COMPLETE GENOMICS, INC. Patent applications |
Patent application number | Title | Published |
20150379192 | Processing and Analysis of Complex Nucleic Acid Sequence Data - The present invention is directed to logic for analysis of nucleic acid sequence data that employs algorithms that lead to a substantial improvement in sequence accuracy and that can be used to phase sequence variations, e.g., in connection with the use of the long fragment read (LFR) process. | 12-31-2015 |
20140356865 | Methods and Compositions for Efficient Base Calling in Sequencing Reactions - The present invention is directed to methods and compositions for acquiring nucleotide sequence information of target sequences. In particular, the present invention provides methods and compositions for improving the efficiency of sequencing reactions by using fewer labels to distinguish between nucleotides and by detecting nucleotides at multiple detection positions in a target sequence. | 12-04-2014 |
20140323316 | MULTIPLE TAGGING OF INDIVIDUAL LONG DNA FRAGMENTS - This disclosure provides methods and compositions for tagging long fragments of a target nucleic acid for sequencing and analyzing the resulting sequence information in order to reduce errors and perform haplotype phasing, for example. | 10-30-2014 |
20140232845 | METHOD AND SYSTEM FOR IMAGING HIGH DENSITY BIOCHEMICAL ARRAYS WITH SUB-PIXEL ALIGNMENT - A method and associated system for imaging high density biochemical arrays comprises one or more imaging channels that share a common objective lens and a corresponding one or more time delay integration-type imaging cameras with optical alignment mechanisms that permit independent inter-channel and intra-channel adjustment of each of four degrees: X, Y, rotation and scale. The imaging channels are configured to independently examine different spectra of the image of the biochemical arrays. | 08-21-2014 |
20140213461 | EFFICIENT BASE DETERMINATION IN SEQUENCING REACTIONS - The present invention is directed to compositions and methods for nucleic acid identification and detection. Compositions and methods of the present invention include extracting and fragmenting target nucleic acids from a sample, using the fragmented target nucleic acids to produce target nucleic acid templates and subjecting those target nucleic acid templates to amplification methods to form nucleic acid nanoballs. The invention also includes methods of detecting and identifying sequences using various sequencing applications, including sequencing by ligation methods. | 07-31-2014 |
20140188396 | OLIGOMER SEQUENCES MAPPING - Mapping oligomer sequences includes receiving a set of related oligomer sequences, applying one or more key patterns derived from a set of oligomer sequence relationships to obtain one or more keys that are consistent with the set of related oligomer sequences, and locating the one or more keys in an index configured to map a plurality of possible keys to their respective candidate and/or validated locations in a reference. | 07-03-2014 |
20140152793 | TECHNIQUES FOR SCANNED ILLUMINATION - Imaging systems are provided for high speed, high resolution imaging of biochemical materials. In an example embodiment, an imaging system comprises an objective lens component, a line generator, a digital camera, a positioning stage, and a scan mirror. The line generator generates a line of light that is scanned across a portion of a substrate that is mounted on the positioning stage. The positioning stage moves the substrate in a particular direction that is substantially normal to an optical axis of the objective lens component. The camera collects an image of the portion of the substrate through the objective lens component. The scan mirror moves in coordination with the positioning stage, while the line of light is being scanned across the portion of the substrate and the substrate is being moved in the particular direction, in order to keep the image still with respect to the camera while the image is being collected by the camera. | 06-05-2014 |
20140115515 | Genome Explorer System to Process and Present Nucleotide Variations in Genome Sequence Data - This disclosure provides a technology for users to gain first-hand knowledge and experience with interpreting whole genomes. The technology graphically depicts variations in genome sequences in an expandable display, and provides a platform whereby the user may find and research the biological significance of such variants. The technology also provides a unique collaborative environment designed to capture and improve the collective knowledge of the participating community. | 04-24-2014 |
20140085457 | HIGH-DENSITY ARRAY CHIPS WITH SYNCHRONOUS TRACKS - An array chip design is provided where the chip includes a field region arranged with sites according to a first pitch and at least one track region having a one-dimensional site pattern arranged according to a second pitch that is less dense and is an integer multiple of the first pitch so that observation through pixel-based sensors using one-dimensional quad-cell averaging can be applied in the track region, thereby to attain alignment of the chip to pixel-based optical instrumentation with a higher density of sites. | 03-27-2014 |
