Patents Assigned to NuGen Technologies, Inc.
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Patent number: 10190155Abstract: Described herein are methods, compositions and kits for identifying modifications that could lead to false positive detections in nucleic acid sequencing. In some embodiments, the methods, compositions and kits provided herein are useful for reducing potential of false positive detection of variants caused by errors during sample preparation or sequencing.Type: GrantFiled: October 14, 2016Date of Patent: January 29, 2019Assignee: NuGEN Technologies, Inc.Inventors: Douglas A. Amorese, Stephanie C. Huelga, Bin Li
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Patent number: 10102337Abstract: Disclosed herein are methods, compositions and kits for quantitating one or more specific nucleic acids within a plurality of nucleic acids. In some embodiments, a sequencing library is constructed from enriched probe extension products specific for the specific nucleic acids and sequenced. In some embodiments, the resulting reads are used for removing duplicate reads. In some embodiments, counting of verified probes is used to quantitate or determine the number of specific nucleic acid molecules in the starting nucleic acid sample.Type: GrantFiled: August 6, 2015Date of Patent: October 16, 2018Assignee: NuGEN Technologies, Inc.Inventors: Jonathan Scolnick, Benjamin Schroeder, Douglas Amorese, Stephanie C. Huelga
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Patent number: 9822408Abstract: Described herein are improved methods, compositions and kits for next generation sequencing (NGS). The methods, compositions and kits described herein enable phasing of two or more nucleic acid sequences in a sample, i.e. determining whether the nucleic acid sequences (which can comprise regions of sequence variation) are located on the same chromosome and/or the same chromosomal fragment. Phasing information can be obtained by performing multiple, successive sequencing reactions from the same immobilized nucleic acid template. The methods, compositions and kits provided herein can be useful, for example, for haplotyping, SNP phasing, or for determining downstream exons in RNA-seq.Type: GrantFiled: March 14, 2014Date of Patent: November 21, 2017Assignee: Nugen Technologies, Inc.Inventors: Doug Amorese, Benjamin G. Schroeder, Jonathan Scolnick
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Patent number: 8852867Abstract: The invention provides methods for amplification of polynucleotide sequences using primers containing single-stranded RNA. The methods employ use of an enzyme capable of cleaving single-stranded RNA, such as RNase I, to degrade a first RNA-containing primer prior to addition of a second RNA-containing primer. The invention also provides compositions and kits for practicing the amplification methods, as well as methods which use the amplification products.Type: GrantFiled: May 9, 2011Date of Patent: October 7, 2014Assignee: Nugen Technologies, Inc.Inventors: Nurith Kurn, Shenglong Wang
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Publication number: 20140274729Abstract: The invention provides methods and compositions, including kits, for the construction of directional nucleic acid libraries. The invention further provides methods and compositions for the amplification and sequencing of directional cDNA libraries.Type: ApplicationFiled: September 18, 2013Publication date: September 18, 2014Applicant: NuGEN Technologies, Inc.Inventors: Nurith Kurn, Bin Li
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Publication number: 20140274738Abstract: The present invention provides improved methods, compositions and kits for short read next generation sequencing (NGS). The methods, compositions and kits of the present invention enable phasing of two or more nucleic acid sequences in a sample, i.e. determining whether the nucleic acid sequences (typically comprising regions of sequence variation) are located on the same chromosome and/or the same chromosomal fragment. Phasing information is obtained by performing multiple, successive sequencing reactions from the same immobilized nucleic acid template. The methods, compositions and kits provided herein are useful, for example, for haplotyping, SNP phasing, or for determining downstream exons in RNA-seq.Type: ApplicationFiled: March 14, 2014Publication date: September 18, 2014Applicant: NuGEN Technologies, Inc.Inventors: Doug Amorese, Benjamin G. Schroeder, Jonathan Scolnick
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Patent number: 8551709Abstract: The invention provides methods, compositions, and kits for fragmentation and labeling of nucleic acids. More particularly, the invention relates to methods for fragmentation of nucleic acids to produce fragments with 3? end hydroxyl groups within a desired size range. In methods of the invention, nucleic acids are fragmented at abasic sites to produce fragments with blocked 3? ends. The 3? ends are unblocked to produce polynucleotide fragments with hydroxyl groups at their 3? ends. Methods, kits, and compositions for carrying out fragmentation of a polynucleotide template in a single reaction mixture to yield fragments with 3?-hydroxyl ends within the desired size range are disclosed.Type: GrantFiled: March 2, 2012Date of Patent: October 8, 2013Assignee: NuGEN Technologies, Inc.Inventors: Nurith Kurn, Pengchin Chen
