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1. 发明申请

US20170233724A1 Partitioning of DNA Sequencing Libraries into Host and Microbial Components 审中-公开
公开(公告)号：US20170233724A1
公开(公告)日：2017-08-17
申请号：US15583928
申请日：2017-05-01
申请人： The Board of Trustees of the Leland Stanford Junior University
发明人： Carlos D. Bustamante , Meredith L. Carpenter
IPC分类号： C12N15/10
CPC分类号： C12N15/1065 , C12N15/1006 , C12N15/1013 , C12Q2525/191 , C12Q2537/159
摘要： Described herein is a method for isolating microbial DNA from a sample that comprises host DNA and microbial DNA. In some embodiments, the method may comprise: obtaining a tagged DNA sample, wherein the tagged DNA sample contains host DNA and microbial DNA, both comprising an appended universal adaptor; b) hybridizing the extracted DNA, in solution, with affinity-tagged RNA probes generated by in vitro transcribing, in the presence of an affinity-tagged ribonucleotide, a library of fragmented host DNA that has been ligated to an RNA promoter adaptor; c) binding the product of step b) with a capture agent that is tethered to a substrate, in the presence of RNA oligonucleotides that are complementary to or have the same sequence as one or more strands of the universal adaptor, thereby capturing the host DNA on the substrate; and d) collecting the unbound DNA, wherein the unbound DNA comprises the microbial DNA.

2. 发明授权

US09670485B2 Partitioning of DNA sequencing libraries into host and microbial components 有权
公开(公告)号：US09670485B2
公开(公告)日：2017-06-06
申请号：US14619011
申请日：2015-02-10
申请人： The Board of Trustees of the Leland Stanford Junior University
发明人： Carlos D. Bustamante , Meredith L. Carpenter
IPC分类号： C12Q1/68 , C12P19/34 , C12N15/10
CPC分类号： C12N15/1065 , C12N15/1006 , C12N15/1013 , C12Q2525/191 , C12Q2537/159
摘要： Described herein is a method for isolating microbial DNA from a sample that comprises host DNA and microbial DNA. In some embodiments, the method may comprise: obtaining a tagged DNA sample, wherein the tagged DNA sample contains host DNA and microbial DNA, both comprising an appended universal adaptor; b) hybridizing the extracted DNA, in solution, with affinity-tagged RNA probes generated by in vitro transcribing, in the presence of an affinity-tagged ribonucleotide, a library of fragmented host DNA that has been ligated to an RNA promoter adaptor; c) binding the product of step b) with a capture agent that is tethered to a substrate, in the presence of RNA oligonucleotides that are complementary to or have the same sequence as one or more strands of the universal adaptor, thereby capturing the host DNA on the substrate; and d) collecting the unbound DNA, wherein the unbound DNA comprises the microbial DNA.

3. 发明授权

US10576446B2 Enrichment of DNA sequencing libraries from samples containing small amounts of target DNA 有权
公开(公告)号：US10576446B2
公开(公告)日：2020-03-03
申请号：US14653748
申请日：2014-05-02
申请人： The Board of Trustees of the Leland Stanford Junior University
发明人： Carlos D. Bustamante , Meredith L. Carpenter , Jason D. Buenrostro , William J. Greenleaf
IPC分类号： C12Q1/68 , B01J19/00 , C12Q1/6806 , C12N15/10 , C12Q1/6809
摘要： Provided herein is a method for capturing DNA molecules in solution. The method may comprise: extracting DNA from a sample that comprises endogenous DNA and environmental DNA to produce extracted DNA; ligating universal adaptors to the extracted DNA; hybridizing the extracted DNA, in solution, with affinity-tagged RNA probes generated by: in vitro transcribing a library of fragmented reference genomic DNA that has been ligated to an RNA promoter adaptor, in the presence of an affinity-tagged ribonucleotide; binding the product with a capture agent that is tethered to a substrate in the presence of RNA oligonucleotides that are complementary to the adaptors, thereby capturing the hybridized DNA molecules on the substrate; washing the substrate to remove any unbound DNA molecules; and releasing the captured DNA molecules. A kit for performing the method is also provided.

