Provided herein are methods and compositions to make guide nucleic acids (gNAs), nucleic acids encoding gNAs, collections of gNAs, and nucleic acids encoding for a collection of gNAs from any source nucleic acid. Also provided herein are methods and compositions to use the resulting gNAs, nucleic acids encoding gNAs, collections of gNAs, and nucleic acids encoding for a collection of gNAs in a variety of applications.
Provided herein are methods and compositions to make guide nucleic acids (gNAs), nucleic acids encoding gNAs, collections of gNAs, and nucleic acids encoding for a collection of gNAs from any source nucleic acid. Also provided herein are methods and compositions to use the resulting gNAs, nucleic acids encoding gNAs, collections of gNAs, and nucleic acids encoding for a collection of gNAs in a variety of applications.
Provided herein are methods and compositions for a simplified and cost effective method for removing unwanted nucleic acids from a sample using RNase H.
Provided herein are methods and compositions for depleting targeted nucleic acid sequences from a sample, enriching for sequences of interest from a sample, and/or partitioning of sequences from a sample. The methods and compositions are applicable to biological, clinical, forensic, and environmental samples.
Provided herein are methods and compositions for the detection and identification of targets in a sample, using target-specific guide nucleic acids and nucleic acid-guided nuclease system proteins.
Provided herein are methods and compositions for analysis of a transcriptome, for example detection of a RNA isoform, of a cell, tissue, organ, or subject.
C12Q 1/6886 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
Disclosed herein are compositions and methods related to the detection and/or elimination of a first nucleic acid and enrichment of a second nucleic acid in a sample, for example to exclude the first nucleic acid from downstream analysis or sequencing, or to exclude such sequences from a downstream data set.
C12Q 1/6886 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
8.
CAPTURE OF NUCLEIC ACIDS USING A NUCLEIC ACID-GUIDED NUCLEASE-BASED SYSTEM
Disclosed herein are compositions and methods related to the fast and efficient generation of cDNA library from RNA. The method allows integration of the method in an automation adaptable system.
C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
C12Q 1/6881 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for tissue or cell typing, e.g. human leukocyte antigen [HLA] probes
C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
C12Q 1/70 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving virus or bacteriophage
C12Q 1/6811 - Selection methods for production or design of target specific oligonucleotides or binding molecules
C12Q 1/48 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving transferase
Disclosed herein are compositions and methods related to the elimination of molecules of a selected sequence from a nucleic acid sample or from an sequence dataset resulting from the sequencing of a sample, for example to exclude such molecules from downstream analysis or sequencing, or to exclude such sequences from a downstream data set.
01 - Chemical and biological materials for industrial, scientific and agricultural use
05 - Pharmaceutical, veterinary and sanitary products
42 - Scientific, technological and industrial services, research and design
Goods & Services
Reagent kits containing chemicals for laboratory use, for
non-medical and non-veterinary purposes; reagents and
chemicals for use in molecular biology applications for
non-medical and non-veterinary purposes; reagent kits
comprising specialized enzymes, buffers, and nucleotides for
use with sequencing technologies for non-medical and
non-veterinary purposes; kits primarily comprised of
reagents and also including a protocol for use thereof for
non-medical and non-veterinary purposes. Reagent kits containing chemicals for medical purposes;
reagents and reagent chemicals for use in molecular biology
applications for medical purposes; kits comprising reagents
for use with sequencing technologies for medical purposes;
kits primarily comprised of reagents and also including a
protocol for use thereof for medical purposes; reagent kits
containing chemicals for medical laboratory use. Providing temporary use of on-line non-downloadable software
for storing, organizing and manipulating data for molecular
biology, sequencing and bioinformatics applications.
01 - Chemical and biological materials for industrial, scientific and agricultural use
05 - Pharmaceutical, veterinary and sanitary products
42 - Scientific, technological and industrial services, research and design
Goods & Services
(1) Reagent kits containing chemicals for laboratory use, for non-medical and non-veterinary purposes; reagents and chemicals for use in molecular biology applications for non-medical and non-veterinary purposes; reagent kits comprising specialized enzymes, buffers, and nucleotides for use with sequencing technologies for non-medical and non-veterinary purposes; kits primarily comprised of reagents and also including a protocol for use thereof for non-medical and non-veterinary purposes.