20140051588 | Sequencing Small Amounts of Complex Nucleic Acids - The present invention provides methods and compositions for sequencing small amounts of complex nucleic acids such as human genomes and for analyzing the resulting sequence information in order to reduce sequencing errors and perform haplotype phasing, for example. | 02-20-2014 |
20140005056 | METHODS AND COMPOSITIONS FOR LONG FRAGMENT READ SEQUENCING | 01-02-2014 |
20130323652 | METHOD OF FABRICATING PATTERNED FUNCTIONAL SUBSTRATES - Methods of preparing organosilane-functionalized regions on a substrate surface and more specifically fabricating patterned functionalized substrates suitable to be optically read, the methods generally comprising employing a vapor deposition process of an organosilane gas onto a lithographically patterned silicon surface followed by removal of the patterning media in a bath of organic solvents and ultrasonic excitation. The inventive methods provide optimized surface density of functional species while avoiding deleterious effects that can occur when lithographically patterned substrates are exposed to various gaseous species during the functionalization process. | 12-05-2013 |
20130281305 | FLOW CELLS FOR HIGH DENSITY ARRAY CHIPS - Biochemical flow cells having sealed inlets and outlets are provided for performing high-volume assays on macromolecules. In one example embodiment, a flow cell with detachable inlet and outlet connectors comprises an inlet manifold, a coverslip, and a substrate disposed below the coverslip to form a reaction chamber, where the substrate is disposed to partially cover the inlet manifold such that a slit is formed along an entire edge of the substrate where fluids can flow from the inlet manifold through the slit, around substantially the entire edge of the substrate, and into the reaction chamber at equalized pressure and without bubbles. In another embodiment, a flow cell comprises an outlet manifold, two or more flow regions each connected to its own loading port via its own flow distribution funnel, each loading port connected to the outlet manifold, and plugs in a wall of the outlet manifold opposite each loading port, such that when a plug is absent from the wall of the outlet manifold, a loading tip may be inserted in its place, passing through the outlet manifold and connecting directly to a loading port. | 10-24-2013 |
20130222570 | METHOD AND SYSTEM FOR IMAGING HIGH DENSITY BIOCHEMICAL ARRAYS WITH SUB-PIXEL ALIGNMENT - A method and associated system for imaging high density biochemical arrays comprises one or more imaging channels that share a common objective lens and a corresponding one or more time delay integration-type imaging cameras with optical alignment mechanisms that permit independent inter-channel and intra-channel adjustment of each of four degrees: X, Y, rotation and scale. The imaging channels are configured to independently examine different spectra of the image of the biochemical arrays. | 08-29-2013 |
20130178369 | TREATMENT FOR STABILIZING NUCLEIC ACID ARRAYS - The present invention is directed to treatment of nucleic acid molecules that are attached or associated with solid supports for biochemical analysis, including nucleic acid sequencing. After loading on the solid support, the nucleic acid molecules are treated with a composition comprising a condensing agent, a volume excluding agent, or both, then treated with a composition comprising a protein. | 07-11-2013 |
20130124100 | Processing and Analysis of Complex Nucleic Acid Sequence Data - The present invention is directed to logic for analysis of nucleic acid sequence data that employs algorithms that lead to a substantial improvement in sequence accuracy and that can be used to phase sequence variations, e.g., in connection with the use of the long fragment read (LFR) process. | 05-16-2013 |
20130110407 | DETERMINING VARIANTS IN GENOME OF A HETEROGENEOUS SAMPLE | 05-02-2013 |
20130096841 | IDENTIFICATION OF DNA FRAGMENTS AND STRUCTURAL VARIATIONS - Various short reads can be grouped and identified as coming from a same long DNA fragment (e.g., by using wells with a relatively low-concentration of DNA). A histogram of the genomic coverage of a group of short reads can provide the edges of the corresponding long fragment (pulse). The knowledge of these pulses can provide an ability to determine the haploid genome and to identify structural variations. | 04-18-2013 |
20130059740 | Sequencing Small Amounts of Complex Nucleic Acids - The present invention provides methods and compositions for sequencing small amounts of complex nucleic acids such as human genomes and for analyzing the resulting sequence information in order to reduce sequencing errors and perform haplotype phasing, for example. | 03-07-2013 |
20130059737 | EFFICIENT SHOTGUN SEQUENCING METHODS - Methods are provided for efficient shotgun sequencing to allow efficient selection and sequencing of nucleic acids of interest contained in a library. The nucleic acids of interest can be defined any time before or after preparation of the library. One example of nucleic acids of interest is missing or low confidence genome sequences resulting from an initial sequencing procedure. Other nucleic acids of interest include subsets of genomic DNA, RNA or cDNAs (exons, genes, gene sets, transciptomes). By designing an efficient (simple to implement, speedy, high specificity, low cost) selection procedure, a more complete sequence is achieved with less effort than by using highly redundant shotgun sequencing in an initial sequencing procedure | 03-07-2013 |
