公开(公告)号：US20250059593A1

公开(公告)日：2025-02-20

申请号：US18776428

申请日：2024-07-18

Applicant: ULTIMA GENOMICS, INC.

Inventor： Linda LEE ,  Steven MENCHEN ,  Theo NIKIFOROV ,  Gilad ALMOGY ,  Florian OBERSTRASS

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

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

公开(公告)号：US20250012778A1

公开(公告)日：2025-01-09

申请号：US18776046

申请日：2024-07-17

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 ,  G01N1/22 ,  G01Q10/04

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：US20240328947A1

公开(公告)日：2024-10-03

申请号：US18635829

申请日：2024-04-15

Applicant: Ultima Genomics, Inc.

Inventor： Robert ONO ,  Aklilu WORKU ,  Stephanie KUBECKA ,  Florian OBERSTRASS ,  Gilad ALMOGY

IPC: G01N21/64 ,  C12Q1/6806 ,  C12Q1/6834

CPC classification number: G01N21/6456 ,  C12Q1/6806 ,  C12Q1/6834

Abstract: Disclosed herein are buffer solutions for decreasing the size of particles during imaging. The buffer solutions may comprise polymers, ions, or a combination thereof. The buffer solutions may decrease the sizes of particles to facilitate the resolution of individual particles during imaging. Also provided herein are methods and systems of using the same.

公开(公告)号：US20240120025A1

公开(公告)日：2024-04-11

申请号：US18362754

申请日：2023-07-31

Applicant: Ultima Genomics, Inc.

Inventor： Yoav ETZIONI ,  Simchon FAIGLER ,  Gilad ALMOGY ,  Mark PRATT ,  Florian OBERSTRASS

IPC: G16B20/20 ,  C12Q1/6874 ,  G06F17/00 ,  G16B20/00 ,  G16B30/00 ,  G16B30/10

CPC classification number: G16B20/20 ,  C12Q1/6874 ,  G06F17/00 ,  G16B20/00 ,  G16B30/00 ,  G16B30/10 ,  C12Q2600/156 ,  C12Q2600/158 ,  G01N2021/6439

Abstract: Methods for detecting a short genetic variant in a test sample are described herein. In some exemplary methods, the short genetic variant is called using one or match scores, which are determined using one or more sequencing data sets obtained from a test nucleic acid molecule, wherein the test sequencing data sets are determined by sequencing the test nucleic acid molecule using non-terminating nucleotides provided in separate nucleotide flows according to a flow-cycle order. Also described herein are methods of sequencing a test nucleic acid molecule using two or more different flow-cycle orders and/or extended flow cycle orders having five or more nucleotide flows per flow cycle.

公开(公告)号：US20240043833A1

公开(公告)日：2024-02-08

申请号：US18488731

申请日：2023-10-17

Applicant: ULTIMA GENOMICS, INC.

Inventor： Florian OBERSTRASS ,  Ron Saar DOVER ,  Zohar SHIPONY ,  Gilad ALMOGY ,  Daniel MAZUR

IPC: C12N15/10

CPC classification number: C12N15/1065

Abstract: Provided herein are methods, systems, compositions, and kits that can determine spatial information between a plurality of analytes in a sample by tagging such analytes with tags, where identities and/or locations of such tags are previously unknown prior to tagging. Each of a plurality of analyte sequences may be tagged with multiple spatial tags, such that each analyte sequence is associated with a set of two or more spatial tags. The sets of spatial tags may be analyzed to generate a map of analyte sequences. The map may comprise information about the respective absolute positions of each of a set of sequences with respect to a reference sequence. The map may comprise information about the respective probability cloud (or likely location) of each of a set of sequences with respect to a reference sequence.

公开(公告)号：US20220162696A1

公开(公告)日：2022-05-26

申请号：US17543521

申请日：2021-12-06

Applicant: Ultima Genomics, Inc.

Inventor： Nathan BECKETT ,  Gilad ALMOGY ,  Nathan CASWELL ,  Jacob A. WOLF ,  Kristopher BARBEE ,  Denis PRISTINSKI ,  Mark PRATT ,  Gene POLOVY ,  Osip SCHWARTZ ,  Stephanie KUBECKA ,  Steven MENCHEN ,  Joseph ANTHONY ,  Jose Martin SOSA ,  Phillip You Fai LEE

IPC: C12Q1/6874 ,  G01N35/10

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：US20220064728A1

公开(公告)日：2022-03-03

申请号：US17487804

申请日：2021-09-28

Applicant: Ultima Genomics, Inc.

Inventor： Gilad ALMOGY ,  Linda LEE

IPC: C12Q1/6874

Abstract: The present disclosure provides methods for nucleic acid sequence identification. The methods may comprise bringing a plurality of nucleic acid molecules in contact with a reaction mixture including a concentration of nucleotides that results in fractional labeling of the nucleic acid molecules. The methods may comprise starting a next reversibly-terminated, sequencing cycle prior to completion of unblocking of reversible terminators in a previous sequencing cycle.

公开(公告)号：US20210383895A1

公开(公告)日：2021-12-09

申请号：US17406464

申请日：2021-08-19

Applicant: ULTIMA GENOMICS, INC.

Inventor： Mark PRATT ,  Gilad ALMOGY ,  Avishai BARTOV

IPC: G16B40/10 ,  C12Q1/6806 ,  G16B45/00 ,  G16B30/10 ,  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：US20210363572A1

公开(公告)日：2021-11-25

申请号：US17395382

申请日：2021-08-05

Applicant: Ultima Genomics, Inc.

Inventor： Linda G. LEE ,  Gilad ALMOGY ,  Steven MENCHEN

IPC: C12Q1/6823 ,  C12Q1/6876 ,  C12Q1/6869

Abstract: The present disclosure provides labeling reagents for labeling substrates such as nucleotides, proteins, antibodies, lipids, and cells. The labeling reagents provided herein may comprise fluorescent labels and semi-rigid linkers. Methods for nucleic acid sequencing using materials comprising such labeling reagents are also provided here

公开(公告)号：US20210054442A1

公开(公告)日：2021-02-25

申请号：US17086203

申请日：2020-10-30

Applicant: Ultima Genomics, Inc.

Inventor： Mark PRATT ,  Gilad ALMOGY ,  Dumitru BRINZA ,  Eliane TREPAGNIER ,  Omer BARAD ,  Yoav ETZIONI ,  Florian OBERSTRASS

IPC: 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.