(2) Reagent kits containing chemicals for medical purposes; reagents and reagent chemicals for use in molecular biology applications for medical purposes; kits comprising reagents for use with sequencing technologies for medical purposes; kits primarily comprised of reagents and also including a protocol for use thereof for medical purposes; reagent kits containing chemicals for medical laboratory use. (1) Providing temporary use of on-line non-downloadable software for storing, organizing and manipulating data for molecular biology, sequencing and bioinformatics applications.
Disclosed herein are compositions and methods related to the elimination of a first nucleic acid and/or enrichment of a second nucleic acid in a sample, for example to exclude the first nucleic acid from downstream analysis or sequencing, or to exclude such sequences from a downstream data set.
C12Q 1/689 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms for bacteria
Provided herein are methods and compositions for a simplified and cost effective method for removing unwanted nucleic acids from a sample using RNase H.
Provided herein are methods and compositions for analysis of a transcriptome, for example detection of a RNA isoform, of a cell, tissue, organ, or subject.
Methods and compositions related to the use of Mobile Element Insertions and their adjacent genomic sequences. Methods using MEIs as markers for cellular proliferation, as targets for pharmaceuticals, as markers for tissue fingerprinting and in related methods and compositions are disclosed herein. Methods and compositions relate to the detection, treatment and ongoing monitoring of cell proliferation events, cancer, and deleterious effects of mobile elements in aging, and to the selection, use and monitoring of the success of treatment regimens to address these conditions.
C12Q 1/6886 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
G16H 15/00 - ICT specially adapted for medical reports, e.g. generation or transmission thereof
C12Q 1/6809 - Methods for determination or identification of nucleic acids involving differential detection
C12Q 1/6883 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
A61K 31/7072 - Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides containing six-membered rings with nitrogen as a ring hetero atom containing condensed or non-condensed pyrimidines having oxo groups directly attached to the pyrimidine ring, e.g. cytidine, cytidylic acid having two oxo groups directly attached to the pyrimidine ring, e.g. uridine, uridylic acid, thymidine, zidovudine
A61K 31/7056 - Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides containing five-membered rings with nitrogen as a ring hetero atom
01 - Chemical and biological materials for industrial, scientific and agricultural use
Goods & Services
Reagent kits containing chemicals for laboratory use, for non-medical and non-veterinary purposes; reagents and chemicals for use in molecular biology applications for non-medical and non-veterinary purposes; reagent kits comprising specialized enzymes, buffers, and nucleotides for use with sequencing technologies for non-medical and non-veterinary purposes; kits primarily comprised of reagents and also including a protocol for use thereof for non-medical and non-veterinary purposes; Reagent kits containing chemicals for medical laboratory use
42 - Scientific, technological and industrial services, research and design
Goods & Services
Providing temporary use of on-line non-downloadable software for storing, organizing and manipulating data for molecular biology, sequencing and bioinformatics applications
05 - Pharmaceutical, veterinary and sanitary products
Goods & Services
Reagent kits containing chemicals for medical purposes; reagents and reagent chemicals for use in molecular biology applications for medical purposes; kits comprising reagents for use with sequencing technologies for medical purposes; kits primarily comprised of reagents and also including a protocol for use thereof for medical purposes
Provided herein are methods of normalizing a population of nucleic acid samples. Methods herein can comprise: contacting a plurality of nucleic acid samples to a normalizing agent, wherein each nucleic acid of the plurality comprises a sample-specific barcode, and wherein the normalizing agent comprises a plurality of labeled enzymes capable of binding to each sample specific barcode; contacting the product to a capture agent to capture the nucleic acids that are bound to the normalizing agent; and treating the product with a protease to release the bound nucleic acids, thereby creating a normalized library having more even representation of each nucleic acid sample than the plurality of nucleic acid samples before normalization.