20130054508 | ANALYZING GENOME SEQUENCING INFORMATION TO DETERMINE LIKELIHOOD OF CO-SEGREGATING ALLELES ON HAPLOTYPES - Sequencing information is used to correlate alleles at certain locations to alleles at other locations. The statistical information from the reads of fragments in a sample can be used to determine the phasing of haplotypes and to correct or confirm based calls at the locations. In one example, a confidence value (strength score) is determined for a particular hypothesis, which can include whether two alleles are on a same haplotype at two particular loci, as well as what the alleles are on another haplotype (e.g. for a diploid organism). The strength can include a positive contribution from data that is consistent with the hypothesis and a negative contribution from data is that inconsistent with the hypothesis, where both values can be used in a formula to determine the strength. | 02-28-2013 |
20130054151 | PHASING OF HETEROZYGOUS LOCI TO DETERMINE GENOMIC HAPLOTYPES - Haplotypes of one or more portions of a chromosome of an organism from sequencing information of DNA or RNA fragments can be determined. Heterozygous loci (hets) can be used to determine haplotypes. One allele on a first het can be connected (likely to be on the same haplotype) to an allele on a second het, thereby defining a particular orientation between the hets. Haplotypes can be assembled through these connections. Errors can be identified through redundant connection information, particularly using a confidence value (strength) for a particular connection. The connections among a set of hets can be analyzed to determine likely haplotypes for that set, e.g., an optimal tree of a graph containing the hets. Furthermore, haplotypes of different contiguous sections (contig) of the chromosome can be matched to a particular chromosome copy (e.g., to a particular parental copy). Thus, the phase of an entire chromosome can be determined. | 02-28-2013 |
20120224050 | HIGH-DENSITY BIOCHEMICAL ARRAY CHIPS - An array chip useful for biochemical assays is provided wherein the chip includes a field region arranged with attachment sites according to a first pitch and at least one track region having a one-dimensional spot pattern arranged according to a second pitch that is less dense and is a non-integer multiple of the first pitch so that one-dimensional Moiré averaging may be applied in the track region, thereby to attain alignment of the chip to the optical instrumentation with a higher density of attachment sites. | 09-06-2012 |
20120197533 | IDENTIFYING REARRANGEMENTS IN A SEQUENCED GENOME - Methods, apparatuses, and systems for identification of junctions (e.g., resulting from large-scale rearrangements) of a sequenced genome with respect to a human genome reference sequence is provided. For example, false positives can be distinguished from actual junctions. Such false positives can result from many sources, including mismapping, chimeric reactions among the DNA of a sample, and problems with the reference genome. As part of the filtering processes, a base pair resolution (or near base pair resolution) of a junction can be provided. In various implementations, junctions can be identified using discordant mate pairs and/or using a statistical analysis of the length distributions of fragments for local regions of the sample genome. Clinically significant junctions can also be identified so that further analysis can be focused on genomic regions that may have more of an impact on the health of a patient. | 08-02-2012 |
20120135893 | High throughput genome sequencing on DNA arrays - The present invention is directed to methods and compositions for acquiring nucleotide sequence information of target sequences using adaptors interspersed in target polynucleotides. The sequence information can be new, e.g. sequencing unknown nucleic acids, re-sequencing, or genotyping. The invention preferably includes methods for inserting a plurality of adaptors at spaced locations within a target polynucleotide or a fragment of a polynucleotide. Such adaptors may serve as platforms for interrogating adjacent sequences using various sequencing chemistries, such as those that identify nucleotides by primer extension, probe ligation, and the like. Encompassed in the invention are methods and compositions for the insertion of known adaptor sequences into target sequences, such that there is an interruption of contiguous target sequence with the adaptors. By sequencing both “upstream” and “downstream” of the adaptors, identification of entire target sequences may be accomplished. | 05-31-2012 |
20120122721 | METHOD FOR NUCLEIC ACID DETECTION USING VOLTAGE ENHANCEMENT - Methods are provided for carrying out nucleic acid analysis, including sequence identification, employing voltage and/or controlled electric charge to enhance operation. A device comprises substrates for nucleic acid analysis, a first electrically conductive layer, a first electrically insulative layer of dielectric material on the first conductive layer, a second electrically conductive layer disposed upon the first insulative layer in a pattern to define discrete attachment sites for macromolecules on the first insulative layer, the second conductive layer provided with means for resisting affinity for the macromolecules to impede their attachment to sites on the second conductive layer, and terminals for the first and second conductive layers for applying a voltage pattern between the first and the second conductive layers to control affinity between the macromolecules and the discrete attachment sites. | 05-17-2012 |
