33 results about "Sequencing by synthesis" patented technology

The invention provides methods and compositions, including, without limitation, algorithms, computer readable media, computer programs, apparatus, and systems for determining the identity of nucleic acids in nucleotide sequences using, for example, data obtained from sequencing by synthesis methods. A plurality of smaller flow cells is employed, each with a relatively small area to be imaged, in order to provide greater flexibility and efficiency.

Embodiments of the present disclosure relate to methods and kits for sequencing by synthesis utilizing biorthogonal chemical reactions between unlabeled nucleotides and post incorporation labeling reagents.

The invention provides various orthogonal nucleotide analogues and methods for using combinations of said various orthogonal nucleotide analogues for sequencing by synthesis.

The invention is directed to methods for massively parallel template-free enzymatic synthesis of a plurality of different polynucleotides of predetermined sequences. In one aspect, methods of the invention employ large scale arrays of reaction sites each associated with at least one working electrode for controlling deprotection and deblocking steps at predetermined user selected sites. In another aspect, the invention provides template-free enzymatic synthesis with proofreading, wherein completed polynucleotides at predetermined reaction sites are sequenced using a sequencing by synthesis technique, particularly employing electrochemically labile blocking groups.

The invention is directed to methods for massively parallel template-free enzymatic synthesis of a plurality of different polynucleotides of predetermined sequences. In one aspect, methods of the invention employ large scale arrays of reaction sites each associated with at least one working electrode for controlling deprotection and deblocking steps at predetermined user selected sites. In another aspect, the invention provides template-free enzymatic synthesis with proofreading, wherein completed polynucleotides at predetermined reaction sites are sequenced using a sequencing by synthesis technique, particularly employing electrochemically labile blocking groups.

Embodiments of the present disclosure relate to compositions and methods for labeling of nucleotides, oligonucleotides, or polynucleotides with conjugated polymers or polymer dots. In particular, conjugated polymers or polymer dots can be used as detectable labels for nucleotides, oligonucleotides, or polynucleotides in sequencing by synthesis.

The invention provides methods and compositions, including, without limitation, algorithms, computer readable media, computer programs, apparatus, and systems for determining the identity of nucleic acids in nucleotide sequences using, for example, data obtained from sequencing by synthesis methods. The methods of the invention include correcting one or more phenomena that are encountered during nucleotide sequencing, such as using sequencing by synthesis methods. These phenomena include, without limitation, sequence lead, sequence lag, spectral crosstalk, and noise resulting from variations in illumination and / or filter responses.

Embodiments of the present disclosure relate to methods and kits for sequencing by synthesis utilizing orthogonal or biorthogonal chemical reactions between unlabeled nucleotides and multi-dye labeled post incorporation labeling reagents containing water-soluble polymer scaffolds.

Embodiments of the present disclosure relate to multi-dye labeled polyphosphodiester scaffolds, as well as methods and kits for sequencing by synthesis utilizing such multi-dye labeled, scaffolds as post-incorporation labeling reagents.

Embodiments of the present disclosure relate to compositions and methods for labeling of nucleotides, oligonucleotides, or polynucleotides with nanoparticles. In particular, labeled nanoparticles can be used to label nucleotides, oligonucleotides, or polynucleotides in sequencing by synthesis.

Embodiments of the present disclosure relate to methods and kits for sequencing by synthesis utilizing biorthogonal chemical reactions between unlabeled nucleotides and post incorporation labeling reagents.

Embodiments of the present disclosure relate to nucleotide molecules having an enzymatically cleavable self-immolative linker group. Also provided herein are methods and kits for sequencing applications using such nucleotides.

The present application relates to the technical field of organic compound reagent, specifically relates to a silicon-based rhodamine compound and a preparation method thereof, fluorescent modified nucleotide and kit, wherein the fluorescent modified nucleotide can be applied to the nucleic acid sequencing reaction of sequencing by synthesis. The present application creatively improves -COR 11 The connection structure between the fluorescent compound dye core structure adopts a heteroalkyl structure containing dioxygen -O-(CH2) m -O-(CH2) n -COR 11 As the connection structure, the connecting group -COR The silicon-based rhodamine compound is connected to the fluorescent compound core structure, and the fluorescence stability, fluorescence intensity and incorporation efficiency of the modified nucleotide formed by the silicon-based rhodamine compound as a modified molecule used in the nucleic acid sequencing reaction are improved.

A method for real-time sequence analysis of DNA fragments includes providing a DNA fragments sample and connecting first and second adapter oligonucleotides to 5′ and 3′ ends of a DNA strand of the DNA fragments, respectively. A first adapter oligonucleotide includes from 5′ to 3′ a) a first flow cell binding sequence, b) a read 1 sequencing primer site, c) optionally a random sequence, and d) a sample-specific barcoding sequence. A second adapter oligonucleotide includes from 5′ to 3′ d) a sequence complementary to the sample-specific barcoding sequence, c) optionally a sequence complementary to the random sequence, b) a read 2 sequencing primer site that might be complementary to the read 1 sequencing primer site, and a) a second flow cell binding sequence. First and second adapter oligonucleotides of one kind have complementary barcoding sequences. A sequencing by synthesis process is used for sequencing the connected adapter oligonucleotides.

Random arrays of single molecules are provided for carrying out large scale analyzes, 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 μm2 and have nearest neighbor distances that permit optical resolution of on the order of 109 single molecules per cm2. Many analytical chemistries can be applied to random arrays of the invention, including sequencing by hybridization chemistries, sequencing by synthesis chemistries, SNP detection chemistries, and the like, to greatly expand the scale and potential applications of such techniques.