C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
C12N 9/16 - Hydrolases (3.) acting on ester bonds (3.1)
C12Q 1/37 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving hydrolase involving peptidase or proteinase
C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
Provided herein are methods and compositions for creating a sequencing library comprising a target nucleic acid. Methods herein can comprise: contacting a nucleic acid sample to a first population of primers, a polymerase, dNTPs, and labeled ddNTPs; performing an extension reaction thereby creating an labeled extension product; contacting the extension product to a second population of primers to create a double stranded extension product comprising the target nucleic acid; contacting the double stranded extension product to a target specific enzyme under conditions allowing cleavage of at least a subset of the double stranded extension product thereby creating a cleaved target nucleic acid; and isolating the cleaved target nucleic acid.
Provided are methods for preparing samples for sequencing. Also provided are methods for sequence analysis. Also provided are methods for classifying multiple aspects of a nucleotide repeat expansion disorder in a single sequencing assay. Also provided are methods for genotyping a target nucleic acid sequence.
C12Q 1/6883 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
23.
DE-NOVO K-MER ASSOCIATIONS BETWEEN MOLECULAR STATES
Provided are methods for preparation and analysis of nucleic acids. Some embodiments include reverse transcribing the RNA with barcoded primers to produce cDNA while maintaining the DNA in the sample, sequencing the DNA and cDNA together, and differentiating the sequenced DNA and cDNA using the barcode or barcodes of the primers. Some embodiments include analyzing the DNA and cDNA sequences of multiple samples separating reads into k-mers, and comparing the k-mers between samples to identify differential sequences between the sequences of the samples.
Disclosed herein are methods, compositions, and systems that utilize the consensus sequencing of rolling circle amplified short templates. Methods of determining a nucleic acid sequence can include one or more steps of contacting a nucleic acid in a sample to an endonuclease to cleave a target nucleic acid; ligating the target nucleic acid sequence to form a circular target nucleic acid; hybridizing at least one primer to the circular target molecule to form amplified nucleic acid through rolling circle amplification; and performing sequence analysis of the amplified nucleic acid.
Disclosed herein are compositions and methods related to the detection and/or elimination of a first nucleic acid and enrichment of a second nucleic acid in a sample, for example to exclude the first nucleic acid from downstream analysis or sequencing, or to exclude such sequences from a downstream data set.
Disclosed herein are methods of long range target specific amplification and sequencing using an RNA intermediate synthesized directly from the target including using hairpin adaptors having a double stranded promoter and an overhang which hybridizes with a reverse-complementary overhang on a target nucleic acid. RNA transcription eliminates clonal amplification of early synthesis errors. Approaches allow for the identification of target-adjacent sequence, such as sequence adjacent to a repeat element target. Also disclosed herein are compositions and kits for amplification and sequencing.
Disclosed herein are compositions and methods related to the elimination of a first nucleic acid and enrichment of a second nucleic acid in a sample, for example to exclude the first nucleic acid from downstream analysis or sequencing, or to exclude such sequences from a downstream data set.
Disclosed herein are compositions and methods related to the elimination of a first nucleic acid and/or enrichment of a second nucleic acid in a sample, for example to exclude the first nucleic acid from downstream analysis or sequencing, or to exclude such sequences from a downstream data set.
Disclosed herein are compositions and methods related to the elimination of molecules of a selected sequence from a nucleic acid sample or from an sequence dataset resulting from the sequencing of a sample, for example to exclude such molecules from downstream analysis or sequencing, or to exclude such sequences from a downstream data set.
Provided herein are methods and compositions for creating a sequencing library comprising a target nucleic acid. Methods herein can comprise: contacting a nucleic acid sample to a first population of primers, a polymerase, dNTPs, and labeled ddNTPs; performing an extension reaction thereby creating an labeled extension product; contacting the extension product to a second population of primers to create a double stranded extension product comprising the target nucleic acid; contacting the double stranded extension product to a target specific enzyme under conditions allowing cleavage of at least a subset of the double stranded extension product thereby creating a cleaved target nucleic acid; and isolating the cleaved target nucleic acid.
Provided herein are methods of normalizing a population of nucleic acid samples. Methods herein can comprise: contacting a plurality of nucleic acid samples to a normalizing agent, wherein each nucleic acid of the plurality comprises a sample-specific barcode, and wherein the normalizing agent comprises a plurality of labeled enzymes capable of binding to each sample specific barcode; contacting the product to a capture agent to capture the nucleic acids that are bound to the normalizing agent; and treating the product with a protease to release the bound nucleic acids, thereby creating a normalized library having more even representation of each nucleic acid sample than the plurality of nucleic acid samples before normalization.