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Patent number: 8512956Abstract: The present method provides methods, libraries, and kits related to the archiving and clonal amplification of sequences related to target polynucleotide sequences. The method allows for the generation and attachment of polynucleotides with defined 3? and 5? ends to solid surfaces. The polynucleotides attached to the solid substrates can be stored or archived as libraries and can subsequently be retrieved for analysis, for example by clonal amplification using a single composite amplification primer comprising a DNA portion and an RNA portion. In some embodiments, nucleotides attached to solid surfaces can be used for sequencing of nucleotide sequences related to the target DNA. The methods are applicable to total RNA and/or total DNA analysis.Type: GrantFiled: August 9, 2011Date of Patent: August 20, 2013Assignee: Nugen Technologies, Inc.Inventor: Nurith Kurn
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Patent number: 8492095Abstract: The invention provides methods for isothermal amplification of RNA. The methods are particularly suitable for amplifying a plurality of RNA species in a sample. The methods employ a composite primer, a second primer and strand displacement to generate multiple copies of DNA products comprising sequences complementary to an RNA sequence of interest. In another aspect, the methods employ a single primer (which is a composite primer) and strand displacement to generate multiple copies of DNA products comprising sequences complementary to an RNA sequence of interest. In some embodiments, a transcription step is included to generate multiple copies of sense RNA of an RNA sequence of interest. The methods are useful for preparation of nucleic acid libraries and substrates for analysis of gene expression of cells in biological samples. The invention also provides compositions and kits for practicing the amplification methods, as well as methods which use the amplification products.Type: GrantFiled: October 27, 2011Date of Patent: July 23, 2013Assignee: Nugen Technologies, Inc.Inventor: Nurith Kurn
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Patent number: 8465950Abstract: The invention relates to the field of polynucleotide amplification. More particularly, the invention provides methods, compositions and kits for amplification of (i.e., making multiple copies of) a multiplicity of different polynucleotide template sequences using a randomly primed RNA/DNA composite primer.Type: GrantFiled: January 13, 2012Date of Patent: June 18, 2013Assignee: Nugen Technologies, Inc.Inventors: Nurith Kurn, Shenglong Wang
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Patent number: 8334116Abstract: The present invention provides novel isothermal methods of generating multiple copies of, detecting and/or quantifying nucleic acid sequences of interest based on limited primer extension or attachment of oligonucleotide pairs using composite RNA/DNA primers. Methods for generating multiple copies of and/or detecting and/or quantifying nucleic acid sequences, wherein products of primer extension or attachment of oligonucleotide pairs comprising a cleavable portion are generated, and wherein cleavage of the products results in dissociation of cleaved products from target polynucleotides, are provided. The invention further provides compositions, kits and systems for practicing these methods.Type: GrantFiled: June 2, 2010Date of Patent: December 18, 2012Assignee: Nugen Technologies, Inc.Inventor: Nurith Kurn
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Publication number: 20120220483Abstract: The invention provides methods, compositions, and kits for fragmentation and labeling of nucleic acids. More particularly, the invention relates to methods for fragmentation of nucleic acids to produce fragments with 3? end hydroxyl groups within a desired size range. In methods of the invention, nucleic acids are fragmented at abasic sites to produce fragments with blocked 3? ends. The 3? ends are unblocked to produce polynucleotide fragments with hydroxyl groups at their 3? ends. Methods, kits, and compositions for carrying out fragmentation of a polynucleotide template in a single reaction mixture to yield fragments with 3?-hydroxyl ends within the desired size range are disclosed.Type: ApplicationFiled: March 2, 2012Publication date: August 30, 2012Applicant: NuGen Technologies, Inc.Inventors: Nurith KURN, Pengchin Chen
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Patent number: 8143001Abstract: The invention relates to methods for analysis of nucleic acid methylation status, and fragmentation and/or labeling and/or immobilization of nucleic acids. More particularly, the invention relates to methods for fragmentation and/or labeling and/or immobilization of nucleic acids comprising labeling and/or cleavage and/or immobilization at abasic sites.Type: GrantFiled: November 30, 2007Date of Patent: March 27, 2012Assignee: NuGEN Technologies, Inc.Inventors: Nurith Kurn, Geoffrey A. Dafforn
