| SEQUENOM, INC. Patent applications |
| Patent application number | Title | Published |
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| 20120115737 | RESTRICTION ENDONUCLEASE ENHANCED POLYMORPHIC SEQUENCE DETECTION - Provided is an improved method for the detection of specific polymorphic alleles in a mixed DNA population. The method comprises enriching the relative percentage of a given polymorphic allele that is exponentially amplifiable by PCR. Also provided are methods for selectively enriching target nucleic acid, for example, fetal nucleic acid in a maternal sample. In the case of detecting fetal nucleic acid in a maternal sample, a restriction enzyme is introduced that can discriminate between the alleles of a polymorphic site. Preferably, the maternal allele is digested and nucleic acid comprising the paternal allele is relatively enriched. | 05-10-2012 |
| 20120046178 | PRODUCTS AND PROCESSES FOR MULTIPLEX NUCLEIC ACID IDENTIFICATION - Provided herein are products and processes for detecting the presence or absence of multiple target nucleic acids. Certain methods include amplifying the target nucleic acids, or portion thereof; extending oligonucleotides that specifically hybridize to the amplicons, where the oligonucleotides include distinguishable labels and a capture agent; capturing the extended oligonucleotides to a solid phase via the capture agent; releasing and detecting the distinguishable label, and thereby determining the presence or absence of each target nucleic acid by the presence or absence of the distinguishable label. | 02-23-2012 |
| 20120015826 | METHODS FOR HIGH LEVEL MULTIPLEXED POLYMERASE CHAIN REACTIONS AND HOMOGENOUS MASS EXTENSION REACTIONS - Provided herein are optimized methods for performing multiplexed detection of a plurality of sequence variations. Also provided are methods for performing multiplexed amplification of target nucleic acid. | 01-19-2012 |
| 20110294699 | METHODS AND COMPOSITIONS FOR UNIVERSAL SIZE-SPECIFIC PCR - Provided herein are products and processes for the amplification, detection and sequencing of short-stranded nucleic acid in the presence of a high background of long-stranded genomic material (e.g., host or maternal nucleic acids). The methods rely on the use of inside and outside primers introduced at varying concentrations, as well as universal amplification reactions that preferentially amplify short, low copy number nucleic acid. | 12-01-2011 |
| 20110269643 | MASS SPECTROMETRIC METHODS FOR DETECTING MUTATIONS IN A TARGET NUCLEIC ACID - Fast and highly accurate mass spectrometry-based processes for detecting particular nucleic acid molecules and mutations in the molecules are provided. | 11-03-2011 |
| 20110263453 | NUCLEIC ACID QUANTIFICATION PRODUCTS AND PROCESSES - Described herein are products and processes for nucleic acid quantification, which are in part useful for detecting and determining the nucleotide sequence of rare nucleic acids (i.e., low copy number nucleic acids) in a sample. Such products and processes are useful for reducing the dynamic range among different nucleic acid species. | 10-27-2011 |
| 20110251076 | NON-INVASIVE DETECTION OF FETAL GENETIC TRAITS - Blood plasma of pregnant women contains fetal and (generally >90%) maternal circulatory extracellular DNA. Most of said fetal DNA contains ≦500 base pairs, said maternal DNA having a greater size. Separation of circulatory extracellular DNA of <500 base pairs results in separation of fetal from maternal DNA. A fraction of a blood plasma or serum sample of a pregnant woman containing, due to size separation (e.g. by chromatography, density gradient centrifugation or nanotechnological methods), extracellular DNA substantially comprising ≦500 base pairs is useful for non-invasive detection of fetal genetic traits (including the fetal RhD gene in pregnancies at risk for HDN; fetal Y chromosome-specific sequences in pregnancies at risk for X chromosome-linked disorders; chromosomal aberrations; hereditary Mendelian genetic disorders and corresponding genetic markers; and traits decisive for paternity determination) by e.g. PCR, ligand chain reaction or probe hybridization techniques, or nucleic acid arrays. | 10-13-2011 |