Provided herein are methods and compositions to make guide nucleic acids (gNAs), nucleic acids encoding gNAs, collections of gNAs, and nucleic acids encoding for a collection of gNAs from any source nucleic acid. Also provided herein are methods and compositions to use the resulting gNAs, nucleic acids encoding gNAs, collections of gNAs, and nucleic acids encoding for a collection of gNAs in a variety of applications.
Provided herein are methods and compositions for depleting targeted nucleic acid sequences from a sample, enriching for sequences of interest from a sample, and/or partitioning of sequences from a sample. The methods and compositions are applicable to biological, clinical, forensic, and environmental samples.
C12N 15/00 - Mutation or genetic engineeringDNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purificationUse of hosts therefor
C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
01 - Chemical and biological materials for industrial, scientific and agricultural use
05 - Pharmaceutical, veterinary and sanitary products
42 - Scientific, technological and industrial services, research and design
Goods & Services
Reagent kits containing chemicals for laboratory use, for
non-medical and non-veterinary purposes; reagents and
chemicals for use in molecular biology applications for
non-medical and non-veterinary purposes; reagent kits
comprising specialized enzymes, buffers, and nucleotides for
use with sequencing technologies for non-medical and
non-veterinary purposes; laboratory research kits primarily
comprised of reagents for non-medical and non-veterinary
purposes; reagent kits containing chemicals for medical
laboratory use. Reagent kits containing chemicals for medical purposes;
reagents and reagent chemicals for use in molecular biology
applications for medical purposes; kits comprising reagents
for use with sequencing technologies for medical purposes;
diagnostic kits primarily comprised of diagnostic reagents
for medical purposes. Providing temporary use of on-line non-downloadable software
for storing, organizing and manipulating data for molecular
biology, sequencing and bioinformatics applications.
Methods, compositions and kits are provided herein for insertional modification of nucleic acids by, for example transposase-mediated covalent insertion of insertion sequence into a sample nucleic acid molecule. Using sequence of the insertion to direct amplification of adjacent nucleic acid sequence, and using bar codes to map amplified sequence to partitions, one can map sample nucleic acid sequence to single molecules of the nucleic acid sample that are derived directly from the sample nucleic acid molecule.
01 - Chemical and biological materials for industrial, scientific and agricultural use
05 - Pharmaceutical, veterinary and sanitary products
42 - Scientific, technological and industrial services, research and design
Goods & Services
Reagent kits containing chemicals for laboratory use, for
non-medical and non-veterinary purposes; reagents and
chemicals for use in molecular biology applications for
non-medical and non-veterinary purposes; reagent kits
comprising specialized enzymes, buffers, and nucleotides for
use with sequencing technologies for non-medical and
non-veterinary purposes; laboratory research kits primarily
comprised of reagents for non-medical and non-veterinary
purposes; reagent kits containing chemicals for medical
laboratory use. Reagent kits containing chemicals for medical purposes;
reagents and reagent chemicals for use in molecular biology
applications for medical purposes; kits comprising reagents
for use with sequencing technologies for medical purposes;
diagnostic kits primarily comprised of diagnostic reagents
for medical purposes. Providing temporary use of on-line non-downloadable software
for storing, organizing and manipulating data for molecular
biology, sequencing and bioinformatics applications.
37.
DE-NOVO K-MER ASSOCIATIONS BETWEEN MOLECULAR STATES
Provided are methods for preparation and analysis of nucleic acids. Some embodiments include reverse transcribing the RNA with barcoded primers to produce cDNA while maintaining the DNA in the sample, sequencing the DNA and cDNA together, and differentiating the sequenced DNA and cDNA using the barcode or barcodes of the primers. Some embodiments include analyzing the DNA and cDNA sequences of multiple samples separating reads into k-mers, and comparing the k-mers between samples to identify differential sequences between the sequences of the samples.
Provided are methods for preparing samples for sequencing. Also provided are methods for sequence analysis. Also provided are methods for classifying multiple aspects of a nucleotide repeat expansion disorder in a single sequencing assay. Also provided are methods for genotyping a target nucleic acid sequence.
