Patents Assigned to NuGen Technologies, Inc.
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Patent number: 11365408Abstract: The disclosure provides DNA library preparation methods that do not require a purification between adapter ligation and PCR amplification. Adaptors are added to DNA fragments to form oligonucleotide extension products and the oligonucleotide extension products are amplified without stopping or interruption for a cleanup step. Excess materials, such as enzymes, adaptors, or co-factors, from the adaptor addition step do not interfere with the amplification step and the amplification step proceeds without regards to the presence of reagents from the ligation step. In preferred embodiments, the ligation and amplification step make use of a common priming sequence e.g., in the form of one of the adaptor oligos.Type: GrantFiled: February 6, 2019Date of Patent: June 21, 2022Assignee: NUGEN TECHNOLOGIES, INC.Inventors: Bin Li, Benjamin G. Schroeder, Manqing Hong, Maureen Peterson
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Patent number: 11028430Abstract: Provided herein are methods, compositions and kits for the generation of bisulfite-converted next generation sequencing (NGS) libraries. The methods, compositions and kits provided herein can be useful, for example, for the production of libraries from genomic DNA that allow for determination of the methylation status across the genome, i.e. the methylome. The methods, compositions and kits provided herein can also be utilized to query methylation status at a particular genomic locus or loci. Moreover, the methods provided herein can be employed for high-throughput sequencing of bisulfite-converted DNA while maintaining the directional (strandedness) information of the original nucleic acid sample.Type: GrantFiled: January 8, 2016Date of Patent: June 8, 2021Assignee: NUGEN TECHNOLOGIES, INC.Inventors: Benjamin G. Schroeder, Doug Amorese
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Patent number: 10927405Abstract: 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: January 11, 2019Date of Patent: February 23, 2021Assignee: NUGEN TECHNOLOGIES, INC.Inventors: Douglas A. Amorese, Stephanie C. Huelga, Bin Li
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Patent number: 10876108Abstract: The present invention provides methods, compositions and kits for targeted nucleic acid sequence enrichment in a nucleic acid sample and for high efficiency nucleic acid library generation for next generation sequencing (NGS). Specifically, the methods, compositions and kits provided herein are useful for the production and capture of amplification-ready, target-specific and strand-specific regions of interest from nucleic acid samples containing complex DNA.Type: GrantFiled: June 25, 2018Date of Patent: December 29, 2020Assignee: NUGEN TECHNOLOGIES, INC.Inventors: Doug Amorese, Chris Armour, Nurith Kurn
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Patent number: 10760123Abstract: 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: GrantFiled: January 7, 2016Date of Patent: September 1, 2020Assignee: NUGEN TECHNOLOGIES, INC.Inventors: Doug Amorese, Benjamin G. Schroeder, Jonathan Scolnick
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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: 10036012Abstract: The present invention provides methods, compositions and kits for targeted nucleic acid sequence enrichment in a nucleic acid sample and for high efficiency nucleic acid library generation for next generation sequencing (NGS). Specifically, the methods, compositions and kits provided herein are useful for the production and capture of amplification-ready, target-specific and strand-specific regions of interest from nucleic acid samples containing complex DNA.Type: GrantFiled: March 28, 2017Date of Patent: July 31, 2018Assignee: NUGEN TECHNOLOGIES, INC.Inventors: Doug Amorese, Chris Armour, Nurith Kurn
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Patent number: 9957549Abstract: The present invention provides methods, compositions and kits for the generation of next generation sequencing (NGS) libraries in which non-desired nucleic acid sequences have been depleted or substantially reduced. The methods, compositions and kits provided herein are useful, for example, for the production of libraries from total RNA with reduced ribosomal RNA and for the reduction of common mRNA species in expression profiling from mixed samples where the mRNAs of interest are present at low levels. The methods of the invention can be employed for the elimination of non-desired nucleic acid sequences in a sequence-specific manner, and consequently, for the enrichment of nucleic acid sequences of interest in a nucleic acid library.Type: GrantFiled: March 15, 2013Date of Patent: May 1, 2018Assignee: NUGEN TECHNOLOGIES, INC.Inventors: Christopher Armour, Doug Amorese, Bin Li, Nurith Kurn
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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: 9745614Abstract: Described herein are methods, compositions and kits for the generation of bisulfite-converted libraries useful for conducting reduced representation bisulfite sequencing (RRBS). The methods described herein can be employed to generate RRBS libraries in a manner that is easier and more cost-efficient than conventional RRBS methods, and can be efficiently sequenced with next generation sequencing (NGS) techniques without the need for genomic, higher diversity sequencing controls such as PhiX spike-ins.Type: GrantFiled: February 27, 2015Date of Patent: August 29, 2017Assignee: NUGEN TECHNOLOGIES, INC.Inventor: Benjamin G. Schroeder
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Patent number: 9650628Abstract: The present invention provides methods, compositions and kits for targeted nucleic acid sequence enrichment in a nucleic acid sample and for high efficiency nucleic acid library generation for next generation sequencing (NGS). Specifically, the methods, compositions and kits provided herein are useful for the production and capture of amplification-ready, target-specific and strand-specific regions of interest from nucleic acid samples containing complex DNA.Type: GrantFiled: January 25, 2013Date of Patent: May 16, 2017Assignee: NUGEN TECHNOLOGIES, INC.Inventors: Doug Amorese, Chris Armour, Nurith Kurn
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Patent number: 9546399Abstract: The present invention provides methods, compositions and kits for detecting duplicate sequencing reads. In some embodiments, the duplicate sequencing reads are removed.Type: GrantFiled: November 13, 2014Date of Patent: January 17, 2017Assignee: NUGEN TECHNOLOGIES, INC.Inventors: Douglas Amorese, Jonathan Scolnick, Ben Schroeder
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Patent number: 9206418Abstract: The invention provides methods and compositions, including kits, for directional nucleic acid amplification and sequencing. The invention further provides methods and compositions for the construction of directional cDNA libraries.Type: GrantFiled: October 19, 2012Date of Patent: December 8, 2015Assignee: NUGEN TECHNOLOGIES, INC.Inventor: Christopher Armour
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Patent number: 9181582Abstract: 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: June 19, 2013Date of Patent: November 10, 2015Assignee: NUGEN TECHNOLOGIES, INC.Inventor: Nurith Kurn
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Patent number: 9175325Abstract: 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: June 14, 2013Date of Patent: November 3, 2015Assignee: NUGEN TECHNOLOGIES, INC.Inventors: Nurith Kurn, Shenglong Wang
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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: 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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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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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