| 20110245482 | NON-INVASIVE DETECTION OF FETAL GENETIC TRAITS - Blood plasma of pregnant women contains fetal and (generally>90%) maternal circulatory extracellular DNA. Most of said fetal DNA contains ≦500 base pairs, said maternal DNA having a greater size. Separation of circulatory extracellular DNA of <500 base pairs results in separation of fetal from maternal DNA. A fraction of a blood plasma or serum sample of a pregnant woman containing, due to size separation (e.g. by chromatography, density gradient centrifugation or nanotechnological methods), extracellular DNA substantially comprising ≦500 base pairs is useful for non-invasive detection of fetal genetic traits (including the fetal RhD gene in pregnancies at risk for HDN; fetal Y chromosome-specific sequences in pregnancies at risk for X chromosome-linked disorders; chromosomal aberrations; hereditary Mendelian genetic disorders and corresponding genetic markers; and traits decisive for paternity determination) by e.g. PCR, ligand chain reaction or probe hybridization techniques, or nucleic acid arrays. | 10-06-2011 |
| 20110172124 | COMPOSITIONS AND PROCESSES FOR IMPROVED MASS SPECTROMETRY ANALYSIS - The invention provides a novel additive for improved analysis by mass spectrometry. More specifically, ascorbic acid has been found to reduce or eliminate the presence of adducts commonly present in mass spectra. The improved processes and compositions of the invention allow for increased accuracy, sensitivity and throughput for samples analyzed by mass spectrometry. | 07-14-2011 |
| 20110172111 | SOLID PHASE SEQUENCING OF BIOPOLYMERS - This invention relates to methods for detecting and sequencing target nucleic acid sequences, to mass modified nucleic acid probes and arrays of probes useful in these methods, and to kits and systems which contain these probes. Useful methods involve hybridizing the nucleic acids or nucleic acids which represent complementary or homologous sequences of the target to an array of nucleic acid probes. These probes comprise a single-stranded portion, an optional double-stranded portion and a variable sequence within the single-stranded portion. The molecular weights of the hybridized nucleic acids of the set can be determined by mass spectroscopy, and the sequence of the target determined from the molecular weights of the fragments. Nucleic acids whose sequences can be determined include DNA or RNA in biological samples such as patient biopsies and environmental samples. Probes may be fixed to a solid support such as a hybridization chip to facilitate automated molecular weight analysis and identification of the target sequence. | 07-14-2011 |
| 20110160093 | DETECTION AND QUANTIFICATION OF BIOMOLECULES USING MASS SPECTROMETRY - The present invention is directed in part to a method for detecting a target nucleic acid using detector oligonucleotides detectable by mass spectrometry. This method takes advantage of the 5′ to 3′ nuclease activity of a nucleic acid polymerase to cleave annealed oligonucleotide probes from hybridized duplexes and releases labels for detection by mass spectrometry. This process is easily incorporated into a polymerase chain reaction (PCR) amplification assay. The method also includes embodiments directed to quantitative analysis of target nucleic acids. | 06-30-2011 |
| 20110124518 | METHODS AND COMPOSITIONS FOR THE ANALYSIS OF BIOLOGICAL MOLECULES - Provided herein are compositions and methods for analysis of nucleic acids, including, methods and compositions for genotyping, haplotyping, sequencing and performing other genetic and epigenetic analyses on nucleic acids, for example. In some embodiments, methods and compositions suitable for whole-genome sequencing on single molecules of nucleic acid are provided. In some embodiments, analysis of single molecules of nucleic acid are performed in conjunction with nanopores and/or nanopore devices. | 05-26-2011 |
| 20110027773 | MASS SPECTROMETRIC METHODS FOR DETECTING MUTATIONS IN A TARGET NUCLEIC ACID - Fast and highly accurate mass spectrometry-based processes for detecting particular nucleic acid molecules and mutations in the molecules are provided. In some embodiments, a process comprises: amplifying a nucleic acid from a biological sample; ionizing and volatilizing the amplified product; analyzing the product by mass spectrometry to determine an observed molecular mass of the product; and comparing the observed molecular mass of the product to a calculated molecular mass of at least one nucleic acid having a known sequence, wherein the calculated molecular mass of the at least one nucleic acid having a known sequence is derived from the base composition of the at least one nucleic acid having a known sequence; whereby the presence or absence of the target nucleic acid is detected based on the comparison. | 02-03-2011 |