Disclosed herein are methods, compositions, and systems that utilize the consensus sequencing of rolling circle amplified short templates. Methods of determining a nucleic acid sequence can include one or more steps of contacting a nucleic acid in a sample to an endonuclease to cleave a target nucleic acid; ligating the target nucleic acid sequence to form a circular target nucleic acid; hybridizing at least one primer to the circular target molecule to form amplified nucleic acid through rolling circle amplification; and performing sequence analysis of the amplified nucleic acid.
01 - Chemical and biological materials for industrial, scientific and agricultural use
05 - Pharmaceutical, veterinary and sanitary products
42 - Scientific, technological and industrial services, research and design
Goods & Services
(1) Kits containing reagent chemicals for laboratory, non-medical and non-veterinary purposes namely for gene sequencing; chemical reagents for use in molecular biology applications for non-medical and non-veterinary purposes namely for gene sequencing; kits containing reagents with specialized enzymes, buffers, and nucleotides for use with gene sequencing for non-medical and non-veterinary purposes; kits containing reagents for laboratory research for non-medical and non-veterinary purposes namely for gene sequencing; kits containing reagent chemicals for medical laboratory use for gene sequencing.
(2) Kits containing reagent chemicals for medical purposes namely for gene sequencing; cell culture reagents and chemical reagents for use in molecular biology applications for medical purposes namely for gene sequencing; kits comprising reagents for use with sequencing technologies for medical purposes; kits comprised of chemical reagents for diagnostic medical purposes in gene sequencing.
01 - Chemical and biological materials for industrial, scientific and agricultural use
05 - Pharmaceutical, veterinary and sanitary products
42 - Scientific, technological and industrial services, research and design
Goods & Services
(1) Non-medical and non-veterinary reagent kits comprising chemical diagnostic reagents for laboratory research use; non-medical and non-veterinary chemical diagnostic reagents and bio-chemical reagents for use in molecular biology applications for laboratory research use; non-medical and non-veterinary reagent kits comprising enzymes, buffers, and nucleotides for use with sequencing technologies, for scientific research use; non-medical and non-veterinary laboratory research kits comprising chemical diagnostic reagents for scientific research use; reagent kits comprising chemical diagnostic reagents for laboratory research use.
(2) Reagent kits comprising diagnostic chemical reagents for medical purposes; reagents and reagent chemicals, namely, diagnostic reagents, for use in molecular biology applications for medical purposes; kits comprising diagnostic reagents for use with sequencing technologies for medical purposes; diagnostic kits comprising diagnostic reagents for medical purposes. (1) Providing temporary use of on-line non-downloadable software for storing, organizing and manipulating data for molecular biology, sequencing and bioinformatics applications.
01 - Chemical and biological materials for industrial, scientific and agricultural use
Goods & Services
Reagent kits containing chemicals for laboratory use, for non-medical and non-veterinary purposes; reagents and chemicals for use in molecular biology applications for non-medical and non-veterinary purposes; reagent kits comprising specialized enzymes, buffers, and nucleotides for use with sequencing technologies for non-medical and non-veterinary purposes; kits primarily comprised of reagents and also including a protocol for use thereof for non-medical and non-veterinary purposes; Reagent kits containing chemicals for medical laboratory use
05 - Pharmaceutical, veterinary and sanitary products
Goods & Services
Reagent kits containing chemicals for medical purposes; reagents and reagent chemicals for use in molecular biology applications for medical purposes; kits comprising reagents for use with sequencing technologies for medical purposes; kits primarily comprised of reagents and also including a protocol for use thereof for medical purposes
01 - Chemical and biological materials for industrial, scientific and agricultural use
Goods & Services
Reagent kits containing chemicals for laboratory use, for non-medical and non-veterinary purposes; reagents and chemicals for use in molecular biology applications for non-medical and non-veterinary purposes; reagent kits comprising specialized enzymes, buffers, and nucleotides for use with sequencing technologies for non-medical and non-veterinary purposes; kits primarily comprised of reagents and also including a protocol for use thereof for non-medical and non-veterinary purposes; Reagent kits containing chemicals for medical laboratory use
05 - Pharmaceutical, veterinary and sanitary products
Goods & Services
Reagent kits containing chemicals for medical purposes; reagents and reagent chemicals for use in molecular biology applications for medical purposes; kits comprising reagents for use with sequencing technologies for medical purposes; kits primarily comprised of reagents and also including a protocol for use thereof for medical purposes
Disclosed herein are compositions and methods related to the elimination of a first nucleic acid and enrichment of a second nucleic acid in a sample, for example to exclude the first nucleic acid from downstream analysis or sequencing, or to exclude such sequences from a downstream data set.
