134 results about "Sequence variation" patented technology

The invention provides methods for determining genome-wide sequence variations associated with a phenotype of a species in a hypothesis-free manner. In the methods of the invention, a set of restriction fragments for each of a sub-population of individuals having the phenotype are generated by digesting nucleic acids from the individual using one or more different restriction enzymes. A set of restriction sequence tags for the individual is then determined from the set of restriction fragments. The restriction sequence tags for the sub-population of organisms are compared and grouped into one or more groups, each of which comprising restriction sequence tags that comprise homologous sequences. The obtained one or more groups of restriction sequence tags identify the sequence variations associated with the phenotype. The methods of the invention can be used for, e.g., analysis of large numbers of sequence variants in many patient samples to identify subtle genetic risk factors.

Methods of generating cell lines with a sequence variation or copy number variation of a gene of interest, methods of use thereof, and cell lines with a sequence variation or copy number variation of a gene of interest are provided.

The present invention provides a technology called Pulse-Multiline Excitation or PME. This technology provides a novel approach to fluorescence detection with application for high-throughput identification of informative SNPs, which could lead to more accurate diagnosis of inherited disease, better prognosis of risk susceptibilities, or identification of sporadic mutations. The PME technology has two main advantages that significantly increase fluorescence sensitivity: (1) optimal excitation of all fluorophores in the genomic assay and (2) “color-blind” detection, which collects considerably more light than standard wavelength resolved detection. Successful implementation of the PME technology will have broad application for routine usage in clinical diagnostics, forensics, and general sequencing methodologies and will have the capability, flexibility, and portability of targeted sequence variation assays for a large majority of the population.

Systems and method for determining variants can receive mapped reads, align flow space information to a flow space representation of a corresponding portion of the reference. Reads spanning a position with a potential variant can be evaluated in a context specific manner. A list of probable variants can be provided.

The present invention is a method for detecting DNA sequence differences including single nucleotide mutations or polymorphisms, one or more nucleotide insertions, and one or more nucleotide deletions. Labeled heteroduplex PCR fragments containing base mismatches are prepared. Endonuclease cleaves the heteroduplex PCR fragments both at the position containing the variation (one or more mismatched bases) and to a lesser extent, at non-variant (perfectly matched) positions. Ligation of the cleavage products with a DNA ligase corrects non-variant cleavages and thus substantially reduces background. This is then followed by a detection step in which the reaction products are detected, and the position of the sequence variations are determined.

Systems and method for determining variants can receive mapped reads, and call variants. In embodiments, flow space information for the reads can be aligned to a flow space representation of a corresponding portion of the reference. Reads spanning a position with a potential variant can be grouped and a score can be calculated for the variant. Based on the scores, a list of probable variants can be provided. In various embodiments, low frequency variants can be identified where multiple potential variants are present at a position.

The invention discloses a method for detecting mutation information in a multiplex amplification sequencing product of a genome. The method comprises steps as follows: sequencing data are subjected to quality assessment and preprocessing; a recognizable sequencing sequence is selected for sequence assembling; the recognizable sequencing sequence or a sequence obtained through assembling is compared with a reference gene sequence, and preliminary variation information is obtained; fine calibration of sequence variation is performed according to different types of conditions; a calibrated sequencing fragment is obtained; the homozygosis or heterozygosis state of a target fragment is obtained according to the type of the sequencing fragment with the highest abundance; finally, the mutation information in the multiplex amplification sequencing product of the genome is obtained. By means of the method, the amplification product can be rapidly, efficiently and accurately recognized, and the calculation resources are saved; the sequence assembling process is compatible, and the problem of reduction of the quality value of basic groups produced in the sequencing process can be effectively solved; the homozygosis / heterozygosis state of variation information can be more effectively and stably judged, and random errors introduced in the PCR (polymerase chain reaction) process and the sequencing process are eliminated.

The claimed invention provides for new sample preparation methods enabling direct sequencing of PCR products using pyrophosphate sequencing techniques. The PCR products may be specific regions of a genome. The techniques provided in this disclosure allows for SNP (single nucleotide polymorphism) detection, classification, and assessment of individual allelic polymorphisms in one individual or a population of individuals. The results may be used for diagnostic and treatment of patients as well as assessment of viral and bacterial population identification.

The invention relates to the field of nucleic acid analysis. More particularly, the invention relates to compositions and methods used for the detection of sequence variations or single nucleotide polymorphisms (SNPs) in a nucleic acid of interest.

The present invention is directed to various methods for detecting DNA sequence differences, including single nucleotide mutations or polymorphisms, one or more nucleotide insertions, and one or more nucleotide deletions. Labeled heteroduplex PCR fragments containing base mismatches are prepared. Endonuclease cleaves the heteroduplex PCR fragments both at the position containing the variation (one or more mismatched bases) and, to a lesser extent, at non-variant (perfectly matched) positions. Ligation of the cleavage products with a DNA ligase corrects non-variant cleavages and thus substantially reduces background. This is then followed by a detection step in which the reaction products are detected, and the position of the sequence variations are determined.