20120122699 | Methods and Oligonucleotide Designs for Insertion of Multiple Adaptors Employing Selective Methylation - Aspects described and claimed herein provide methods to insert multiple DNA adaptors into a population of circular target DNAs at defined positions and orientations with respect to one another. The resulting multi-adaptor constructs are then used in massively-parallel nucleic acid sequencing techniques. | 05-17-2012 |
20120100534 | EFFICIENT BASE DETERMINATION IN SEQUENCING REACTIONS - The present invention is directed to compositions and methods for nucleic acid identification and detection. Compositions and methods of the present invention include extracting and fragmenting target nucleic acids from a sample, using the fragmented target nucleic acids to produce target nucleic acid templates and subjecting those target nucleic acid templates to amplification methods to form nucleic acid nanoballs. The invention also includes methods of detecting and identifying sequences using various sequencing applications, including sequencing by ligation methods. | 04-26-2012 |
20120099852 | METHOD AND SYSTEM FOR IMAGING HIGH DENSITY BIOCHEMICAL ARRAYS WITH SUB-PIXEL ALIGNMENT - A system and associated method for imaging high density biochemical arrays comprises one or more imaging channels that share a common objective lens and a corresponding one or more time delay integration-type imaging cameras with optical alignment mechanisms that permit independent inter-channel and intra-channel adjustment of each of four degrees: X, Y, rotation and scale. The imaging channels are configured to independently examine different spectra of the image of the biochemical arrays. | 04-26-2012 |
20120004140 | FLOW CELLS FOR BIOCHEMICAL ANALYSIS - Assay flow cells used as part of an overall system for biological assays include, in various configurations, a carrier in which an assay substrate may be provided, where a substantial portion of the assay substrate can be used for biochemical analysis, since the carrier component of the flow cell is designed to provide functionalities that in prior art systems were performed by the assay substrate itself The flow cells may be used in automated systems, are flat for imaging and various configurations of the components of the flow cells minimize evaporation, yet allow for precise control of fluid intake and evacuation. | 01-05-2012 |
20120004139 | FLOW CELLS FOR BIOCHEMICAL ANALYSIS - Assay flow cells used as part of an overall system for biological assays include, in various configurations, a carrier in which an assay substrate may be provided, where a substantial portion of the assay substrate can be used for biochemical analysis, since the carrier component of the flow cell is designed to provide functionalities that in prior art systems were performed by the assay substrate itself The flow cells may be used in automated systems, are flat for imaging and various configurations of the components of the flow cells minimize evaporation, yet allow for precise control of fluid intake and evacuation. | 01-05-2012 |
20120004126 | Efficient Arrays of Amplified Polynucleotides - The present invention is related generally to analysis of polynucleotides, particularly polynucleotides derived from genomic DNA. The invention provides methods, compositions and systems for such analysis. Encompassed by the invention are arrays of polynucleotides in which the polynucleotides have undergone multiple rounds of amplification in order to increase the strength of signals associated with single polynucleotide molecules. | 01-05-2012 |
20110281736 | Nucleic Acid Sequencing and Process - The present invention is directed to compositions and methods for nucleic acid identification and detection. Compositions and methods of the present invention include extracting and fragmenting target nucleic acids from a sample, using the fragmented target nucleic acids to produce target nucleic acid templates and subjecting those target nucleic acid templates to amplification methods to form nucleic acid nanoballs. The invention also includes methods of detecting and identifying sequences using various sequencing applications, including sequencing by ligation methods. | 11-17-2011 |
20110269644 | STRUCTURES FOR ENHANCED DETECTION OF FLUORESCENCE - Substrates are provided for use in the detection, identification and analysis of biologic or chemical samples that are labeled with a fluorescent label, in which the plane of maximum fluorescence is displaced from a reflective substrate surface so that the intensity maximum of the standing wave interference pattern of incident and reflected probe radiation is enhanced. The format of the substrates includes substantially planar surfaces as well as substrates with introduced variations to the substrate surface, e.g., depressions, wells, pedestals and the like, disposed in arrays or other similar structures such that one or more fluorophore-comprising objects can be attached thereto. | 11-03-2011 |
