公开(公告)号：US20240257906A1

公开(公告)日：2024-08-01

申请号：US18617448

申请日：2024-03-26

Applicant: Ultima Genomics, Inc.

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

IPC: G16B20/20 ,  C12Q1/6874 ,  G06F17/00 ,  G16B20/00 ,  G16B30/00 ,  G16B30/10 ,  G01N21/64

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：US20240255428A1

公开(公告)日：2024-08-01

申请号：US18623877

申请日：2024-04-01

Applicant: Ultima Genomics, Inc.

Inventor： Osip SCHWARTZ ,  Gilad ALMOGY ,  Rongwen LU ,  Gene POLOVY ,  Amy Elizabeth FRANTZ

IPC: G01N21/64

CPC classification number: G01N21/6456 ,  G01N21/6428 ,  G01N2021/6439 ,  G01N2201/02

Abstract: Provided herein are systems and methods that combine the use of first and second optical transformations (e.g., implemented using optical photon reassignment (OPRA)) with time delay and integration (TDI) imaging to provide high throughput imaging while maintaining a high signal to noise ratio and providing enhanced image resolution.

公开(公告)号：US20240026446A1

公开(公告)日：2024-01-25

申请号：US18480416

申请日：2023-10-03

Applicant: ULTIMA GENOMICS, INC.

Inventor： Gilad ALMOGY ,  Mark PRATT ,  Florian OBERSTRASS ,  Ron Saar DOVER ,  Zohar SHIPONY

IPC: C12Q1/6874 ,  C12N15/10

CPC classification number: C12Q1/6874 ,  C12N15/1068

Abstract: Despite the advance of screening technology, omic-based studies with spatial resolution still requires laborious efforts, hampering the analysis of biology and disease. The present disclosure provides methods, systems, reagents, and platforms to increase the throughput of analyte screening with spatial resolution.

公开(公告)号：US20230407385A1

公开(公告)日：2023-12-21

申请号：US18035073

申请日：2021-11-03

Applicant: Ultima Genomics, Inc.

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

IPC: C12Q1/6874

CPC classification number: C12Q1/6874

Abstract: Described herein are methods synchronizing sequencing primers within a sequencing cluster and methods of generating long-range sequencing reads. The methods can include hybridizing primers to polynucleotide copies within a sequencing cluster; extending the primers through a first region of the polynucleotide copies using labeled nucleotides according to a sequencing flow order; extending the primers through a second region of the polynucleotide copies using one or more re-phasing flow steps that each include at least two different types of nucleotide bases; and extending the primers through a third region of the polynucleotide copies using labeled nucleotides according to the sequencing cycle. The rephasing flow steps may be initiated after a predetermined number of sequencing flow steps, after a measured sequencing signal strength falls below a predetermined sequencing signal strength threshold, or a measured sequencing signal-to-noise ratio falls below a sequencing signal-to-noise ratio threshold.

公开(公告)号：US20220170089A1

公开(公告)日：2022-06-02

申请号：US17453481

申请日：2021-11-03

Applicant: Ultima Genomics, Inc.

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

IPC: C12Q1/6869

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：US20210147930A1

公开(公告)日：2021-05-20

申请号：US17158953

申请日：2021-01-26

Applicant: Ultima Genomics, Inc.

Inventor： Florian OBERSTRASS ,  Gilad ALMOGY

IPC: C12Q1/6874

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：US20210139980A1

公开(公告)日：2021-05-13

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：US20210079465A1

公开(公告)日：2021-03-18

申请号：US17032023

申请日：2020-09-25

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：US20200372971A1

公开(公告)日：2020-11-26

申请号：US16864981

申请日：2020-05-01

Applicant: Ultima Genomics, Inc.

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

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

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：US20200303039A1

公开(公告)日：2020-09-24

申请号：US16845278

申请日：2020-04-10

Applicant: ULTIMA GENOMICS, INC.

Inventor： Mark PRATT ,  Gilad ALMOGY ,  Avishai BARTOV

IPC: G16B40/10 ,  C12Q1/6869 ,  G16B30/10 ,  C12Q1/6806 ,  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.