulty of effective information is effectively reduced, and on the basis, the accuracy of data analysis is improved. By comparing and analyzing composition differences of microbial communities in production fluid samples of a water injection well and a production well under different time scales, the connectivity between the injection wells and the production wells is judged, and dynamic monitoring of the connectivity between the wells in a long-term and large-range mode is achieved.

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.

The invention relates to a method for screening FMT (intestinal flora transplantation) donors easy to colonize. Comprising the following steps: collecting excrement of a receptor before intestinal flora transplantation, performing full-length 16s DNA sequencing on the excrement and a donor library, calculating the abundance and satisfaction degree of the donor and the receptor, and the like. The method provided by the invention can be used for screening a donor sample library easy to colonize for the FMT and screening and matching proper donors for patients, so that the colonization of donor strains after the FMT and the effectiveness of the FMT are ensured.

The invention belongs to the field of oncology and computational biology, and discloses a method for reconstructing tumor clone heterogeneity and evolutionary relationship based on tumor DNA sequencing data. Comprising the steps of mutation multiplicity and cancer cell fraction calculation, subcloning clustering and recognition, clustering post-processing, tumor cloning evolutionary tree inference, subcloning proportion calculation and tumor sample evolutionary tree inference. According to the method, the mutation multiplicity of SNV is calculated through the Euclidean distance to accurately represent the CCF, and the subcloning clustering result is post-processed to evaluate the credibility and rationality of the subcloning clustering result. Secondly, quickly deducing a tumor cloning evolutionary tree by adopting a greedy strategy, and calculating a subcloning proportion according to an evolutionary relationship;

The invention discloses a fluid production profile dynamic interpretation method based on microorganism DNA sequencing diagnosis in the technical field of oil exploration and exploitation, and the method comprises the steps: obtaining stratum microorganism baselines with high-resolution characteristics of different stratums through sampling and DNA sequencing of fluid production and rock debris of different well types; by comparing five evaluation indexes of accuracy, precision, recall rate, F1-score and calculation time of three clustering methods of naive Bayes, random forest and bp neural network, the random forest algorithm is optimized and improved, a liquid production profile interpretation model based on the stratum and liquid production strain feature PSO-random forest algorithm is constructed, and the liquid production profile of each stratum can be accurately described. The fluid production profile interpretation method is high in calculation precision and short in time consumption, production does not need to be stopped in the testing process, operation is easy, no pollution is caused to the stratum, and meanwhile the purpose of long-term effective dynamic monitoring of the oil reservoir can be achieved by sampling the produced fluid at different stages.

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 invention relates to a target tumor DNA fragment screening method based on deep learning, and belongs to the technical field of target tumor DNA fragment screening. A tumor DNA fragment screening model is constructed through a deep neural network, a training set is used for model establishment, and a test set is used for model performance testing. And obtaining to-be-identified positive tumor sample DNA sequencing data, carrying out positioning analysis on the to-be-identified positive tumor sample DNA sequencing data according to the trained tumor DNA fragment screening model, obtaining the position of a target tumor DNA fragment, and displaying the position according to a preset mode. According to the method, the training sample data in which a plurality of different types of tumor DNA fragments exist is processed, so that the interference of the plurality of different types of tumor DNA fragments in the same tumor training sample data on model training can be reduced to the greatest extent, the prediction precision of the model can be improved, and the screening precision of the tumor DNA fragments can be improved.

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.

Methods and systems are provided for genotyping a gene sequence. The method comprises obtaining first genotyping call data representing a query gene sequence. A numerical score is assigned to each of a plurality of allele calls of second genotyping call data by matching the first genotyping call data with the second genotyping call data. the second genotyping call data representing a plurality of candidate gene sequences. A match score is determined for each of the plurality of candidate gene sequences based on the numerical score assigned to each of the plurality of allele calls of the second genotyping call data, and a genotyping call is made for the query gene sequence based on a highest match score from among the match score determined for each of the plurality of candidate gene sequences.

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 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.

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.

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.