20110268347 | METHOD AND SYSTEM FOR ACCURATE ALIGNMENT AND REGISTRATION OF ARRAY FOR DNA SEQUENCING - In a genome sequencing system and methodology, a protocol is provided to achieve precise alignment and accurate registration of an image of a planar array of nanoballs subject to optical analysis. Precise alignment correcting for fractional offsets is achieved by correcting for errors in subperiod x-y offset, scale and rotation by use of minimization techniques and Moiré averaging. In Moiré averaging, magnification is intentionally set so that the pixel period of the imaging element is a noninteger multiple of the site period. Accurate registration is achieved by providing for pre-defined pseudo-random sets of sites, herein deletion or reserved sites, where nanoballs are prevented from attachment to the substrate so that the sites of the array can be used in a pattern matching scheme as registration markers for absolute location identification. Information can be extracted with a high degree of confidence that it is correlated to a known location, while at the same time the amount of information that can be packed on a chip is maximized. | 11-03-2011 |
20110033854 | METHODS AND COMPOSITIONS FOR LONG FRAGMENT READ SEQUENCING - The present invention is directed to methods and compositions for long fragment read sequencing. The present invention encompasses methods and compositions for preparing long fragments of genomic DNA, for processing genomic DNA for long fragment read sequencing methods, as well as software and algorithms for processing and analyzing sequence data. | 02-10-2011 |
20110004413 | METHOD AND SYSTEM FOR CALLING VARIATIONS IN A SAMPLE POLYNUCLEOTIDE SEQUENCE WITH RESPECT TO A REFERENCE POLYNUCLEOTIDE SEQUENCE - Embodiments for calling variations in a sample polynucleotide sequence compared to a reference polynucleotide sequence are provided. Aspects of the embodiments include executing an application on at least one computer that locates local areas in the reference polynucleotide sequence where a likelihood exists that one or more bases of the sample polynucleotide sequence are changed from corresponding bases in the reference polynucleotide sequence, where the likelihood is determined at least in part based on mapped mated reads of the sample polynucleotide sequence; generating at least one sequence hypothesis for each of the local areas, and optimizing the at least one sequence hypothesis for at least a portion of the local areas to find one or more optimized sequence hypotheses of high probability for the local areas; and analyzing the optimized sequence hypotheses to identify a series of variation calls in the sample polynucleotide sequence. | 01-06-2011 |
20100199155 | METHOD AND APPARATUS FOR QUANTIFICATION OF DNA SEQUENCING QUALITY AND CONSTRUCTION OF A CHARACTERIZABLE MODEL SYSTEM USING REED-SOLOMON CODES - Data extracted from fluorosphore responses of fluorophore labeled bases in genetic material used in sequencing of unknown fragments from a defined set of for example a model system are converted into a class of block codes that are then employed in a computer-based process to compare and correct preliminary calls of calls of the categorically known genetic material. In a specific embodiment, the Reed-Solomon codes are employed to identify one or more errors as may occur in a finite block of codes. The methodology is also useful to identify elements of a real system containing known elements in the form of a tag. Reed-Solomon sensors may be employed with and in addition to other types of genome sensors. | 08-05-2010 |
20100105052 | Nucleic acid sequencing and process - The present invention is directed to compositions and methods for nucleic acid identification and detection. Compositions and methods of the present invention include extracting and fragmenting target nucleic acids from a sample, using the fragmented target nucleic acids to produce target nucleic acid templates and subjecting those target nucleic acid templates to amplification methods to form nucleic acid nanoballs. The invention also includes methods of detecting and identifying sequences using various sequencing applications, including sequencing by ligation methods. | 04-29-2010 |
20090318304 | Efficient Shotgun Sequencing Methods - Methods are provided for efficient shotgun sequencing to allow efficient selection and sequencing of nucleic acids of interest contained in a library. The nucleic acids of interest can be defined any time before or after preparation of the library. One example of nucleic acids of interest is missing or low confidence genome sequences resulting from an initial sequencing procedure. Other nucleic acids of interest include subsets of genomic DNA, RNA or cDNAs (exons, genes, gene sets, transciptomes). By designing an efficient (simple to implement, speedy, high specificity, low cost) selection procedure, a more complete sequence is achieved with less effort than by using highly redundant shotgun sequencing in an initial sequencing procedure | 12-24-2009 |
20090270273 | ARRAY STRUCTURES FOR NUCLEIC ACID DETECTION - Devices formed as optically readable substrates are provided having a high feature density (e.g., attachment or deposition sites) in arrays comprising macromolecules, specifically amplicons, and devices and methods are provided for analysis of target nucleic acids having an undetermined sequence. High density arrayed nucleic acids are provided which are amenable to individual or multiple nucleotide interrogation, and which are particularly useful to determine the nucleotide sequence of a complex target nucleic acid sequence | 10-29-2009 |