| 20100297710 | METHODS AND COMPOSITIONS FOR THE EXTRACTION AND AMPLIFICATION OF NUCLEIC ACID FROM A SAMPLE - Provided herein are methods, compositions and kits to extract and relatively enrich by physical separation or amplification short base pair nucleic acid in the presence of a high background of genomic material (e.g., host or maternal nucleic acids). | 11-25-2010 |
| 20100292930 | METHODS FOR GENERATING DATABASES AND DATABASES FOR IDENTIFYING POLYMORPHIC GENETIC MARKERS - Processes and methods for creating a database of genomic samples from healthy human donors, methods that use the database to identify and correlate polymorphic genetic markers and other markers with diseases and conditions are provided. | 11-18-2010 |
| 20100279295 | USE OF THERMOSTABLE ENDONUCLEASES FOR GENERATING REPORTER MOLECULES - Provided are compositions and methods for amplifying, capturing and/or detecting target nucleic acids using cleavable oligonucleotides. | 11-04-2010 |
| 20100273165 | PROCESSES AND COMPOSITIONS FOR METHYLATION-BASED ENRICHMENT OF FETAL NUCLEIC ACID FROM A MATERNAL SAMPLE USEFUL FOR NON INVASIVE PRENATAL DIAGNOSES - Provided are compositions and processes that utilize genomic regions that are differentially methylated between a mother and her fetus to separate, isolate or enrich fetal nucleic acid from a maternal sample. The compositions and processes described herein are particularly useful for non-invasive prenatal diagnostics, including the detection of chromosomal aneuplodies. | 10-28-2010 |
| 20100120035 | METHOD FOR ACCURATE ASSESSMENT OF DNA QUALITY AFTER BISULFITE TREATMENT - The present invention is directed to methods useful for determining DNA quality after bisulfite treatment. The methods include a PCR-based assay, which allows ab-initio assessment of the DNA quality after bisulfite treatment and can help to prevent inaccurate quantitative measurement resulting from poor bisulfite treatment. | 05-13-2010 |
| 20100105049 | PROCESSES AND COMPOSITIONS FOR METHYLATION-BASED ENRICHMENT OF FETAL NUCLEIC ACID FROM A MATERNAL SAMPLE USEFUL FOR NON INVASIVE PRENATAL DIAGNOSES - Provided are compositions and processes that utilize genomic regions differentially methylated between a mother and her fetus to separate, isolate or enrich fetal nucleic acid from a maternal sample. The compositions and processes described herein are useful for non-invasive prenatal diagnostics, including the detection of chromosomal aneuplodies. | 04-29-2010 |
| 20090317818 | RESTRICTION ENDONUCLEASE ENHANCED POLYMORPHIC SEQUENCE DETECTION - Provided in part herein is an improved method for the detection of specific polymorphic alleles in a mixed DNA population. The method comprises enriching the relative percentage of a given polymorphic allele that is exponentially amplifiable by PCR. Provided also are methods for selectively enriching target nucleic acid, for example, fetal nucleic acid in a maternal sample. In the case of detecting fetal nucleic acid in a maternal sample, a restriction enzyme is introduced that can discriminate between the alleles of a polymorphic site. In some embodiments, the maternal allele is digested and nucleic acid comprising the paternal allele is relatively enriched. | 12-24-2009 |
| 20090317817 | NUCLEIC ACID-BASED TESTS FOR PRENATAL GENDER DETERMINATION - Provided herein are compositions, processes and kits for noninvasive, early determination of fetal sex from, and/or amount of fetal nucleic acid in, an extracellular nucleic acid sample from a pregnant female. Such compositions, processes and kits are useful for detection of low genomic copy numbers of male fetal nucleic acid in a high copy number background of female nucleic acid, thereby determining the sex of a fetus and/or amount of fetal nucleic acid in a sample. | 12-24-2009 |
| 20090317816 | METHODS FOR IDENTIFYING RISK OF BREAST CANCER AND TREATMENTS THEREOF - Provided herein are methods for identifying risk of breast cancer in a subject and/or a subject at risk of breast cancer, reagents and kits for carrying out the methods, methods for identifying candidate therapeutics for treating breast cancer, and therapeutic methods for treating breast cancer in a subject. These embodiments are based upon an analysis of polymorphic variations in nucleotide sequences within the human genome. | 12-24-2009 |