4. 发明申请

US20180285593A1 Techniques for Determining Whether an Individual Is Included in Ensemble Genomic Data 审中-公开
公开(公告)号：US20180285593A1
公开(公告)日：2018-10-04
申请号：US15766611
申请日：2016-10-06
申请人： The Board of Trustees of the Leland Stanford Junior University
发明人： Suyash Shringarpure , Carlos D. Bustamante
IPC分类号： G06F21/62 , G06F19/28 , G06F19/18 , G16H10/60 , G06F17/30
摘要： Techniques to determine if an individual is a member of an ensemble contributing to combined genomic data include determining a site frequency spectrum (SFS) for alleles in the combined genomic data, and a number N of individuals contributing to the combined genomic data. Based on the SFS and N, both a number of queries NQ and a number of yeses NY are determined. NY is a number of yes responses to NQ queries, which indicates a particular likelihood that the individual is a member of the ensemble. Output is based on at least one of NQ and NY. For example, fewer than NQ queries from a single source are answered from a beacon. Alternatively, the likelihood that an individual is a member of the ensemble is determined based on responses to NQ queries about NQ different alleles present in the individual and NY.

5. 发明授权

US10981137B2 Enrichment of DNA sequencing libraries from samples containing small amounts of target DNA 有权
公开(公告)号：US10981137B2
公开(公告)日：2021-04-20
申请号：US16743501
申请日：2020-01-15
申请人： The Board of Trustees of the Leland Stanford Junior University
发明人： Carlos D. Bustamante , Meredith L. Carpenter , Jason D. Buenrostro , William J. Greenleaf
IPC分类号： B01J19/00 , C12Q1/6806 , C12N15/10 , C12Q1/6809
摘要： Provided herein is a method for capturing DNA molecules in solution. The method may comprise: extracting DNA from a sample that comprises endogenous DNA and environmental DNA to produce extracted DNA; ligating universal adaptors to the extracted DNA; hybridizing the extracted DNA, in solution, with affinity-tagged RNA probes generated by: in vitro transcribing a library of fragmented reference genomic DNA that has been ligated to an RNA promoter adaptor, in the presence of an affinity-tagged ribonucleotide; binding the product with a capture agent that is tethered to a substrate in the presence of RNA oligonucleotides that are complementary to the adaptors, thereby capturing the hybridized DNA molecules on the substrate; washing the substrate to remove any unbound DNA molecules; and releasing the captured DNA molecules. A kit for performing the method is also provided.

6. 发明申请

US20150360194A1 Enrichment of DNA Sequencing Libraries from Samples Containing Small Amounts of Target DNA 审中-公开
标题翻译：从含有少量靶DNA的样品中富集DNA测序文库
公开(公告)号：US20150360194A1
公开(公告)日：2015-12-17
申请号：US14653748
申请日：2014-05-02
申请人： THE BOARD OF TRUSTEES OF THE LELAND STANFORD JUNIOR UNIVERSITY
发明人： Carlos D. Bustamante , Meredith L. Carpenter , Jason D. Buenrostro , William J. Greenleaf
IPC分类号： B01J19/00 , C12Q1/68
CPC分类号： B01J19/0046 , B01J2219/00585 , B01J2219/00596 , B01J2219/00722 , C12N15/1006 , C12N15/1034 , C12Q1/6806 , C12Q1/6809 , C12Q2525/143 , C12Q2525/191 , C12Q2535/122 , C12Q2537/159 , C12Q2563/131
摘要： Provided herein is a method for capturing DNA molecules in solution. The method may comprise: extracting DNA from a sample that comprises endogenous DNA and environmental DNA to produce extracted DNA; ligating universal adaptors to the extracted DNA; hybridizing the extracted DNA, in solution, with affinity-tagged RNA probes generated by: in vitro transcribing a library of fragmented reference genomic DNA that has been ligated to an RNA promoter adaptor, in the presence of an affinity-tagged ribonucleotide; binding the product with a capture agent that is tethered to a substrate in the presence of RNA oligonucleotides that are complementary to the adaptors, thereby capturing the hybridized DNA molecules on the substrate; washing the substrate to remove any unbound DNA molecules; and releasing the captured DNA molecules. A kit for performing the method is also provided.
摘要翻译：本文提供了一种在溶液中捕获DNA分子的方法。该方法可以包括：从包含内源DNA和环境DNA的样品中提取DNA以产生提取的DNA; 将通用接头连接到提取的DNA; 将提取的DNA在溶液中与通过以下方式产生的亲和标记的RNA探针杂交：在亲和标记的核糖核苷酸的存在下体外转录已连接到RNA启动子衔接子的片段参考基因组文库; 在与衔接子互补的RNA寡核苷酸的存在下将产物与捕获剂结合，所述捕获剂被束缚于底物，从而在底物上捕获杂交的DNA分子; 洗涤底物以除去任何未结合的DNA分子; 并释放所捕获的DNA分子。还提供了用于执行该方法的套件。

