公开(公告)号：US12152277B2

公开(公告)日：2024-11-26

申请号：US18132693

申请日：2023-04-10

Applicant: ULTIMA GENOMICS, INC.

Inventor： Gilad Almogy ,  Mark Pratt ,  Florian Oberstrass

IPC: C12Q1/68 ,  C12Q1/6806 ,  C12Q1/6869

Abstract: Recognized herein is the need for methods and processes for increasing the efficiency and accuracy of paired end sequencing.

公开(公告)号：US12119087B2

公开(公告)日：2024-10-15

申请号：US17574260

申请日：2022-01-12

Applicant: ULTIMA GENOMICS, INC.

Inventor： Mark Pratt ,  Gilad Almogy ,  Avishai Bartov

IPC: G16B40/10 ,  C12Q1/6806 ,  C12Q1/6869 ,  G16B30/10 ,  G16B45/00

CPC classification number: G16B40/10 ,  C12Q1/6806 ,  C12Q1/6869 ,  G16B30/10 ,  G16B45/00

Abstract: The present disclosure provides methods and systems for accurate and efficient context-aware base calling of sequences. In an aspect, disclosed herein is a method for sequencing a nucleic acid molecule, comprising: (a) sequencing the nucleic acid molecule to generate a plurality of sequence signals; and (b) determining base calls of the nucleic acid molecule based at least in part on (i) the plurality of sequence signals and (ii) quantified context dependency for at least a portion of the plurality of sequence signals.

公开(公告)号：US11904322B2

公开(公告)日：2024-02-20

申请号：US17673444

申请日：2022-02-16

Applicant: Ultima Genomics, Inc.

Inventor： Jose Martin Sosa ,  Joseph Anthony ,  Nathan Beckett ,  Gilad Almogy ,  Chandan Shee ,  Phillip You Fai Lee ,  Yuto Watanabe

IPC: B01L7/00 ,  B01L3/00 ,  B01L99/00 ,  C12Q1/686

CPC classification number: B01L7/52 ,  B01L3/508 ,  B01L2200/0647 ,  B01L2300/1805 ,  B01L2400/0415 ,  C12Q1/686

Abstract: The present disclosure provides methods and processes for increasing the efficiency and accuracy of nucleic acid sequencing using techniques such as polymerase chain reaction (PCR). Methods and systems provided herein may facilitate performing reactions such as emulsion PCR (ePCR) on samples comprising nucleic acids and beads. The methods provided herein may provide a higher throughput compared to existing technologies.

公开(公告)号：US11655501B2

公开(公告)日：2023-05-23

申请号：US16842584

申请日：2020-04-07

Applicant: ULTIMA GENOMICS, INC.

Inventor： Gilad Almogy ,  Mark Pratt ,  Florian Oberstrass

IPC: C12Q1/68 ,  C12Q1/6869 ,  C12Q1/6806

CPC classification number: C12Q1/6869 ,  C12Q1/6806

Abstract: Recognized herein is the need for methods and processes for increasing the efficiency and accuracy of paired end sequencing.

公开(公告)号：US20230060685A1

公开(公告)日：2023-03-02

申请号：US17822760

申请日：2022-08-26

Applicant: Ultima Genomics, Inc.

Inventor： Mark Pratt ,  Gilad Almogy ,  Dumitru Brinza ,  Eliane Trepagnier ,  Omer Barad ,  Yoav Etzioni ,  Florian Oberstrass

IPC: C12Q1/6869 ,  G16B30/00 ,  C12Q1/6827

Abstract: Described herein are methods of generating a coupled sequencing read pair for a polynucleotide, and methods of analyzing the coupled sequencing read pair. The coupled sequencing read pair can be analyzed to detect polynucleotide variants, including at loci that are not directly sequenced within the coupled sequencing read pair. Other analytical methods can include using coupled sequencing read pairs to construct or validate a consensus sequence. The coupled sequencing read pair may be generated for a polynucleotide by generating sequencing data for a first region by extending a primer using labeled nucleotides; further extending the primer through a second region using nucleotides provided in a second region flow order, wherein primer extension through the second region is faster than primer extension through the first region; and generating sequencing data associated with a sequence of a third region of the polynucleotide by further extending the primer using labeled nucleotides.

公开(公告)号：US11220710B2

公开(公告)日：2022-01-11

申请号：US17158960

申请日：2021-01-26

Applicant: Ultima Genomics, Inc.

Inventor： Florian Oberstrass ,  Gilad Almogy

IPC: C12Q1/6869 ,  C12Q1/6874 ,  C12N15/10

Abstract: Described herein are methods for determining a sequence of a region of interest from an mRNA molecule. Sequenced polynucleotides can include a barcode region, a homopolymer region (e.g., a poly-A region), and a target region associated with the mRNA molecule. According to some methods, the barcode region omits the same base present in the homopolymer region. According to some methods, extension of the primer used for sequencing is stalled within the homopolymer region. According to some methods, sequencing flow cycles and the different barcode regions of the polynucleotides configured are such that the primer is extended to the end of the barcode region across the plurality of polynucleotides before being extended into the homopolymer region. According to some methods, two primers or a cleavable primer is used to separately sequence the barcode region and the target region.