| 20090317801 | METHODS AND COMPOSITIONS FOR DISEASE PROGNOSIS BASED ON NUCLEIC ACID METHYLATION - A large scale DNA methylation study was performed in patients with acute myeloid leukemia (AML) that revealed quantitative methylation patterns correlated with patient survival. Based on these results, a prognostic model was built which categorizes a patient's risk—either in a good or poor prognosis group. The findings provided herein support the use of genomic methylation markers for improved molecular classification and disease management in adult AML. Also, the results provide insight into the pathophysiology of AML and offer novel AML gene targets. Thus provided are methods and compositions for the prognosis of a subject suffering from acute myeloid leukemia (AML) based on the methylation state of nucleic acids. The methods may used alone to determine a patient's prognosis or in combination with other prognostic factors or markers such as gene expression. | 12-24-2009 |
| 20090305284 | Methods for Identifying Risk of Breast Cancer and Treatments Thereof - Provided herein are methods for identifying risk of breast cancer in a subject and/or a subject at risk of breast cancer, reagents and kits for carrying out the methods, methods for identifying candidate therapeutics for treating breast cancer, and therapeutic methods for treating breast cancer in a subject. These embodiments are based upon an analysis of polymorphic variations in nucleotide sequences within the human genome. | 12-10-2009 |
| 20090258793 | TARGET-SPECIFIC COMPOMERS AND METHODS OF USE - Provided herein are libraries of nucleic acid species each comprising a transcription unit having a promoter region operatively linked to a coding sequence. The coding sequence of each nucleic acid species encodes a RNA cleavage substrate comprising a unique compomer species and a cleavage site. Each compomer species has a molecular mass distinguishable from the molecular mass of other compomer species in the library, and cleavage at a cleavage site releases a polynucleotide comprising the compomer species from the RNA cleavage substrate. | 10-15-2009 |
| 20090258344 | METHODS FOR IDENTIFYING RISK OF BREAST CANCER AND TREATMENTS THEREOF - Provided herein are methods for identifying risk of breast cancer in a subject and/or a subject at risk of breast cancer, reagents and kits for carrying out the methods, methods for identifying candidate therapeutics for treating breast cancer, and therapeutic methods for treating breast cancer in a subject. These embodiments are based upon an analysis of polymorphic variations in nucleotide sequences within the human genome. | 10-15-2009 |
| 20090202984 | SINGLE MOLECULE NUCLEIC ACID SEQUENCE ANALYSIS PROCESSES AND COMPOSITIONS - Improved solid supports and methods for analyzing target nucleotide sequences are provided herein. Certain improvements are directed to efficiently preparing nucleic acids that comprise nucleotide sequences identical to or substantially identical to one or more target nucleotide sequences, or complement thereof. The prepared nucleic acids include a reference sequence that facilitates sequence analysis. The solid supports and methods provided herein minimize the number of steps required by published sequence analysis methodologies, and thereby offer improved sequence analysis efficiency. | 08-13-2009 |
| 20090155846 | KINASE ANCHOR PROTEIN MUTEINS, PEPTIDES THEREOF AND RELATED METHODS - A-kinase anchor protein (AKAPS) muteins, peptides thereof, and nucleic acids encoding the peptides are provided herein. Also provided are transgenic animals, cells comprising transgenes and various methods employing such peptides. | 06-18-2009 |
| 20090111712 | DETECTION AND QUANTIFICATION OF BIOMOLECULES USING MASS SPECTROMETRY - The present invention is directed in part to a method for detecting a target nucleic acid using detector oligonucleotides detectable by mass spectrometry. This method takes advantage of the 5′ to 3′ nuclease activity of a nucleic acid polymerase to cleave annealed oligonucleotide probes from hybridized duplexes and releases labels for detection by mass spectrometry. This process is easily incorporated into a polymerase chain reaction (PCR) amplification assay. The method also includes embodiments directed to quantitative analysis of target nucleic acids. | 04-30-2009 |
