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：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：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：US11276480B2

公开(公告)日：2022-03-15

申请号：US17406464

申请日：2021-08-19

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：US10267790B1

公开(公告)日：2019-04-23

申请号：US15974441

申请日：2018-05-08

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

Abstract: Provided are systems for biological sample processing and analysis. A system can comprise a substrate configured to rotate. The substrate can comprise an array configured to immobilize a biological analyte. A fluid flow unit comprising a fluid channel can be configured to dispense a solution comprising a plurality of probes. The solution 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 in optical communication with the array can be configured to detect one or more signals from the at least one probe coupled to the biological analyte.

公开(公告)号：US11747323B2

公开(公告)日：2023-09-05

申请号：US17962163

申请日：2022-10-07

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

CPC classification number: G01N33/492 ,  G01N1/02 ,  G01Q10/04 ,  G01N2001/2291

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：US11505820B2

公开(公告)日：2022-11-22

申请号：US16936619

申请日：2020-07-23

Applicant: ULTIMA GENOMICS, INC.

Inventor： Eliane Trepagnier ,  Mark Pratt ,  Theo Nikiforov ,  Gilad Almogy

IPC: C12Q1/6818 ,  C12Q1/6869

Abstract: The present disclosure provides methods and systems for sequencing nucleic acid molecules in a manner that enables higher sequencing accuracy. Methods and systems provided herein may enable sequences that may have low-accuracy reads, such as homopolymer sequences or other repeating sequences, to be determined at a higher accuracy and efficiency.