20090264299 | High throughput genome sequencing on DNA arrays - The present invention is directed to methods and compositions for acquiring nucleotide sequence information of target sequences using adaptors interspersed in target polynucleotides. The sequence information can be new, e.g. sequencing unknown nucleic acids, re-sequencing, or genotyping. The invention preferably includes methods for inserting a plurality of adaptors at spaced locations within a target polynucleotide or a fragment of a polynucleotide. Such adaptors may serve as platforms for interrogating adjacent sequences using various sequencing chemistries, such as those that identify nucleotides by primer extension, probe ligation, and the like. Encompassed in the invention are methods and compositions for the insertion of known adaptor sequences into target sequences, such that there is an interruption of contiguous target sequence with the adaptors. By sequencing both “upstream” and “downstream” of the adaptors, identification of entire target sequences may be accomplished. | 10-22-2009 |
20090263872 | Methods and compositions for preventing bias in amplification and sequencing reactions - The present invention is directed to compositions and methods for nucleic acid identification and detection. Compositions and methods of the present invention include template nucleic acids with stabilizing sequences. The present invention also includes concatemers formed from template nucleic acids that have stabilizing sequences, arrays of such concatemers, as well as methods for identifying and detecting sequences of such concatemers. | 10-22-2009 |
20090263802 | Methods and compositions for efficient base calling in sequencing reactions - The present invention is directed to methods and compositions for acquiring nucleotide sequence information of target sequences. In particular, the present invention provides methods and compositions for improving the efficiency of sequencing reactions by using fewer labels to distinguish between nucleotides and by detecting nucleotides at multiple detection positions in a target sequence. | 10-22-2009 |
20090203551 | Methods and Oligonucleotide Designs for Insertion of Multiple Adaptors Employing Selective Methylation - Aspects described and claimed herein provide methods to insert multiple DNA adaptors into a population of circular target DNAs at defined positions and orientations with respect to one another. The resulting multi-adaptor constructs are then used in massively-parallel nucleic acid sequencing techniques. | 08-13-2009 |
20090176652 | Methods and Oligonucleotide Designs for Insertion of Multiple Adaptors into Library Constructs - Aspects described and claimed herein provide methods to insert multiple DNA adaptors into a population of circular target DNAs at defined positions and orientations with respect to one another. The resulting multi-adaptor constructs are then used in massively-parallel nucleic acid sequencing techniques. | 07-09-2009 |
20090176234 | Efficient base determination in sequencing reactions - The present invention is directed to compositions and methods for nucleic acid identification and detection. Compositions and methods of the present invention include extracting and fragmenting target nucleic acids from a sample, using the fragmented target nucleic acids to produce target nucleic acid templates and subjecting those target nucleic acid templates to amplification methods to form nucleic acid nanoballs. The invention also includes methods of detecting and identifying sequences using various sequencing applications, including sequencing by ligation methods. | 07-09-2009 |
20090155793 | APPARATUS FOR HIGH THROUGHPUT SEQUENCING OF NUCLEIC ACIDS - A scalable reaction and detection system for automated high throughput sequencing of nucleic acids involving a combination of chemical processes and observation processes independent of the chemistry processes. Discrete functional units may be configured in a manner that allows the system to interchangeably utilize different sequencing reaction components in conjunction with discrete apparatus components for optical image collection and/or analysis. | 06-18-2009 |
20090155781 | High throughput genome sequencing on DNA arrays - The present invention is directed to methods and compositions for acquiring nucleotide sequence information of target sequences using adaptors interspersed in target polynucleotides. The sequence information can be new, e.g. sequencing unknown nucleic acids, re-sequencing, or genotyping. The invention preferably includes methods for inserting a plurality of adaptors at spaced locations within a target polynucleotide or a fragment of a polynucleotide. Such adaptors may serve as platforms for interrogating adjacent sequences using various sequencing chemistries, such as those that identify nucleotides by primer extension, probe ligation, and the like. Encompassed in the invention are methods and compositions for the insertion of known adaptor sequences into target sequences, such that there is an interruption of contiguous target sequence with the adaptors. By sequencing both “upstream” and “downstream” of the adaptors, identification of entire target sequences may be accomplished. | 06-18-2009 |