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Publication number: 20120045797Abstract: The invention provides methods for amplification of polynucleotide sequences using primers containing single-Cstranded RNA. The methods employ use of an enzyme capable of cleaving single-stranded RNA, such as RNase I, to degrade a first RNA-containing primer prior to addition of a second RNA-containing primer. The invention also provides compositions and kits pl. for practicing the amplification methods, as well as methods which use the amplification products.Type: ApplicationFiled: May 9, 2011Publication date: February 23, 2012Applicant: Nugen Technologies, Inc.Inventors: Nurith Kurn, Shenglong Wang
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Publication number: 20110319290Abstract: Adapters are joined to target polynucleotides to create adapter-tagged polynucleotides. Adapter-tagged polynucleotides are sequenced simultaneously and sample sources are identified on the basis of barcode sequences.Type: ApplicationFiled: June 8, 2011Publication date: December 29, 2011Applicant: NuGEN Technologies, Inc.Inventors: Christopher Raymond, Nurith Kurn, Jill Magnus
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Patent number: 8071311Abstract: The invention provides methods for isothermal amplification of RNA. The methods are particularly suitable for amplifying a plurality of RNA species in a sample. The methods employ a composite primer, a second primer and strand displacement to generate multiple copies of DNA products comprising sequences complementary to an RNA sequence of interest. In another aspect, the methods employ a single primer (which is a composite primer) and strand displacement to generate multiple copies of DNA products comprising sequences complementary to an RNA sequence of interest. In some embodiments, a transcription step is included to generate multiple copies of sense RNA of an RNA sequence of interest. The methods are useful for preparation of nucleic acid libraries and substrates for analysis of gene expression of cells in biological samples. The invention also provides compositions and kits for practicing the amplification methods, as well as methods which use the amplification products.Type: GrantFiled: November 10, 2009Date of Patent: December 6, 2011Assignee: NuGEN Technologies, Inc.Inventor: Nurith Kurn
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Publication number: 20110294132Abstract: The present method provides methods, libraries, and kits related to the archiving and clonal expansion of sequences related to target polynucleotide sequences. The method allow for the attachment of polynucleotides with defined 3? and or 5? sequences to solid surfaces. The polynucleotides attached to the solid substrates can be stored or archived as libraries and can subsequently be retrieved for analysis, for example by clonal expansion. In some embodiments, nucleotides attached to solid surfaces can be used for sequencing of nucleotide sequences related to target RNA or target RNA. The methods are applicable to total RNA and/or total DNA analysis.Type: ApplicationFiled: August 9, 2011Publication date: December 1, 2011Applicant: NuGen Technologies, Inc.Inventor: Nurith Kurn
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Patent number: 8034568Abstract: Methods and compositions are provided related to the amplification of target polynucleotide sequences as well as total RNA and total DNA amplification. In some embodiments, the methods and compositions also allow for the immobilization and capture of target polynucleotides with defined 3? and or 5? sequences to solid surfaces. The polynucleotides attached to the solid surfaces can be amplified or eluted for downstream processing. In some cases, nucleotides attached to solid surfaces can be used for high throughput sequencing of nucleotide sequences related to target DNA or target RNA.Type: GrantFiled: February 12, 2009Date of Patent: October 11, 2011Assignee: NuGEN Technologies, Inc.Inventors: Nurith Kurn, Shenglong Wang
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Publication number: 20110224105Abstract: Methods, kits, and compositions are provided herein for the generation of double stranded DNA products suitable for downstream analysis.Type: ApplicationFiled: August 12, 2010Publication date: September 15, 2011Applicant: NuGEN Technologies, Inc.Inventors: Nurith Kurn, Shenglong Wang
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Publication number: 20110189679Abstract: The present invention provides methods and compositions, including kits, for the generation of cDNA from mRNA with reduced ribosomal RNA representation.Type: ApplicationFiled: September 10, 2010Publication date: August 4, 2011Applicant: NuGEN Technologies, Inc.Inventors: Nurith Kurn, Shenglong Wang, Leah R. Turner, Victor Sementchenko