In some embodiments, the present inventions relates generally to compositions, methods and kits for use in discriminating sequence variation between different alleles. More specifically, in some embodiments, the present invention provides for compositions, methods and kits for quantitating rare (e.g., mutant) allelic variants, such as SNPs, or nucleotide (NT) insertions or deletions, in samples comprising abundant (e.g., wild type) allelic variants with high specificity and selectivity. In particular, in some embodiments, the invention relates to a highly selective method for mutation detection referred to as competitive allele-specific TaqMan PCR ('cast-PCR').

This invention relates to ‘genome partitioning’ and nucleic library construction, for example for sequence variation discovery and screening. The method employs a plurality of restriction enzymes in order to reliably reproduce a representative partition of the entirety of a sample nucleic acid based on the restriction ends of one or more ‘layers’ of the fragments present. In preferred embodiments there is provided a method for producing a nucleic acid library, which library contains a plurality of different nucleic acid fragments, the method comprising: (i) digesting the sample nucleic acid with a plurality of different restriction enzymes to generate a plurality of different layers of fragments, wherein each layer is a group of fragments having a unique combination of restriction ends, and wherein the combination of layers represents the entirety of the sample nucleic acid, (ii) optionally purifying said fragments, (iii) selecting a desired sub-set of layers according to the unique restriction ends of said layers, (iv) ligating said sub-set of layers into vectors adapted to receive it, (v) transforming host cells with the vectors (vi) culturing said host cells to provide said library containing said partition of the sample nucleic acid. The invention also provides systems, methods and functions for designing and optimising such libraries, and genotyping ‘chips’ based on the genome partitioning methods.

We describe here an in vitro method of redistributing sequence variations between non-identical polynucleotide sequences, by making a heteroduplex polynucleotide from two non-identical polynucleotides; introducing a nick in one strand at or near a base pair mismatch site; removing mismatched base(s) from the mismatch site where the nick occurred; and using the opposite strand as template to replace the removed base(s) with bases that complement base(s) in the first strand. By this method, information is transferred from one strand to the other at sites of mismatch.

Provided herein are optimized methods for performing multiplexed detection of a plurality of sequence variations. Also provided are methods for performing multiplexed amplification of target nucleic acid.

Fragmentation-based methods and systems, particularly mass spectrometry based methods and systems, for the analysis of sequence variations including haplotypes are provided. Also provided are methods for obtaining a specific allele from a nucleic acid mixture, such as genomic DNA.

Certain sequence variants have been found to be useful for correcting Prostate Specific Antigen levels in humans. The invention provides diagnostic applications based on such correction, including methods of diagnosis of prostate cancer.

The present invention provides a technology called Pulse-Multiline Excitation or PME. This technology provides a novel approach to fluorescence detection with application for high-throughput identification of informative SNPs, which could lead to more accurate diagnosis of inherited disease, better prognosis of risk susceptibilities, or identification of sporadic mutations. The PME technology has two main advantages that significantly increase fluorescence sensitivity: (1) optimal excitation of all fluorophores in the genomic assay and (2) “color-blind” detection, which collects considerably more light than standard wavelength resolved detection. This technology differs significantly from the current state-of-the-art DNA sequencing instrumentation, which features single source excitation and color dispersion for DNA sequence identification. Successful implementation of the PME technology will have broad application for routine usage in clinical diagnostics, forensics, and general sequencing methodologies and will have the capability, flexibility, and portability of targeted sequence variation assays for a large majority of the population.

The invention provides a method for predicting the susceptibility of an individual to pulmonary tuberculosis, the method comprising amplifying genomic DNA of pulmonary tuberculosis patients and normal control individuals using oligonuecleotide primers, sequencing the amplified PCR product and identifying the sequence variation computationally by comparing it with the already existing sequence of human SP-A2 gene.

The invention provides methods for determining genome-wide sequence variations associated with a phenotype of a species in a hypothesis-free manner. In the methods of the invention, a set of restriction fragments for each of a sub-population of individuals having the phenotype are generated by digesting nucleic acids from the individual using one or more different restriction enzymes. A set of restriction sequence tags for the individual is then determined from the set of restriction fragments. The restriction sequence tags for the sub-population of organisms are compared and grouped into one or more groups, each of which comprising restriction sequence tags that comprise homologous sequences. The obtained one or more groups of restriction sequence tags identify the sequence variations associated with the phenotype. The methods of the invention can be used for, e.g., analysis of large numbers of sequence variants in many patient samples to identify subtle genetic risk factors.