20090143235 | EFFICIENT ARRAYS OF AMPLIFIED POLYNUCLEOTIDES - The present invention is related generally to analysis of polynucleotides, particularly polynucleotides derived from genomic DNA. The invention provides methods, compositions and systems for such analysis. Encompassed by the invention are arrays of polynucleotides in which the polynucleotides have undergone multiple rounds of amplification in order to increase the strength of signals associated with single polynucleotide molecules. | 06-04-2009 |
20090137414 | Single molecule arrays for genetic and chemical analysis - Random arrays of single molecules are provided for carrying out large scale analyses, particularly of biomolecules, such as genomic DNA, cDNAs, proteins, and the like. In one aspect, arrays of the invention comprise concatemers of DNA fragments that are randomly disposed on a regular array of discrete spaced apart regions, such that substantially all such regions contain no more than a single concatemer. Preferably, such regions have areas substantially less than 1 μm | 05-28-2009 |
20090137404 | Single molecule arrays for genetic and chemical analysis - Random arrays of single molecules are provided for carrying out large scale analyses, particularly of biomolecules, such as genomic DNA, cDNAs, proteins, and the like. In one aspect, arrays of the invention comprise concatemers of DNA fragments that are randomly disposed on a regular array of discrete spaced apart regions, such that substantially all such regions contain no more than a single concatemer. Preferably, such regions have areas substantially less than 1 μm | 05-28-2009 |
20090118488 | High throughput genome sequencing on DNA arrays - The present invention is directed to methods and compositions for acquiring nucleotide sequence information of target sequences using adaptors interspersed in target polynucleotides. The sequence information can be new, e.g. sequencing unknown nucleic acids, re-sequencing, or genotyping. The invention preferably includes methods for inserting a plurality of adaptors at spaced locations within a target polynucleotide or a fragment of a polynucleotide. Such adaptors may serve as platforms for interrogating adjacent sequences using various sequencing chemistries, such as those that identify nucleotides by primer extension, probe ligation, and the like. Encompassed in the invention are methods and compositions for the insertion of known adaptor sequences into target sequences, such that there is an interruption of contiguous target sequence with the adaptors. By sequencing both “upstream” and “downstream” of the adaptors, identification of entire target sequences may be accomplished. | 05-07-2009 |
20090117006 | STRUCTURES FOR ENHANCED DETECTION OF FLUORESCENCE - Substrates are provided for use in the detection, identification and analysis of biologic or chemical samples that are labeled with a fluorescent label, in which the plane of maximum fluorescence is displaced from a reflective substrate surface so that the intensity maximum of the standing wave interference pattern of incident and reflected probe radiation is enhanced. The format of the substrates includes substantially planar surfaces as well as substrates with introduced variations to the substrate surface, e.g., depressions, wells, pedestals and the like, disposed in arrays or other similar structures such that one or more fluorophore-comprising objects can be attached thereto. | 05-07-2009 |
20090111706 | SELECTION OF DNA ADAPTOR ORIENTATION BY AMPLIFICATION - Aspects described and claimed herein provide methods to insert multiple DNA adaptors into a population of circular target DNAs at defined positions and orientations with respect to one another by employing amplification procedures. The resulting multi-adaptor constructs are then used in massively-parallel nucleic acid sequencing techniques. | 04-30-2009 |
20090111705 | SELECTION OF DNA ADAPTOR ORIENTATION BY HYBRID CAPTURE - Aspects described and claimed herein provide methods to insert multiple DNA adaptors into a population of circular target DNAs at defined positions and orientations with respect to one another by employing selective capture of defined molecules. The resulting multi-adaptor constructs are then used in massively-parallel nucleic acid sequencing techniques. | 04-30-2009 |
20090111115 | SEQUENCE ANALYSIS USING DECORATED NUCLEIC ACIDS - The present invention provides a sequence interrogation chemistry that combines the accuracy and haplotype integrity of long-read sequencing with improved methods of preparing genomic nucleic acids and analyzing sequence information generated from those nucleic acids. The present invention encompasses compositions comprising decorated nucleic acids stretched on substrates. The present invention further encompasses methods of making stretched decorated nucleic acids and methods of using decorated nucleic acids to obtain sequence information. | 04-30-2009 |
20090105961 | METHODS OF NUCLEIC ACID IDENTIFICATION IN LARGE-SCALE SEQUENCING - The present invention provides methods for determining a base probability in a target nucleic acid within an experimental data set. The methods of the invention provide specific methods of improving accuracy of base calling for experimental sequencing data compared to conventional methods. The experimental base values used in the methods of the present invention provide relative base probabilities within an experimental data set that are robust and uniformly optimal regardless of the experimental conditions. | 04-23-2009 |