7. 发明授权

US10954509B2 Partitioning of DNA sequencing libraries into host and microbial components 有权
公开(公告)号：US10954509B2
公开(公告)日：2021-03-23
申请号：US15583928
申请日：2017-05-01
申请人： The Board of Trustees of the Leland Stanford Junior University
发明人： Carlos D. Bustamante , Meredith L. Carpenter
IPC分类号： C12Q1/68 , C12N15/10
摘要： Described herein is a method for isolating microbial DNA from a sample that comprises host DNA and microbial DNA. In some embodiments, the method may comprise: obtaining a tagged DNA sample, wherein the tagged DNA sample contains host DNA and microbial DNA, both comprising an appended universal adaptor; b) hybridizing the extracted DNA, in solution, with affinity-tagged RNA probes generated by in vitro transcribing, in the presence of an affinity-tagged ribonucleotide, a library of fragmented host DNA that has been ligated to an RNA promoter adaptor; c) binding the product of step b) with a capture agent that is tethered to a substrate, in the presence of RNA oligonucleotides that are complementary to or have the same sequence as one or more strands of the universal adaptor, thereby capturing the host DNA on the substrate; and d) collecting the unbound DNA, wherein the unbound DNA comprises the microbial DNA.

8. 发明授权

US10747899B2 Techniques for determining whether an individual is included in ensemble genomic data 有权
公开(公告)号：US10747899B2
公开(公告)日：2020-08-18
申请号：US15766611
申请日：2016-10-06
申请人： The Board of Trustees of the Leland Stanford Junior University
发明人： Suyash Shringarpure , Carlos D. Bustamante
IPC分类号： G06F21/62 , G06F16/00 , G06F16/903 , G16B20/00 , G16B50/00 , G16B20/40 , G16H10/60
摘要： Techniques to determine if an individual is a member of an ensemble contributing to combined genomic data include determining a site frequency spectrum (SFS) for alleles in the combined genomic data, and a number N of individuals contributing to the combined genomic data. Based on the SFS and N, both a number of queries NQ and a number of yeses NY are determined. NY is a number of yes responses to NQ queries, which indicates a particular likelihood that the individual is a member of the ensemble. Output is based on at least one of NQ and NY. For example, fewer than NQ queries from a single source are answered from a beacon. Alternatively, the likelihood that an individual is a member of the ensemble is determined based on responses to NQ queries about NQ different alleles present in the individual and NY.

9. 发明申请

US20150232834A1 PARTITIONING OF DNA SEQUENCING LIBRARIES INTO HOST AND MICROBIAL COMPONENTS 有权
标题翻译：将DNA序列分析成宿主和微生物成分的分类
公开(公告)号：US20150232834A1
公开(公告)日：2015-08-20
申请号：US14619011
申请日：2015-02-10
申请人： The Board of Trustees of the Leland Stanford Junior University
发明人： Carlos D. Bustamante , Meredith L. Carpenter
IPC分类号： C12N15/10
CPC分类号： C12N15/1065 , C12N15/1006 , C12N15/1013 , C12Q2525/191 , C12Q2537/159
摘要： Described herein is a method for isolating microbial DNA from a sample that comprises host DNA and microbial DNA. In some embodiments, the method may comprise: obtaining a tagged DNA sample, wherein the tagged DNA sample contains host DNA and microbial DNA, both comprising an appended universal adaptor; b) hybridizing the extracted DNA, in solution, with affinity-tagged RNA probes generated by in vitro transcribing, in the presence of an affinity-tagged ribonucleotide, a library of fragmented host DNA that has been ligated to an RNA promoter adaptor; c) binding the product of step b) with a capture agent that is tethered to a substrate, in the presence of RNA oligonucleotides that are complementary to or have the same sequence as one or more strands of the universal adaptor, thereby capturing the host DNA on the substrate; and d) collecting the unbound DNA, wherein the unbound DNA comprises the microbial DNA.
摘要翻译：本文描述了从包含宿主DNA和微生物DNA的样品中分离微生物DNA的方法。在一些实施方案中，所述方法可以包括：获得标记的DNA样品，其中所述标记的DNA样品含有宿主DNA和微生物DNA，其均包含附加的通用适配器; b）将已提取的DNA在溶液中与在亲和标记的核糖核苷酸存在下通过体外转录产生的亲和标记的RNA探针杂交，已经连接到RNA启动子衔接子的片段化宿主DNA文库; c）在与通用衔接子的一条或多条链互补或具有相同序列的RNA寡核苷酸的存在下，将步骤b）的产物与束缚于底物的捕获剂结合，从而捕获宿主DNA 在基材上和d）收集未结合的DNA，其中未结合的DNA包含微生物DNA。

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