公开(公告)号：US20210142869A1

公开(公告)日：2021-05-13

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：US10830703B1

公开(公告)日：2020-11-10

申请号：US16677067

申请日：2019-11-07

Applicant: Ultima Genomics, Inc.

Inventor： Gilad Almogy ,  Nathan Beckett ,  Nathan Caswell ,  Gene Polovy

IPC: G01N21/65 ,  G02B21/00

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：US10512911B1

公开(公告)日：2019-12-24

申请号：US16440026

申请日：2019-06-13

Applicant: Ultima Genomics, Inc.

Inventor： Nathan Beckett ,  Nathan Caswell

IPC: B01L3/00 ,  G01N7/02 ,  G01N33/487

Abstract: Provided herein are methods for processing and/or detecting a sample. A method can comprise providing a barrier between a first region and a second region, wherein the first region comprises the sample, wherein the barrier maintains the first region at a first atmosphere that is different than a second atmosphere of the second region, wherein a portion of the barrier comprises a fluid in coherent motion; and using a detector at least partially contained in the first region to detect one or more signals from the sample while the first region is maintained at the first atmosphere that is different than the second atmosphere of the second region. The portion of the barrier comprising fluid may have a pressure lower than the first atmosphere, the second atmosphere, or both.

公开(公告)号：US12209278B2

公开(公告)日：2025-01-28

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: C12Q1/68 ,  C12Q1/6827 ,  C12Q1/6869 ,  G16B30/00

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：US12195797B2

公开(公告)日：2025-01-14

申请号：US18737230

申请日：2024-06-07

Applicant: Ultima Genomics, Inc.

Inventor： Daniel Mazur

IPC: C12Q1/68 ,  C12Q1/6844 ,  C12Q1/6869

Abstract: The present disclosure provides compositions, methods, and systems for preparing nucleic acid samples for sequencing, including attaching adapters to a template nucleic acid molecule having a first and second strands; attaching the template nucleic acid molecule to a support; detaching the first and second strands from each other; generating a reverse complement copy of the second strand using a primer coupled to the support; generating amplified copies of the first strand and the reverse complement copy of the second strand using primers coupled to the support; and identifying the sequences of the first strand and the reverse complement copy of the second strand. Further provided herein are methods of error correction by preserving both strands of a template nucleic acid molecule during amplification.

公开(公告)号：US20240386998A1

公开(公告)日：2024-11-21

申请号：US18426104

申请日：2024-01-29

Applicant: Ultima Genomics, Inc.

Inventor： Simchon FAIGLER ,  Eyal NEISTEIN ,  Mark PRATT

IPC: G16B30/00 ,  G06T5/20 ,  G06T5/50 ,  G06T7/00 ,  G06T7/194 ,  G06V20/69 ,  G06V20/70

Abstract: The present disclosure relates generally to sequencing techniques, and more specifically to methods, systems, devices, and non-transitory computer-readable storage media for processing images of biological samples (e.g., to obtain sequencing data). An exemplary method of determining nucleic acid sequences of a plurality of sequencing colonies comprises: obtaining an input image of a surface, wherein the plurality of sequencing colonies are attached to the surface; detecting a set of sequencing colonies of the plurality of sequencing colonies in the input image; executing in parallel, using a graphics processor, a plurality of iterative processes to obtain signal amplitudes for the detected set of sequencing colonies, wherein each iterative process corresponds to a respective detected sequencing colony in the set; and determining, at least partially based on the signal amplitudes for the detected set of sequencing colonies, portions of nucleic acid sequences of the plurality of sequencing colonies.

公开(公告)号：US20240287483A1

公开(公告)日：2024-08-29

申请号：US18651565

申请日：2024-04-30

Applicant: Ultima Genomics, Inc.

Inventor： Daniel MAZUR ,  Eileen Collins TOZER ,  Theo NIKIFOROV ,  Denise Sanchez TOPACIO-HALL

IPC: C12N9/12 ,  C12Q1/6825

CPC classification number: C12N9/1252 ,  C12Q1/6825 ,  C12Y207/07007

Abstract: Mutant nucleic acid polymerases are described herein. Also described are methods for screening or assaying the mutant nucleic acid polymerases.

公开(公告)号：US12071653B2

公开(公告)日：2024-08-27

申请号：US17712765

申请日：2022-04-04

Applicant: Ultima Genomics, Inc.

Inventor： Linda Lee ,  Steven Menchen ,  Theo Nikiforov ,  Gilad Almogy ,  Florian Oberstrass

IPC: C12Q1/68 ,  C12Q1/6806 ,  C12Q1/6823 ,  C12Q1/6869 ,  G01N21/64

CPC classification number: C12Q1/6823 ,  C12Q1/6806 ,  C12Q1/6869 ,  G01N21/6428 ,  G01N2021/6439

Abstract: The disclosure provides methods for sequencing nucleic acids using, including with nucleotide analogs and subsequently appended labels.

公开(公告)号：US20240117411A1

公开(公告)日：2024-04-11

申请号：US18540604

申请日：2023-12-14

Applicant: Ultima Genomics, Inc.

Inventor： Robert ONO ,  Daniel MAZUR ,  Florian OBERSTRASS

IPC: C12Q1/6806

CPC classification number: C12Q1/6806

Abstract: Methods of controlling the density or number of nucleic acid molecules coupled to solid supports are provided. Capture substrates produced thereby or comprising a predetermined density or number of nucleic acids coupled thereto are also provided.

公开(公告)号：US20240043918A1

公开(公告)日：2024-02-08

申请号：US18035081

申请日：2021-11-03

Applicant: Ultima Genomics, Inc.

Inventor： Omer BARAD ,  Yoav ETZIONI

IPC: C12Q1/6869 ,  C12Q1/6809

CPC classification number: C12Q1/6869 ,  C12Q1/6809

Abstract: Described herein are methods of sequencing a polynucleotide and methods of analyzing sequencing data obtained from such sequencing methods. The sequencing methods can include accelerated primer extension through a region of the polynucleotide using labeled nucleotides provided according to a flow order, measuring a signal from labeled nucleotides incorporated into the primer, and determining distance information that indicates the length of the region using the measured signal.