公开(公告)号：WO2021081235A1

公开(公告)日：2021-04-29

申请号：PCT/US2020/056904

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.

公开(公告)号：WO2022212559A1

公开(公告)日：2022-10-06

申请号：PCT/US2022/022619

申请日：2022-03-30

Applicant: JUMPCODE GENOMICS, INC.

Inventor： BROWN, Keith ,  ARMSTRONG, Jon ,  SIDDIQUE, Azeem

IPC: C12Q1/68

Abstract: Disclosed herein are compositions and methods related to the detection and/or elimination of a first nucleic acid and enrichment of a second nucleic acid in a sample, for example to exclude the first nucleic acid from downstream analysis or sequencing, or to exclude such sequences from a downstream data set.

公开(公告)号：WO2021146534A1

公开(公告)日：2021-07-22

申请号：PCT/US2021/013598

申请日：2021-01-15

Applicant: JUMPCODE GENOMICS, INC.

Inventor： BROWN, Keith

IPC: C12Q1/6806 ,  C12Q1/6853 ,  C12Q1/6876

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：WO2022035950A2

公开(公告)日：2022-02-17

申请号：PCT/US2021/045521

申请日：2021-08-11

Applicant: JUMPCODE GENOMICS, INC.

Inventor： BROWN, Keith

IPC: C12Q1/6806 ,  C12N15/10 ,  C12Q1/6869 ,  C12Q1/6851 ,  C12Q1/6855 ,  C40B30/06

Abstract: Disclosed herein are compositions and methods related to the elimination of a first nucleic acid and/or enrichment of a second nucleic acid in a sample, for example to exclude the first nucleic acid from downstream analysis or sequencing, or to exclude such sequences from a downstream data set.

公开(公告)号：WO2021062107A1

公开(公告)日：2021-04-01

申请号：PCT/US2020/052652

申请日：2020-09-25

Applicant: JUMPCODE GENOMICS, INC.

Inventor： BROWN, Keith

IPC: C12Q1/6869 ,  C12N15/09 ,  C12N15/10 ,  C12N15/113

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：AU2020372488A1

公开(公告)日：2022-05-19

申请号：AU2020372488

申请日：2020-10-23

Applicant: JUMPCODE GENOMICS INC

Inventor： BROWN KEITH

IPC: C40B40/08 ,  A61K31/70 ,  A61K38/45 ,  A61P43/00 ,  C12Q1/68

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：AU2020354648A1

公开(公告)日：2022-04-14

申请号：AU2020354648

申请日：2020-09-25

Applicant: JUMPCODE GENOMICS INC

Inventor： BROWN KEITH

IPC: C12Q1/6869 ,  C12N15/09 ,  C12N15/10 ,  C12N15/113

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：PL3110975T3

公开(公告)日：2021-12-13

申请号：PL15754498

申请日：2015-02-27

Applicant: JUMPCODE GENOMICS INC

Inventor： BROWN KEITH

IPC: A61K38/45 ,  A61P43/00 ,  C12Q1/6809 ,  C12Q1/6869 ,  C12Q1/6886 ,  G16H15/00

公开(公告)号：AU2015222802A1

公开(公告)日：2016-10-13

申请号：AU2015222802

申请日：2015-02-27

Applicant: JUMPCODE GENOMICS INC

Inventor： BROWN KEITH

IPC: C12Q1/68

Abstract: Methods and compositions related to the use of Mobile Element Insertions and their adjacent genomic sequences. Methods using MEIs as markers for cellular proliferation, as targets for pharmaceuticals, as markers for tissue fingerprinting and in related methods and compositions are disclosed herein. Methods and compositions relate to the detection, treatment and ongoing monitoring of cell proliferation events, cancer, and deleterious effects of mobile elements in aging, and to the selection, use and monitoring of the success of treatment regimens to address these conditions.

公开(公告)号：US11761039B2

公开(公告)日：2023-09-19

申请号：US17506431

申请日：2021-10-20

Applicant: JumpCode Genomics, Inc.

Inventor： Keith Brown ,  Peter Dansky

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

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.