Disclosed herein are compositions and methods related to the elimination of molecules of a selected sequence from a nucleic acid sample or from an sequence dataset resulting from the sequencing of a sample, for example to exclude such molecules from downstream analysis or sequencing, or to exclude such sequences from a downstream data set.
Provided herein are methods and compositions to make guide nucleic acids (gNAs), nucleic acids encoding gNAs, collections of gNAs, and nucleic acids encoding for a collection of gNAs from any source nucleic acid. Also provided herein are methods and compositions to use the resulting gNAs, nucleic acids encoding gNAs, collections of gNAs, and nucleic acids encoding for a collection of gNAs in a variety of applications.
C12N 15/00 - Mutation or genetic engineeringDNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purificationUse of hosts therefor
C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
Disclosed herein are methods of long range target specific amplification and sequencing using an RNA intermediate synthesized directly from the target including using hairpin adaptors having a double stranded promoter and an overhang which hybridizes with a reverse-complementary overhang on a target nucleic acid. RNA transcription eliminates clonal amplification of early synthesis errors. Approaches allow for the identification of target-adjacent sequence, such as sequence adjacent to a repeat element target. Also disclosed herein are compositions and kits for amplification and sequencing.
Provided herein are methods and compositions for depleting targeted nucleic acid sequences from a sample, enriching for sequences of interest from a sample, and/or partitioning of sequences from a sample. The methods and compositions are applicable to biological, clinical, forensic, and environmental samples.
Provided herein are methods and compositions for depleting targeted nucleic acid sequences from a sample, enriching for sequences of interest from a sample, and/or partitioning of sequences from a sample. The methods and compositions are applicable to biological, clinical, forensic, and environmental samples.
Methods, compositions and kits are provided herein for insertional modification of nucleic acids by, for example transposase-mediated covalent insertion of insertion sequence into a sample nucleic acid molecule. Using sequence of the insertion to direct amplification of adjacent nucleic acid sequence, and using bar codes to map amplified sequence to partitions, one can map sample nucleic acid sequence to single molecules of the nucleic acid sample that are derived directly from the sample nucleic acid molecule.
Disclosed herein are methods of long range target specific amplification and sequencing using an RNA intermediate synthesized directly from the target to eliminate clonal amplification of early synthesis errors. Approaches allow for the identification of target-adjacent sequence, such as sequence adjacent to a repeat element target. Also disclosed herein are compositions and kits for amplification and sequencing.
Disclosed herein are compositions and methods related to the elimination of molecules of a selected sequence from a nucleic acid sample or from an sequence dataset resulting from the sequencing of a sample, for example to exclude such molecules from downstream analysis or sequencing, or to exclude such sequences from a downstream data set.
Methods, compositions and kits are provided herein for insertional modification of nucleic acids by, for example transposase-mediated covalent insertion of insertion sequence into a sample nucleic acid molecule. Using sequence of the insertion to direct amplification of adjacent nucleic acid sequence, and using bar codes to map amplified sequence to partitions, one can map sample nucleic acid sequence to single molecules of the nucleic acid sample that are derived directly from the sample nucleic acid molecule.
Disclosed herein are methods, compositions, and systems that utilize the consensus sequencing of rolling circle amplified short templates. Methods of determining a nucleic acid sequence can include one or more steps of contacting a nucleic acid in a sample to an endonuclease to cleave a target nucleic acid; ligating the target nucleic acid sequence to form a circular target nucleic acid; hybridizing at least one primer to the circular target molecule to form amplified nucleic acid through rolling circle amplification; and performing sequence analysis of the amplified nucleic acid.