| 20090092977 | MASS SPECTROMETRIC METHODS FOR DETECTING MUTATIONS IN A TARGET NUCLEIC ACID - Fast and highly accurate mass spectrometry-based processes for detecting particular nucleic acid molecules and mutations in the molecules are provided. | 04-09-2009 |
| 20090042203 | Mass Spectrometric Methods for Detecting Mutations in a Target Nucleic Acid - Fast and highly accurate mass spectrometry-based processes for detecting particular nucleic acid molecules and mutations in the molecules are provided. | 02-12-2009 |
| 20090023150 | DNA Diagnostics Based on Mass Spectrometry - Fast and highly accurate mass spectrometry-based processes for detecting a particular nucleic acid sequence in a biological sample are provided. Depending on the sequence to be detected, the processes can be used, for example, to diagnose a genetic disease or chromosomal abnormality; a predisposition to a disease or condition, infection by a pathogenic organism, or for determining identity or heredity. | 01-22-2009 |
| 20090006002 | COMPARATIVE SEQUENCE ANALYSIS PROCESSES AND SYSTEMS - Provided herein are processes for rapidly identifying or determining sequence information in a sample nucleic acid by comparing sample nucleic acid sequence information to reference nucleic acid sequence information or information obtained from reference samples. Also provided are automated systems for conducting comparative sequence analyses. | 01-01-2009 |
| 20080305479 | DETECTION AND QUANTIFICATION OF BIOMOLECULES USING MASS SPECTROMETRY - The present invention is directed in part to a method for detecting a target nucleic acid using detector oligonucleotides detectable by mass spectrometry. This method uses the 5′ to 3′ nuclease activity of a nucleic acid polymerase to cleave annealed oligonucleotide probes from hybridized duplexes and release labels for detection by mass spectrometry. This process is easily incorporated into a PCR amplification assay. The method also includes embodiments directed to quantitative analysis of target nucleic acids. | 12-11-2008 |
| 20080299562 | NUCLEIC ACID-BASED TESTS FOR RHD TYPING, GENDER DETERMINATION AND NUCLEIC ACID QUANTIFICATION - The invention in part provides nucleic acid-based assays, which are particularly useful for non-invasive prenatal testing. The invention in part provides compositions and methods for RhD typing, detecting the presence of fetal nucleic in a sample, determining the relative amount of fetal nucleic acid in a sample and determining the sex of a fetus, wherein each of the assays may be performed alone or in combination. | 12-04-2008 |
| 20080286161 | Methods and Devices for Performing Chemical Reactions on a Solid Support - Apparatus and methods for carrying out biochemical processes directly on a substrate are provided. A substrate assembly includes a cartridge that removably supports a substrate in a fixed position, and a reaction containment member that is removably located on top of the substrate. The reaction containment member includes one or more cavities that form chambers directly above one or more target locations on the surface of the substrate. The chambers can be used to conduct biochemical processes directly over the substrate, as well as to perform thermal cycling of material contained inside the chamber using a heating element disposed directly on the substrate. The substrate assembly is preferably used in combination with a processing machine that dispenses materials into the chambers and that conducts biochemical reactions of materials contained within the chambers, without requiring the substrate assembly to be moved from one location to another location during the processes. | 11-20-2008 |
| 20080248968 | MATRIX-ASSISTED LASER DESORPTION IONIZATION MASS SPECTROMETRY SUBSTRATES HAVING LOW VOLUME MATRIX ARRAY ELEMENTS - Provided herein are substrates for matrix-assisted laser-desorption ionization (MALDI) mass spectrometric analysis. Each spot includes 3-hydroxypicolinic acid matrix and no analyte. | 10-09-2008 |
| 20080199480 | Methods for Identifying Risk of Type II Diabetes and Treatments Thereof - Provided herein are methods for identifying a risk of type II diabetes in a subject, reagents and kits for carrying out the methods, methods for identifying candidate therapeutics for treating type II diabetes, and therapeutic and preventative methods applicable to type II diabetes. These embodiments are based upon an analysis of polymorphic variations in nucleotide sequences within the human genome. | 08-21-2008 |
