公开(公告)号：US20220348994A1

公开(公告)日：2022-11-03

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: C12Q1/6823 ,  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：US11459609B2

公开(公告)日：2022-10-04

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: C12Q1/68 ,  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：USD956263S1

公开(公告)日：2022-06-28

申请号：US29740346

申请日：2020-07-02

Applicant: Ultima Genomics, Inc.

Designer： Nathan Beckett ,  Joseph Anthony ,  Phillip You Fai Lee ,  Jose Martin Sosa

公开(公告)号：US20220199201A1

公开(公告)日：2022-06-23

申请号：US17574260

申请日：2022-01-12

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：US20220168745A1

公开(公告)日：2022-06-02

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

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：US20220154272A1

公开(公告)日：2022-05-19

申请号：US17515958

申请日：2021-11-01

Applicant: Ultima Genomics, Inc.

Inventor： Florian OBERSTRASS ,  Gilad ALMOGY ,  Linda LEE ,  Eliane TREPAGNIER ,  Geunwon JUNG

IPC: C12Q1/6874 ,  C12Q1/6876 ,  C12Q1/6853 ,  C12N9/12 ,  G01N21/64

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：US11326207B2

公开(公告)日：2022-05-10

申请号：US16683841

申请日：2019-11-14

Applicant: Ultima Genomics, Inc.

Inventor： Gilad Almogy ,  Linda Lee

IPC: C12Q1/6869 ,  C12Q1/6806

Abstract: The present disclosure provides methods and systems for nucleic acid sequencing. Such systems and methods may achieve context-independent incorporation, have reduced context-dependence or have context-dependence that is amenable to calibration and modeling. Such systems and methods may also reduce misincorporation.

公开(公告)号：US11268143B2

公开(公告)日：2022-03-08

申请号：US17308241

申请日：2021-05-05

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: C12Q1/68 ,  G01N35/10 ,  C12Q1/6874

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：US11118223B2

公开(公告)日：2021-09-14

申请号：US16953071

申请日：2020-11-19

Applicant: Ultima Genomics, Inc.

Inventor： Gilad Almogy ,  Nathan Beckett ,  Stephanie Kubecka

IPC: G01N35/00 ,  C12Q1/6874 ,  G01N35/10 ,  C12Q1/68

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：US20210277464A1

公开(公告)日：2021-09-09

申请号：US17308241

申请日：2021-05-05

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.