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    Nucleic acid enrichment using Cas9
    22.
    发明授权
    Nucleic acid enrichment using Cas9 有权

    公开(公告)号：US11414695B2

    公开(公告)日：2022-08-16

    申请号：US14290901

    申请日：2014-05-29

    Applicant: Agilent Technologies, Inc.

    Inventor： Brian Jon Peter ,  Robert A. Ach

    IPC: C12Q1/6806 ,  C12N9/22 ,  C12N15/10 ,  C12Q1/6869

    Abstract: A method of enriching for a fragment of a genome, as well as corresponding compositions and kits, are provided. In certain embodiments, the method comprises: (a) contacting a sample comprising fragmented DNA with a Cas9-gRNA complex comprising mutant Cas9 protein that has inactivated nuclease activity and a Cas9-associated guide RNA that is complementary to a site in the DNA, to produce a Cas9-fragment complex that comprises a fragment of the fragmented DNA; and (b) isolating the complex. In addition, other methods and compositions for Cas9/CRISPR-mediated nucleic acid manipulation are also provided.

    Spatial molecular barcoding of in situ nucleic acids
    24.
    发明授权
    Spatial molecular barcoding of in situ nucleic acids 有权

    公开(公告)号：US09834814B2

    公开(公告)日：2017-12-05

    申请号：US14493127

    申请日：2014-09-22

    Applicant: Agilent Technologies, Inc.

    Inventor： Brian Jon Peter ,  Robert A. Ach ,  Alicia Scheffer-Wong ,  Carolina Caffaro

    IPC: C12Q1/68 ,  G01N33/53 ,  C07H21/00

    CPC classification number: C12Q1/6841 ,  C12Q2565/513 ,  C12Q2565/514

    Abstract: This disclosure provides, among other things, a method for analyzing a planar cellular sample. In some embodiments, the method comprises: (a) indirectly or directly attaching nucleic acid tags to binding sites in a planar cellular sample; (b) contacting the planar cellular sample with a solid support comprising an array of spatially addressed features that comprise oligonucleotides, wherein each oligonucleotide comprises a molecular barcode that identifies the feature in which the oligonucleotides is present; (c) hybridizing the nucleic acid tags, or a copy of the same, with the oligonucleotides to produce duplexes; and (d) extending the oligonucleotides in the duplexes to produce extension products that each comprises (i) a molecular barcode and (ii) a copy of a nucleic acid tag. Other embodiments, e.g., kits and the like, are also described.

    Nanofluidic device for charge analysis of straightened molecules
    26.
    发明授权
    Nanofluidic device for charge analysis of straightened molecules 有权

    公开(公告)号：US09683958B2

    公开(公告)日：2017-06-20

    申请号：US14482803

    申请日：2014-09-10

    Applicant: Agilent Technologies, Inc.

    Inventor： John Mannion ,  Bo Curry ,  Brian Jon Peter

    IPC: G01N27/414 ,  G01N27/447

    CPC classification number: G01N27/4145 ,  G01N27/4473

    Abstract: This disclosure provides, among other things, a nanofluidic device sensing device is provided. In certain embodiments, the device contains: a) a channel comprising a floor and a ceiling, b) an array of charge sensors in the floor and/or ceiling of the channel, arranged along the longitudinal axis of the channel; c) a capture area in the floor and/or ceiling of the channel at the entrance end of the channel; and d) a first electrode and a second electrode, wherein the first and second electrodes are positioned to provide an electrophoretic force along the longitudinal axis of the channel. Other embodiments, e.g., methods, are also described.

    POLYMERASE IDLING METHOD FOR SINGLE MOLECULE DNA SEQUENCING
    27.
    发明申请
    POLYMERASE IDLING METHOD FOR SINGLE MOLECULE DNA SEQUENCING 审中-公开
    用于单分子DNA测序的聚合酶识别方法

    公开(公告)号：US20170067103A1

    公开(公告)日：2017-03-09

    申请号：US15353592

    申请日：2016-11-16

    Applicant: Agilent Technologies, Inc.

    Inventor： Brian Jon Peter ,  Joel Myerson

    IPC: C12Q1/68

    CPC classification number: C12Q1/6869 ,  C12Q1/6816 ,  C12Q1/6834 ,  C12Q2525/125 ,  C12Q2525/186 ,  C12Q2537/157

    Abstract: A method for sequencing a nucleic acid is provided. In certain embodiments the method comprises obtaining a duplex comprising a nucleic acid and a primer, wherein the primer has a nuclease resistant 3′ end, combining the duplex with a chain terminator nucleotide and a proof-reading polymerase to produce a reaction in which the polymerase idles on the added chain terminator nucleotide, identifying the chain terminator nucleotide added to the end of the primer; and adding a nuclease-resistant nucleotide to the end of the primer after the polymerase has idled on and removed the added chain terminator nucleotide, thereby producing a duplex comprising the template and an extended primer that has a nuclease resistant 3′ end.