The present invention provides improved methods, compositions and kits for short read next generation sequencing (NGS). The methods, compositions and kits of the present invention enable phasing of two or more nucleic acid sequences in a sample, i.e. determining whether the nucleic acid sequences (typically comprising regions of sequence variation) are located on the same chromosome and / or the same chromosomal fragment. Phasing information is obtained by performing multiple, successive sequencing reactions from the same immobilized nucleic acid template. The methods, compositions and kits provided herein are useful, for example, for haplotyping, SNP phasing, or for determining downstream exons in RNA-seq.

A step-wise integrated process for identifying sequence variations in polynucleotide sequences is disclosed. The identification process is composed of three stages, including allele specific hybridization assays of known sequence variations (Stage I), sequence variation locating assays (Stage II), and direct sequencing (Stage III). The methods can be used for efficient and accurate detection of mutations in any test gene sample.

Provided herein are optimized methods for performing multiplexed detection of a plurality of sequence variations. Also provided are methods for performing multiplexed amplification of target nucleic acid.

Methods of generating cell lines with a sequence variation or copy number variation of a gene of interest, methods of use thereof, and cell lines with a sequence variation or copy number variation of a gene of interest are provided.

Described herein are improved methods, compositions and kits for next generation sequencing (NGS). The methods, compositions and kits described herein enable phasing of two or more nucleic acid sequences in a sample, i.e. determining whether the nucleic acid sequences (which can comprise regions of sequence variation) are located on the same chromosome and / or the same chromosomal fragment. Phasing information can be obtained by performing multiple, successive sequencing reactions from the same immobilized nucleic acid template. The methods, compositions and kits provided herein can be useful, for example, for haplotyping, SNP phasing, or for determining downstream exons in RNA-seq.

Recent developments in cost-effective DNA sequencing allows for individualized genomic screening of a subject for genetic sequence variants. Training a pathogenicity prediction model using semi-supervised training methods produces a better model for predicting the pathogenicity of a test genetic sequence variant. Provided herein are methods for predicting the pathogenicity of a test genetic sequence variant by utilizing a training data set comprising labeled benign genetic sequence variants unlabeled genetic sequence variants, the unlabeled genetic sequence variants comprising a mixture of benign genetic sequence variants and pathogenic genetic sequence variants. The genetic sequences are annotated with one or more features and a machine learning model is trained in a semi-supervised process based on the training data. The test genetic sequence is then annotated using the one or more features and the probability that the test genetic sequence variant is pathogenic is predicted based onthe trained machine learning model.

An automatic musical composition classification device and method that allow automatic classification of a plurality of musical compositions based on melodic similarity. storing chord progression pattern data representing a chord progression sequence for each of the plurality of musical pieces, extracting a chord progression change feature amount for each of the plurality of musical pieces based on the chord progression pattern data, And according to the chord progression sequence and the chord progression change feature quantity represented by the chord progression pattern data of each of the plurality of music pieces, the multiple pieces of music are grouped.

The invention provides a primer and a probe for detecting drug resistance genes mecA in methicillin-resistant staphylococcus aureus (MRSA). The invention also provides a method and a detection kit for detecting drug resistance genes mecA in MRSA. According to the invention, the conserved sequence part of drug resistance genes mecA is directly detected without being affected by the mecA gene variation of strains, and a result is a gold standard of MRSA diagnosis. The specific primer and the probe provided by the invention are applicable to currently known strains containing sequence variation.

In some embodiments, the present invention generally relates to compositions, methods and kits for distinguishing sequence differences between different alleles. More specifically, in some embodiments, the present invention provides methods for quantifying rare (e.g., mutant) alleles in samples containing abundant (e.g., wild-type) allelic variants with high specificity and selectivity. Compositions, methods and kits for genetic variants such as SNP or nucleotide (NT) insertion or deletion. In particular, in some embodiments, the present invention relates to a highly selective method for detecting mutations known as competitive allele-specific TaqMan PCR ("cast-PCR").

The invention relates to an intersection short-lane queue overflow identification method based on electric police data. The intersection short-lane queue overflow identification method based on the electric police data comprises the steps of: (1), obtaining the electric police data, and calculating the departure time headway of a vehicle; (2), in combination with the timestamp information that thevehicle passes through a parking line and the departure time headway obtained by calculation, describing double characteristics of proximity spacing and time headway fluctuation, so that a departuretime headway sequence variation point is identified, and estimating the vehicle queue length on each lane; and (3), analyzing a possible queue overflow type of an intersection in a condition that a left-turn short lane and an adjacent straight lane are different in queue length; and furthermore, performing subdivision by judging whether driving of a vehicle on an adjacent lane is blocked or not. The queue length of each lane is obtained by calculation based on a variable point analyzing theory; under different phase release rules, queue overflow identification algorithms based on rules are respectively established; therefore, queue overflow states in different types can be identified; and the intersection short-lane queue overflow identification method based on the electric police data inthe invention has the advantages of being definite in queue overflow classification, little in input data, wide in applicability and the like.