20090075343 | SELECTION OF DNA ADAPTOR ORIENTATION BY NICKING - Aspects described and claimed herein provide methods to insert multiple DNA adaptors into a population of circular target DNAs at defined positions and orientations with respect to one another using nicking reactions. The resulting multi-adaptor constructs are then used in massively-parallel nucleic acid sequencing techniques. | 03-19-2009 |
20090036316 | Random array DNA analysis by hybridization - The invention relates to methods and devices for analyzing single molecules, i.e. nucleic acids. Such single molecules may be derived from natural samples, such as cells, tissues, soil, air and water without separating or enriching individual components. In certain aspects of the invention, the methods and devices are useful in performing nucleic acid sequence analysis by probe hybridization. | 02-05-2009 |
20090011943 | High throughput genome sequencing on DNA arrays - The present invention is directed to methods and compositions for acquiring nucleotide sequence information of target sequences using adaptors interspersed in target polynucleotides. The sequence information can be new, e.g. sequencing unknown nucleic acids, re-sequencing, or genotyping. The invention preferably includes methods for inserting a plurality of adaptors at spaced locations within a target polynucleotide or a fragment of a polynucleotide. Such adaptors may serve as platforms for interrogating adjacent sequences using various sequencing chemistries, such as those that identify nucleotides by primer extension, probe ligation, and the like. Encompassed in the invention are methods and compositions for the insertion of known adaptor sequences into target sequences, such that there is an interruption of contiguous target sequence with the adaptors. By sequencing both “upstream” and “downstream” of the adaptors, identification of entire target sequences may be accomplished. | 01-08-2009 |
20090011416 | Random array DNA analysis by hybridization - The invention relates to methods and devices for analyzing single molecules, i.e. nucleic acids. Such single molecules may be derived from natural samples, such as cells, tissues, soil, air and water without separating or enriching individual components. In certain aspects of the invention, the methods and devices are useful in performing nucleic acid sequence analysis by probe hybridization. | 01-08-2009 |
20090005259 | Random array DNA analysis by hybridization - The invention relates to methods and devices for analyzing single molecules, i.e. nucleic acids. Such single molecules may be derived from natural samples, such as cells, tissues, soil, air and water without separating or enriching individual components. In certain aspects of the invention, the methods and devices are useful in performing nucleic acid sequence analysis by probe hybridization. | 01-01-2009 |
20090005252 | High throughput genome sequencing on DNA arrays - The present invention is directed to methods and compositions for acquiring nucleotide sequence information of target sequences using adaptors interspersed in target polynucleotides. The sequence information can be new, e.g. sequencing unknown nucleic acids, re-sequencing, or genotyping. The invention preferably includes methods for inserting a plurality of adaptors at spaced locations within a target polynucleotide or a fragment of a polynucleotide. Such adaptors may serve as platforms for interrogating adjacent sequences using various sequencing chemistries, such as those that identify nucleotides by primer extension, probe ligation, and the like. Encompassed in the invention are methods and compositions for the insertion of known adaptor sequences into target sequences, such that there is an interruption of contiguous target sequence with the adaptors. By sequencing both “upstream” and “downstream” of the adaptors, identification of entire target sequences may be accomplished. | 01-01-2009 |
20080234136 | Single molecule arrays for genetic and chemical analysis - Random arrays of single molecules are provided for carrying out large scale analyses, particularly of biomolecules, such as genomic DNA, cDNAs, proteins, and the like. In one aspect, arrays of the invention comprise concatemers of DNA fragments that are randomly disposed on a regular array of discrete spaced apart regions, such that substantially all such regions contain no more than a single concatemer. Preferably, such regions have areas substantially less than 1 μm | 09-25-2008 |
20080221832 | METHODS FOR COMPUTING POSITIONAL BASE PROBABILITIES USING EXPERMINENTALS BASE VALUE DISTRIBUTIONS - Aspects of the various embodiments of the invention relate generally to computing relative base value probabilities using discrete experimental base values to calculate distributions of relative base probabilities. This information can be used with associated experimental measurements to increase the accuracy of the data analysis. | 09-11-2008 |
20080213771 | Methods and Compositions for Large-Scale Analysis of Nucleic Acids Using DNA Deletions - The present invention is related generally to analysis of polynucleotides, particularly polynucleotides derived from genomic DNA. The invention provides methods, compositions and systems for such analysis. Encompassed by the invention are constructs that include pairs of target sequences which are separated by a known distance in the polynucleotide from which they are derived. | 09-04-2008 |