Provided are methods for preparation and analysis of nucleic acids. Some embodiments include reverse transcribing the RNA with barcoded primers to produce cDNA while maintaining the DNA in the sample, sequencing the DNA and cDNA together, and differentiating the sequenced DNA and cDNA using the barcode or barcodes of the primers. Some embodiments include analyzing the DNA and cDNA sequences of multiple samples separating reads into k-mers, and comparing the k-mers between samples to identify differential sequences between the sequences of the samples.
Provided herein are methods and compositions for creating a sequencing library comprising a target nucleic acid. Methods herein can comprise: contacting a nucleic acid sample to a first population of primers, a polymerase, dNTPs, and labeled ddNTPs; performing an extension reaction thereby creating an labeled extension product; contacting the extension product to a second population of primers to create a double stranded extension product comprising the target nucleic acid; contacting the double stranded extension product to a target specific enzyme under conditions allowing cleavage of at least a subset of the double stranded extension product thereby creating a cleaved target nucleic acid; and isolating the cleaved target nucleic acid.
Provided herein are methods of normalizing a population of nucleic acid samples. Methods herein can comprise: contacting a plurality of nucleic acid samples to a normalizing agent, wherein each nucleic acid of the plurality comprises a sample-specific barcode, and wherein the normalizing agent comprises a plurality of labeled enzymes capable of binding to each sample specific barcode; contacting the product to a capture agent to capture the nucleic acids that are bound to the normalizing agent; and treating the product with a protease to release the bound nucleic acids, thereby creating a normalized library having more even representation of each nucleic acid sample than the plurality of nucleic acid samples before normalization.
C12Q 1/6876 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
C12Q 1/6886 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
Provided herein are methods and compositions for a simplified and cost effective method for removing unwanted nucleic acids from a sample using RNase H.
Disclosed herein are compositions and methods related to the elimination of molecules of a selected sequence from a nucleic acid sample or from an sequence dataset resulting from the sequencing of a sample, for example to exclude such molecules from downstream analysis or sequencing, or to exclude such sequences from a downstream data set.
C12P 19/34 - Polynucleotides, e.g. nucleic acids, oligoribonucleotides
C40B 30/04 - Methods of screening libraries by measuring the ability to specifically bind a target molecule, e.g. antibody-antigen binding, receptor-ligand binding
C40B 40/06 - Libraries containing nucleotides or polynucleotides, or derivatives thereof
64.
METHODS FOR ANALYSIS OF SOMATIC MOBILE ELEMENTS, AND USES THEREOF
Methods and compositions related to the use of Mobile Element Insertions and their adjacent genomic sequences. Methods using MEIs as markers for cellular proliferation, as targets for pharmaceuticals, as markers for tissue fingerprinting and in related methods and compositions are disclosed herein. Methods and compositions relate to the detection, treatment and ongoing monitoring of cell proliferation events, cancer, and deleterious effects of mobile elements in aging, and to the selection, use and monitoring of the success of treatment regimens to address these conditions.
C12Q 1/6876 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
C12Q 1/6886 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
65.
METHOD FOR TARGET SPECIFIC RNA TRANSCRIPTION OF DNA SEQUENCES
Disclosed herein are methods of long range target specific amplification and sequencing using an RNA intermediate synthesized directly from the target to eliminate clonal amplification of early synthesis errors. Approaches allow for the identification of target-adjacent sequence, such as sequence adjacent to a repeat element target. Also disclosed herein are compositions and kits for amplification and sequencing.
Provided are methods for preparing samples for sequencing. Also provided are methods for sequence analysis. Also provided are methods for classifying multiple aspects of a nucleotide repeat expansion disorder in a single sequencing assay. Also provided are methods for genotyping a target nucleic acid sequence.
C12Q 1/6883 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
Disclosed herein are compositions and methods related to the elimination of a first nucleic acid and/or enrichment of a second nucleic acid in a sample, for example to exclude the first nucleic acid from downstream analysis or sequencing, or to exclude such sequences from a downstream data set.
C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
C12Q 1/48 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving transferase
C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
C12Q 1/6811 - Selection methods for production or design of target specific oligonucleotides or binding molecules
C12Q 1/6881 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for tissue or cell typing, e.g. human leukocyte antigen [HLA] probes
C12Q 1/70 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving virus or bacteriophage
