Patents Assigned to NuGen Technologies, Inc.
  • Patent number: 10190155
    Abstract: 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: Grant
    Filed: October 14, 2016
    Date of Patent: January 29, 2019
    Assignee: NuGEN Technologies, Inc.
    Inventors: Douglas A. Amorese, Stephanie C. Huelga, Bin Li
  • Patent number: 10102337
    Abstract: 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: Grant
    Filed: August 6, 2015
    Date of Patent: October 16, 2018
    Assignee: NuGEN Technologies, Inc.
    Inventors: Jonathan Scolnick, Benjamin Schroeder, Douglas Amorese, Stephanie C. Huelga
  • Patent number: 9822408
    Abstract: 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: Grant
    Filed: March 14, 2014
    Date of Patent: November 21, 2017
    Assignee: Nugen Technologies, Inc.
    Inventors: Doug Amorese, Benjamin G. Schroeder, Jonathan Scolnick
  • Patent number: 8852867
    Abstract: 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: Grant
    Filed: May 9, 2011
    Date of Patent: October 7, 2014
    Assignee: Nugen Technologies, Inc.
    Inventors: Nurith Kurn, Shenglong Wang
  • Publication number: 20140274729
    Abstract: 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: Application
    Filed: September 18, 2013
    Publication date: September 18, 2014
    Applicant: NuGEN Technologies, Inc.
    Inventors: Nurith Kurn, Bin Li
  • Publication number: 20140274738
    Abstract: 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: Application
    Filed: March 14, 2014
    Publication date: September 18, 2014
    Applicant: NuGEN Technologies, Inc.
    Inventors: Doug Amorese, Benjamin G. Schroeder, Jonathan Scolnick
  • Patent number: 8551709
    Abstract: 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: Grant
    Filed: March 2, 2012
    Date of Patent: October 8, 2013
    Assignee: NuGEN Technologies, Inc.
    Inventors: Nurith Kurn, Pengchin Chen
  • Patent number: 8512956
    Abstract: 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: Grant
    Filed: August 9, 2011
    Date of Patent: August 20, 2013
    Assignee: Nugen Technologies, Inc.
    Inventor: Nurith Kurn
  • Patent number: 8492095
    Abstract: 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: Grant
    Filed: October 27, 2011
    Date of Patent: July 23, 2013
    Assignee: Nugen Technologies, Inc.
    Inventor: Nurith Kurn
  • Patent number: 8465950
    Abstract: 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: Grant
    Filed: January 13, 2012
    Date of Patent: June 18, 2013
    Assignee: Nugen Technologies, Inc.
    Inventors: Nurith Kurn, Shenglong Wang
  • Patent number: 8334116
    Abstract: 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: Grant
    Filed: June 2, 2010
    Date of Patent: December 18, 2012
    Assignee: Nugen Technologies, Inc.
    Inventor: Nurith Kurn
  • Publication number: 20120220483
    Abstract: 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: Application
    Filed: March 2, 2012
    Publication date: August 30, 2012
    Applicant: NuGen Technologies, Inc.
    Inventors: Nurith KURN, Pengchin Chen
  • Patent number: 8143001
    Abstract: 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: Grant
    Filed: November 30, 2007
    Date of Patent: March 27, 2012
    Assignee: NuGEN Technologies, Inc.
    Inventors: Nurith Kurn, Geoffrey A. Dafforn
  • Publication number: 20120045797
    Abstract: 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: Application
    Filed: May 9, 2011
    Publication date: February 23, 2012
    Applicant: Nugen Technologies, Inc.
    Inventors: Nurith Kurn, Shenglong Wang
  • Publication number: 20110319290
    Abstract: 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: Application
    Filed: June 8, 2011
    Publication date: December 29, 2011
    Applicant: NuGEN Technologies, Inc.
    Inventors: Christopher Raymond, Nurith Kurn, Jill Magnus
  • Patent number: 8071311
    Abstract: 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: Grant
    Filed: November 10, 2009
    Date of Patent: December 6, 2011
    Assignee: NuGEN Technologies, Inc.
    Inventor: Nurith Kurn
  • Publication number: 20110294132
    Abstract: 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: Application
    Filed: August 9, 2011
    Publication date: December 1, 2011
    Applicant: NuGen Technologies, Inc.
    Inventor: Nurith Kurn
  • Patent number: 8034568
    Abstract: 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: Grant
    Filed: February 12, 2009
    Date of Patent: October 11, 2011
    Assignee: NuGEN Technologies, Inc.
    Inventors: Nurith Kurn, Shenglong Wang
  • Publication number: 20110224105
    Abstract: Methods, kits, and compositions are provided herein for the generation of double stranded DNA products suitable for downstream analysis.
    Type: Application
    Filed: August 12, 2010
    Publication date: September 15, 2011
    Applicant: NuGEN Technologies, Inc.
    Inventors: Nurith Kurn, Shenglong Wang
  • Publication number: 20110189679
    Abstract: The present invention provides methods and compositions, including kits, for the generation of cDNA from mRNA with reduced ribosomal RNA representation.
    Type: Application
    Filed: September 10, 2010
    Publication date: August 4, 2011
    Applicant: NuGEN Technologies, Inc.
    Inventors: Nurith Kurn, Shenglong Wang, Leah R. Turner, Victor Sementchenko