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.

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.

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.

公开(公告)号：US20240035086A1

公开(公告)日：2024-02-01

申请号：US18446208

申请日：2023-08-08

Applicant: JumpCode Genomics, Inc.

Inventor： Keith Brown ,  Peter Dansky

IPC: C12Q1/6874 ,  C12Q1/6811 ,  C12Q1/68 ,  C12N15/10

CPC classification number: C12Q1/6874 ,  C12Q1/6811 ,  C12Q1/68 ,  C12N15/1093

Abstract: Disclosed herein are compositions and methods related to the elimination of molecules of a selected sequence from a nucleic acid sample or from an sequence dataset resulting from the sequencing of a sample, for example to exclude such molecules from downstream analysis or sequencing, or to exclude such sequences from a downstream data set.

公开(公告)号：US11708606B2

公开(公告)日：2023-07-25

申请号：US16793908

申请日：2020-02-18

Applicant: JumpCode Genomics, Inc.

Inventor： Keith Brown ,  Peter Dansky

IPC: C12Q1/6874 ,  C12N15/10 ,  C12Q1/6811 ,  C12Q1/68

CPC classification number: C12Q1/6874 ,  C12N15/1093 ,  C12Q1/68 ,  C12Q1/6811 ,  C12Q1/6811 ,  C12Q2521/301 ,  C12Q2535/122

Abstract: Disclosed herein are compositions and methods related to the elimination of molecules of a selected sequence from a nucleic acid sample or from an sequence dataset resulting from the sequencing of a sample, for example to exclude such molecules from downstream analysis or sequencing, or to exclude such sequences from a downstream data set.

公开(公告)号：US20220403447A1

公开(公告)日：2022-12-22

申请号：US17770807

申请日：2020-10-23

Applicant: JumpCode Genomics, Inc.

Inventor： Keith Brown

IPC: C12Q1/6806 ,  C12Q1/6869 ,  C12Q1/6883

Abstract: Provided are methods for preparing samples for sequencing. Also provided are methods for sequence analysis. Also provided are methods for classifying multiple aspects of a nucleotide repeat expansion disorder in a single sequencing assay. Also provided are methods for genotyping a target nucleic acid sequence.

公开(公告)号：US20220380755A1

公开(公告)日：2022-12-01

申请号：US17770803

申请日：2020-10-22

Applicant: JumpCode Genomics, Inc.

Inventor： Keith Brown

IPC: C12N15/10 ,  G16B30/20 ,  C12Q1/6869 ,  C12Q1/6855 ,  C12Q1/6806

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.

公开(公告)号：US20220333186A1

公开(公告)日：2022-10-20

申请号：US17761866

申请日：2020-09-25

Applicant: JUMPCODE GENOMICS, INC.

Inventor： Keith BROWN

IPC: C12Q1/6855 ,  C12Q1/6806

Abstract: Disclosed herein are methods, compositions, and systems that utilize the consensus sequencing of rolling circle amplified short templates. Methods of determining a nucleic acid sequence can include one or more steps of contacting a nucleic acid in a sample to an endonuclease to cleave a target nucleic acid; ligating the target nucleic acid sequence to form a circular target nucleic acid; hybridizing at least one primer to the circular target molecule to form amplified nucleic acid through rolling circle amplification; and performing sequence analysis of the amplified nucleic acid.

公开(公告)号：US20220259649A1

公开(公告)日：2022-08-18

申请号：US17724309

申请日：2022-04-19

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.

公开(公告)号：US20200181700A1

公开(公告)日：2020-06-11

申请号：US16793908

申请日：2020-02-18

Applicant: JumpCode Genomics, Inc.

Inventor： Keith Brown ,  Peter Dansky

IPC: C12Q1/6874 ,  C12N15/10 ,  C12Q1/6811 ,  C12Q1/68

Abstract: Disclosed herein are compositions and methods related to the elimination of molecules of a selected sequence from a nucleic acid sample or from an sequence dataset resulting from the sequencing of a sample, for example to exclude such molecules from downstream analysis or sequencing, or to exclude such sequences from a downstream data set.