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    METHODS OF TARGETED SEQUENCING
    32.
    发明申请
    METHODS OF TARGETED SEQUENCING 有权

    公开(公告)号：US20230056763A1

    公开(公告)日：2023-02-23

    申请号：US17758656

    申请日：2021-01-15

    Applicant: JUMPCODE GENOMICS, INC.

    Inventor： Keith BROWN

    IPC: C12Q1/6806 ,  C12Q1/6869 ,  C12Q1/6876 ,  C12Q1/6853 ,  C12N9/12

    Abstract: Provided herein are methods and compositions for creating a sequencing library comprising a target nucleic acid. Methods herein can comprise: contacting a nucleic acid sample to a first population of primers, a polymerase, dNTPs, and labeled ddNTPs; performing an extension reaction thereby creating an labeled extension product; contacting the extension product to a second population of primers to create a double stranded extension product comprising the target nucleic acid; contacting the double stranded extension product to a target specific enzyme under conditions allowing cleavage of at least a subset of the double stranded extension product thereby creating a cleaved target nucleic acid; and isolating the cleaved target nucleic acid.

    Method for target specific RNA transcription of DNA sequences
    33.
    发明授权
    Method for target specific RNA transcription of DNA sequences 有权

    公开(公告)号：US11339427B2

    公开(公告)日：2022-05-24

    申请号：US16101083

    申请日：2018-08-10

    Applicant: JumpCode Genomics, Inc.

    Inventor： Keith Brown

    IPC: C12Q1/6869 ,  C12Q1/6865

    Abstract: Disclosed herein are methods of long range target specific amplification and sequencing using an RNA intermediate synthesized directly from the target including using hairpin adaptors having a double stranded promoter and an overhang which hybridizes with a reverse-complementary overhang on a target nucleic acid. RNA transcription eliminates clonal amplification of early synthesis errors. Approaches allow for the identification of target-adjacent sequence, such as sequence adjacent to a repeat element target. Also disclosed herein are compositions and kits for amplification and sequencing.

    METHOD FOR TARGET SPECIFIC RNA TRANSCRIPTION OF DNA SEQUENCES
    34.
    发明申请
    METHOD FOR TARGET SPECIFIC RNA TRANSCRIPTION OF DNA SEQUENCES 审中-公开

    公开(公告)号：US20190153528A1

    公开(公告)日：2019-05-23

    申请号：US16101083

    申请日：2018-08-10

    Applicant: JumpCode Genomics, Inc.

    Inventor： Keith Brown

    IPC: C12Q1/6869

    Abstract: Disclosed herein are methods of long range target specific amplification and sequencing using an RNA intermediate synthesized directly from the target including using hairpin adaptors having a double stranded promoter and an overhang which hybridizes with a reverse-complementary overhang on a target nucleic acid. RNA transcription eliminates clonal amplification of early synthesis errors. Approaches allow for the identification of target-adjacent sequence, such as sequence adjacent to a repeat element target. Also disclosed herein are compositions and kits for amplification and sequencing.

    Methods of sample normalization
    36.
    发明专利
    Methods of sample normalization 未知

    公开(公告)号：AU2021207685A1

    公开(公告)日：2022-08-25

    申请号：AU2021207685

    申请日：2021-01-15

    Applicant: JUMPCODE GENOMICS INC

    Inventor： BROWN KEITH

    IPC: C12Q1/68 ,  C12N9/22 ,  C12N15/10 ,  C12N15/11 ,  C40B40/08

    Abstract: Provided herein are methods of normalizing a population of nucleic acid samples. Methods herein can comprise: contacting a plurality of nucleic acid samples to a normalizing agent, wherein each nucleic acid of the plurality comprises a sample-specific barcode, and wherein the normalizing agent comprises a plurality of labeled enzymes capable of binding to each sample specific barcode; contacting the product to a capture agent to capture the nucleic acids that are bound to the normalizing agent; and treating the product with a protease to release the bound nucleic acids, thereby creating a normalized library having more even representation of each nucleic acid sample than the plurality of nucleic acid samples before normalization.

    De-novo k-mer associations between molecular states
    37.
    发明专利
    De-novo k-mer associations between molecular states 未知

    公开(公告)号：AU2020371699A1

    公开(公告)日：2022-05-19

    申请号：AU2020371699

    申请日：2020-10-22

    Applicant: JUMPCODE GENOMICS INC

    Inventor： BROWN KEITH

    IPC: C12Q1/68 ,  C12Q1/6809 ,  C12Q1/6876 ,  G16B30/20

    Abstract: Provided are methods for preparation and analysis of nucleic acids. Some embodiments include reverse transcribing the RNA with barcoded primers to produce cDNA while maintaining the DNA in the sample, sequencing the DNA and cDNA together, and differentiating the sequenced DNA and cDNA using the barcode or barcodes of the primers. Some embodiments include analyzing the DNA and cDNA sequences of multiple samples separating reads into k-mers, and comparing the k-mers between samples to identify differential sequences between the sequences of the samples.

    Fraccionamiento del genoma
    38.
    发明专利
    Fraccionamiento del genoma 未知

    公开(公告)号：ES2833299T3

    公开(公告)日：2021-06-14

    申请号：ES15746731

    申请日：2015-02-03

    Applicant: JUMPCODE GENOMICS INC

    Inventor： BROWN KEITH ,  DANSKY PETER

    IPC: C12Q1/6811

    Abstract: Un procedimiento para eliminar una secuencia no deseada de una biblioteca de ácidos nucleicos de cadena doble que comprende: 5 (a) proporcionar dicha biblioteca de ácido nucleico de cadena doble, que comprende una pluralidad de moléculas de ácido nucleico de cadena doble, en la que cada molécula de ácido nucleico de cadena doble comprende una primera región adaptadora, una región de secuencia diana y una segunda región adaptadora, y en la que al menos una de dichas moléculas de ácido nucleico de cadena doble comprende dicha secuencia no deseada; (b) poner en contacto dicha biblioteca de ácidos nucleicos de cadena doble con una fracción modificadora de ácidos nucleicos que se une específicamente a dicha secuencia no deseada; en la que dicha fracción modificadora de ácido nucleico comprende una endonucleasa dirigida por una molécula de ARN guía; (c) escindir dicha secuencia no deseada de modo que dicha primera región adaptadora y dicha segunda región adaptadora no estén unidas físicamente a través de dicha región de secuencia diana; y (d) secuenciar dicha biblioteca de ácidos nucleicos de cadena doble usando un enfoque de secuenciación que requiere dicha primera región adaptadora y dicha segunda región adaptadora que abarca dicha región de secuencia diana.

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