A method for reducing sequencing by synthesis cycle time using a microfluidic device is provided. The microfluidic device comprises a flow cell having an inlet port, an outlet port, and a flow channel extending between the inlet port and the outlet port, wherein the flow channel receives an analyte of interest and one or more reagents for analyzing and detecting molecules. To aid in the acceleration of the reactions, the microfluidic device comprises a mixing device to increase the rates of diffusion of the reagents from the fluid bulk to an active surface of the flow cell. The mixing device comprises at least one of an electrothermal mixing device, an active mechanical mixing device, and a vibrational mixing device.

The application relates to DNA sequencing systems and methods. Systems and methods for determining the nucleotide sequence of a polynucleotide may include introducing a fourth labeled nucleotide in a two-channel sequencing by synthesis system that allows for encoding space for a detecting a fifth labeled nucleotide or empty well detection.

Described are DNA sequencing systems and methods. Systems and methods for determining the nucleotide sequence of a polynucleotide may include determining the sequence of a polynucleotide with more than four types of bases by increasing the number of encoding states in sequencing by synthesis (SBS) systems. The systems and methods may expand the encoding space of current systems by discretizing the amplitude space in a channel into more than two states, and / or by adding additional channels.

The present invention provides compositions and methods for nucleic acid sequencing and other applications. In sequencing by synthesis, an unlabeled reversible terminator is incorporated in each cycle by a polymerase and then labeled after incorporation by binding a directly or indirectly labeled antibody or other affinity reagent to the reversible terminator.

Random arrays of single molecules are provided for carrying out large scale analyzes, 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 μm2 and have nearest neighbor distances that permit optical resolution of on the order of 109 single molecules per cm2. Many analytical chemistries can be applied to random arrays of the invention, including sequencing by hybridization chemistries, sequencing by synthesis chemistries, SNP detection chemistries, and the like, to greatly expand the scale and potential applications of such techniques.

Described are DNA sequencing systems and methods. Systems and methods for determining the nucleotide sequence of a polynucleotide may include determining the sequence of a polynucleotide with more than four types of bases by increasing the number of encoding states in sequencing by synthesis (SBS) systems. The systems and methods may expand the encoding space of current systems by discretizing the amplitude space in a channel into more than two states, and / or by adding additional channels.

The present disclosure provides compositions, methods, kits, systems and apparatus that are useful for nucleic acid polymerization. In particular, recombinant polymerases and biologically active fragments thereof are provided that allow for nucleic acid amplification. In some aspects, the disclosure provides recombinant polymerases that yield lower systematic error rates and / or improved accuracy, when used in sequencing by synthesis reactions as compared to a control polymerase. In one aspect, the disclosure relates to recombinant polymerases useful for nucleic acid sequencing, genotyping, copy number variation analysis, paired-end sequencing and other forms of genetic analysis. In another aspect, the recombinant polymerases are useful for the amplification of nucleic acid templates during PCR, emPCR, isothermal amplification, recombinase polymerase amplification, rolling circle amplification, strand displacement amplification and proximity ligation amplification. In some aspects, the disclosure relates to recombinant polymerases useful for the generation of nucleic acid libraries and / or nucleic acid templates.

Disclosed herein are highly accurate approaches for single molecule electronic nanopore-based SBS.

The present invention relates to a sequencing method that allows for increased sequencing rates and increased sequencing data density. The system can be based on a next generation sequencing method such as sequencing by synthesis (SBS), but uses multiple primers that bind at different positions of the same nucleotide chain.

Systems and methods for nucleic acid sequencing are provided. Polynucleotide strands to be sequenced are immobilized to a surface, clonally amplified and primed for polynucleotide synthesis. Nucleotides modified with cleavable electroactive labels at the 3'-OH of the sugar ring are provided and are incorporated into the growing strand during synthesis. The labels of nucleotides that are successfully incorporated into the growing polynucleotide strand are cleaved via application of a stimulus after incorporation and are detected by an electronic nanosensor. The systems and methods described herein combine the high accuracy of SbS methods combined with the scalability and speed of semiconductor-based electrical detection mechanisms.

Systems and methods for nucleic acid sequencing are provided. Polynucleotide strands to be sequenced are immobilized to a surface, clonally amplified and primed for polynucleotide synthesis. Nucleotides modified with cleavable electroactive labels at the 3′-OH of the sugar ring are provided and are incorporated into the growing strand during synthesis. The labels of nucleotides that are successfully incorporated into the growing polynucleotide strand are cleaved via application of a stimulus after incorporation and are detected by an electronic nanosensor. The systems and methods described herein combine the high accuracy of SbS methods combined with the scalability and speed of semiconductor-based electrical detection mechanisms.

The present disclosure provides a method for sequencing target polynucleotide molecules. In some embodiments, the present disclosure provides a method of sequencing by synthesis where different subsets of nucleotide-conjugate complexes are sequentially formed and detected during each iterative extension of a plurality of nascent nucleic acid copy strands, where each nascent nucleic acid copy strand is complementary to one of a plurality of target polynucleotide molecules. In some embodiments, the plurality of target polynucleotide molecules are arrayed on a solid support.

Embodiments of the present disclosure relate to compositions and methods for labeling of nucleotides, oligonucleotides, or polynucleotides with conjugated polymers or polymer dots. In particular, conjugated polymers or polymer dots can be used as detectable labels for nucleotides, oligonucleotides, or polynucleotides in sequencing by synthesis.