    Abstract translation: 提供了对核酸进行测序的方法。 在某些实施方案中，该方法包括获得包含核酸和引物的双链体，其中引物具有核酸酶抗性3'末端，将双链体与链终止子核苷酸和校对阅读聚合酶组合以产生其中聚合酶 在添加的链终止子核苷酸上空转，鉴定添加到引物末端的链终止子核苷酸; 并在聚合酶空转之后向引物的末端添加核酸酶抗性核苷酸并除去加入的链终止子核苷酸，从而产生包含模板的双链体和具有核酸酶抗性3'末端的延伸引物。

    Method for determining ploidy of a cell
    28.
    发明授权
    Method for determining ploidy of a cell 有权
    确定细胞倍性的方法

    公开(公告)号：US09193992B2

    公开(公告)日：2015-11-24

    申请号：US13894886

    申请日：2013-05-15

    Applicant: Agilent Technologies, Inc.

    Inventor： Bo U. Curry ,  Jayati Ghosh ,  Brian Jon Peter ,  Arjun Vadapalli

    IPC: C12Q1/68 ,  C07H21/00 ,  G06F19/18

    CPC classification number: C12Q1/6827 ,  C12Q1/6883 ,  C12Q2600/156 ,  C12Q2600/158 ,  G06F19/18

    Abstract: A method for determining the ploidy of a test genome is provided. In some embodiments, the method may comprises: a) obtaining a plurality of ratios for polymorphisms that are distributed throughout a test genome, wherein each of the ratios is a ratio of the measured copy number of uncut allele in a polymorphic site relative to the measured copy number of the uncut allele in the reference sample; b) taking the log of the ratios and plotting a distribution of the reference corrected log ratios of the SNP probes; and c) determining the ploidy of said the genome based on the number of peaks in that distribution.

    Abstract translation: 提供了测定基因组倍性的方法。 在一些实施方案中，所述方法可以包括：a）获得分布在整个测试基因组中的多态性的多个比率，其中每个比率是多态性位点中未切割等位基因的测定拷贝数相对于测量的 参考样品中未切割等位基因的拷贝数; b）记录比率对数，并绘制SNP探针的参考校正对数比的分布; 和c）基于该分布中的峰的数目确定所述基因组的倍性。

    METHOD FOR FRAGMENTING GENOMIC DNA USING CAS9
    29.
    发明申请
    METHOD FOR FRAGMENTING GENOMIC DNA USING CAS9 有权
    使用CAS9分离基因组DNA的方法

    公开(公告)号：US20140357523A1

    公开(公告)日：2014-12-04

    申请号：US14290896

    申请日：2014-05-29

    Applicant: Agilent Technologies, Inc.

    Inventor： Gusti Zeiner ,  Derek Lee Lindstrom ,  Brian Jon Peter ,  Robert A. Ach

    IPC: C12Q1/68

    CPC classification number: C12Q1/6806 ,  C12N9/22 ,  C12N15/1003 ,  C12N15/1034 ,  C12Q1/6869 ,  C12Y301/00 ,  Y10T436/143333

    Abstract: A method for fragmenting a genome is provided. In certain embodiments, the method comprises: (a) combining a genomic sample containing genomic DNA with a plurality of Cas9-gRNA complexes, wherein the Cas9-gRNA complexes comprise a Cas9 protein and a set of at least 10 Cas9-associated guide RNAs that are complementary to different, pre-defined, sites in a genome, to produce a reaction mixture; and (b) incubating the reaction mixture to produce at least 5 fragments of the genomic DNA. Also provided is a composition comprising at least 100 Cas9-associated guide RNAs that are each complementary to a different, pre-defined, site in a genome. Kits for performing the method are also provided. In addition, other methods, compositions and kits for manipulating nucleic acids are also provided.

    Abstract translation: 提供了一种分割基因组的方法。 在某些实施方案中，所述方法包括：（a）将含有基因组DNA的基因组样品与多个Cas9-gRNA复合物组合，其中所述Cas9-gRNA复合物包含Cas9蛋白和至少10个Cas9相关导向RNA的集合，其中 与基因组中不同的，预定义的位点互补，以产生反应混合物; 和（b）孵育反应混合物以产生至少5个基因组DNA片段。 还提供了包含至少100种与基因组中不同的，预定义的位点互补的Cas9相关导向RNA的组合物。 还提供了用于执行该方法的套件。 此外，还提供用于操作核酸的其它方法，组合物和试剂盒。

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