公开(公告)号：US11155868B2

公开(公告)日：2021-10-26

申请号：US17155226

申请日：2021-01-22

Applicant: Ultima Genomics, Inc.

Inventor： Gilad Almogy ,  Nathan Beckett ,  Jacob A. Wolf ,  Nathan Caswell ,  Joseph Anthony ,  Jose Martin Sosa ,  Phillip Lee ,  Stephanie Kubecka

IPC: C12Q1/6874 ,  C12Q1/6825 ,  C12Q1/6809 ,  B01J19/00 ,  B01L3/00

Abstract: Provided are systems and methods for analyte detection and analysis. A system can comprise an open substrate. The open substrate may be configured to rotate or otherwise move. The open substrate can comprise an array of individually addressable locations, with analytes immobilized thereto. The substrate may be spatially indexed to identify nucleic acid molecules from one or more sources, and/or sequences thereof, with the respective one or more sources. A solution comprising a plurality of probes may be directed across the array to couple at least one of the plurality of probes with at least one of the analytes to form a bound probe. A detector can be configured to detect a signal from the bound probe via scanning of the substrate while minimizing temperature fluctuations of the substrate or optical aberrations caused by bubbles.

公开(公告)号：US11107554B2

公开(公告)日：2021-08-31

申请号：US17090176

申请日：2020-11-05

Applicant: ULTIMA GENOMICS, INC.

Inventor： Mark Pratt ,  Gilad Almogy ,  Avishai Bartov

IPC: G16B40/10 ,  G16B30/10 ,  G16B45/00 ,  C12Q1/6806 ,  C12Q1/6869

Abstract: The present disclosure provides methods and systems for accurate and efficient context-aware base calling of sequences. In an aspect, disclosed herein is a method for sequencing a nucleic acid molecule, comprising: (a) sequencing the nucleic acid molecule to generate a plurality of sequence signals; and (b) determining base calls of the nucleic acid molecule based at least in part on (i) the plurality of sequence signals and (ii) quantified context dependency for at least a portion of the plurality of sequence signals.

公开(公告)号：US12188924B2

公开(公告)日：2025-01-07

申请号：US18224378

申请日：2023-07-20

Applicant: Ultima Genomics, Inc.

Inventor： Kristopher Barbee ,  Nathan Beckett ,  Denis Pristinski ,  Derek Schulte ,  Avishai Bartov ,  Jamie Sullivan ,  Dumitru Brinza ,  Abizar Lakdawalla ,  Steven Menchen ,  Gilad Almogy ,  Mark Pratt

IPC: G01N33/49 ,  G01N1/02 ,  G01Q10/04 ,  G01N1/22

Abstract: Provided are systems and methods for analyte detection and analysis. A system can comprise an open substrate configured to rotate. The open substrate can comprise an array of immobilized analytes. A solution comprising a plurality of probes may be directed, via centrifugal force, across the array during rotation of the substrate, to couple at least one of the plurality of probes with at least one of the analytes to form a bound probe. A detector can be configured to detect a signal from the bound probe via continuous rotational area scanning of the substrate.

公开(公告)号：US11732298B2

公开(公告)日：2023-08-22

申请号：US16416856

申请日：2019-05-20

Applicant: Ultima Genomics, Inc.

Inventor： Gilad Almogy ,  Kristopher Barbee ,  Nathan Beckett

IPC: C12Q1/6874 ,  C12Q1/6809 ,  C12Q1/6825 ,  B01J19/00 ,  B01L3/00 ,  G01N33/543 ,  C12Q1/6834

CPC classification number: C12Q1/6874 ,  B01J19/0046 ,  B01L3/50273 ,  B01L3/502715 ,  C12Q1/6809 ,  C12Q1/6825 ,  B01J2219/00536 ,  B01J2219/00596 ,  B01J2219/00605 ,  B01J2219/00689 ,  B01J2219/00702 ,  B01J2219/00722 ,  B01L3/5023 ,  B01L2200/026 ,  B01L2200/0647 ,  B01L2300/0654 ,  B01L2400/0409 ,  C12Q1/6834 ,  G01N33/54366 ,  C12Q1/6874 ,  C12Q2565/629 ,  C12Q1/6834 ,  C12Q2565/629

Abstract: Provided are methods for biological sample processing and analysis. A method can comprise providing a substrate configured to rotate. The substrate can comprise an array having immobilized thereto a biological analyte. A solution comprising a plurality of probes may be directed, via centrifugal force, across the substrate during rotation of the substrate, to couple at least one of the plurality of probes with the biological analyte. A detector can be configured to detect a signal from the at least one probe coupled to the biological analyte, thereby analyzing the biological analyte.