Patents by Inventor Benjamin G. SCHROEDER
Benjamin G. SCHROEDER has filed for patents to protect the following inventions. This listing includes patent applications that are pending as well as patents that have already been granted by the United States Patent and Trademark Office (USPTO).
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Patent number: 11697843Abstract: 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: May 14, 2021Date of Patent: July 11, 2023Assignee: Tecan Genomics, Inc.Inventors: Benjamin G. Schroeder, Doug Amorese
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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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Publication number: 20220033896Abstract: Various embodiments of the teachings relate to a system or method for sample preparation or analysis in biochemical or molecular biology procedures. The sample preparation can involve small volume processed in discrete portions or segments or slugs, herein referred to as discrete volumes. A molecular biology procedure can be nucleic acid analysis. Nucleic acid analysis can be an integrated DNA amplification/DNA sequencing procedure.Type: ApplicationFiled: October 19, 2021Publication date: February 3, 2022Applicant: APPLIED BIOSYSTEMS, LLCInventors: Linda G. LEE, Sam L. WOO, Congcong MA, Richard T. REEL, Mark F. OLDHAM, David M. COX, Benjamin G. SCHROEDER, Jon M. SORENSON, Willy WIYATNO
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Patent number: 11162137Abstract: Various embodiments of the teachings relate to a system or method for sample preparation or analysis in biochemical or molecular biology procedures. The sample preparation can involve small volume processed in discrete portions or segments or slugs, herein referred to as discrete volumes. A molecular biology procedure can be nucleic acid analysis. Nucleic acid analysis can be an integrated DNA amplification/DNA sequencing procedure.Type: GrantFiled: August 3, 2018Date of Patent: November 2, 2021Assignee: APPLIED BIOSYSTEMS LLCInventors: Linda G. Lee, Sam L. Woo, Congcong Ma, Richard T. Reel, Mark F. Oldham, David M. Cox, Benjamin G. Schroeder, Jon M. Sorenson, Willy Wiyatno
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Publication number: 20210285040Abstract: 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: ApplicationFiled: May 14, 2021Publication date: September 16, 2021Inventors: Benjamin G. Schroeder, Douglas A. Amorese
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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: 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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Publication number: 20200239953Abstract: The present invention provides methods, compositions and kits for detecting duplicate sequencing reads. In some embodiments, the duplicate sequencing reads are removed.Type: ApplicationFiled: January 15, 2020Publication date: July 30, 2020Inventors: Douglas A. Amorese, Jonathan Scolnick, Benjamin G. Schroeder
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Patent number: 10619206Abstract: 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: November 10, 2017Date of Patent: April 14, 2020Assignee: Tecan GenomicsInventors: Doug Amorese, Benjamin G. Schroeder, Jonathan Scolnick
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Publication number: 20190241887Abstract: 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: ApplicationFiled: February 6, 2019Publication date: August 8, 2019Inventors: Bin Li, Benjamin G. Schroeder, Manqing Hong, Maureen Peterson
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Publication number: 20190119746Abstract: Provided herein are methods and compositions for selective amplification of nucleic acids. The compositions include oligonucleotides with sequence features that allow simultaneous, parallel amplification of multiple targets from a mixture of nucleic acids in a single reaction. Methods of using such oligonucleotides to identify individual targets and create libraries of targets from mixtures of nucleic acids are also provided.Type: ApplicationFiled: October 18, 2018Publication date: April 25, 2019Inventors: Doug Amorese, Benjamin G. Schroeder, Nurith Kurn, Ashesh Saraiya
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Publication number: 20190085387Abstract: Various embodiments of the teachings relate to a system or method for sample preparation or analysis in biochemical or molecular biology procedures. The sample preparation can involve small volume processed in discrete portions or segments or slugs, herein referred to as discrete volumes. A molecular biology procedure can be nucleic acid analysis. Nucleic acid analysis can be an integrated DNA amplification/DNA sequencing procedure.Type: ApplicationFiled: August 3, 2018Publication date: March 21, 2019Inventors: Linda G. Lee, Sam L. Woo, Congcong Ma, Richard T. Reel, Mark F. Oldham, David M. Cox, Benjamin G. Schroeder, Jon M. Sorenson, Willy Wiyatno
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Publication number: 20190005193Abstract: 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: ApplicationFiled: September 7, 2018Publication date: January 3, 2019Inventors: Jonathan Scolnick, Benjamin G. Schroeder, Douglas A. Amorese, Stephanie C. Huelga
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Publication number: 20180291443Abstract: Described herein are methods, compositions, and kits for library quantitation and qualification. Some embodiments relate to a method of library quantitation. For example, the method may include providing DNA fragments, amplifying the DNA fragments by polymerase chain reaction (PCR) in the presence of primers each labeled with a fluorophore. In these instances, only a predetermined number of fluorophores are attached to each DNA fragment. The method may further include detecting a fluorescent signal produced by the amplified DNA fragments and calculating a number of the amplified DNA fragments based on the detected fluorescent signal.Type: ApplicationFiled: April 11, 2017Publication date: October 11, 2018Inventors: Douglas A. Amorese, Bin Li, Benjamin G. Schroeder, Richard A. Fekete
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Patent number: 10041113Abstract: Various embodiments of the teachings relate to a system or method for sample preparation or analysis in biochemical or molecular biology procedures. The sample preparation can involve small volume processed in discrete portions or segments or slugs, herein referred to as discrete volumes. A molecular biology procedure can be nucleic acid analysis. Nucleic acid analysis can be an integrated DNA amplification/DNA sequencing procedure.Type: GrantFiled: October 28, 2015Date of Patent: August 7, 2018Assignee: Applied Biosystems, LLCInventors: Linda G. Lee, Sam L. Woo, Congcong Ma, Richard T. Reel, Mark F. Oldham, David M. Cox, Benjamin G. Schroeder, Jon M. Sorenson, Willy Wiyatno
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Publication number: 20180112264Abstract: 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: ApplicationFiled: November 10, 2017Publication date: April 26, 2018Inventors: Doug Amorese, Benjamin G. Schroeder, Jonathan Scolnick
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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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Publication number: 20160265042Abstract: 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: ApplicationFiled: January 8, 2016Publication date: September 15, 2016Inventors: Benjamin G. Schroeder, Doug Amorese
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Publication number: 20160251711Abstract: 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: ApplicationFiled: March 14, 2014Publication date: September 1, 2016Inventors: Doug AMORESE, Benjamin G. SCHROEDER, Jonathan SCOLNICK