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.

公开(公告)号：US20210054454A1

公开(公告)日：2021-02-25

申请号：US17089781

申请日：2020-11-05

Applicant: Ultima Genomics, Inc.

Inventor： Gilad ALMOGY ,  Kristopher BARBEE ,  Nathan BECKETT

IPC: C12Q1/6874 ,  C12Q1/6809 ,  C12Q1/6825 ,  B01J19/00 ,  B01L3/00

Abstract: Provided are methods for biological sample processing and analysis. A method can comprise providing a substrate configured to rotate. The substrate can comprise an array having immobilized thereto a biological analyte. A solution comprising a plurality of probes 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 can be configured to detect a signal from the at least one probe coupled to the biological analyte, thereby analyzing the biological analyte.

公开(公告)号：US20210047688A1

公开(公告)日：2021-02-18

申请号：US17089876

申请日：2020-11-05

Applicant: Ultima Genomics, Inc.

Inventor： Gilad ALMOGY ,  Kristopher BARBEE ,  Nathan BECKETT

IPC: C12Q1/6874 ,  C12Q1/6809 ,  C12Q1/6825 ,  B01J19/00 ,  B01L3/00

Abstract: Provided are methods for biological sample processing and analysis. A method can comprise providing a substrate configured to rotate. The substrate can comprise an array having immobilized thereto a biological analyte. A solution comprising a plurality of probes 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 can be configured to detect a signal from the at least one probe coupled to the biological analyte, thereby analyzing the biological analyte.

公开(公告)号：US20210040543A1

公开(公告)日：2021-02-11

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.

公开(公告)号：US20210010075A1

公开(公告)日：2021-01-14

申请号：US16925778

申请日：2020-07-10

Applicant: Ultima Genomics, Inc.

Inventor： Florian OBERSTRASS ,  Gilad ALMOGY

IPC: C12Q1/6869

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：US20200216889A1

公开(公告)日：2020-07-09

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：US20190352707A1

公开(公告)日：2019-11-21

申请号：US16358185

申请日：2019-03-19

Applicant: Ultima Genomics, Inc.

Inventor： Gilad ALMOGY ,  Linda LEE

IPC: C12Q1/6869

Abstract: The present disclosure provides methods and systems for determining a nucleic acid sequence of a target nucleic acid molecule. A method for sequencing a target nucleic acid molecule comprises subjecting a plurality of nucleic acid molecules exhibiting sequence homology to the target nucleic acid molecule to at most 4000 cycles a nucleic acid extension reaction while measuring detectable signals from the plurality of nucleic acid molecules. The detectable signals may correspond to individual nucleotides or nucleotide analogs incorporated into the plurality of nucleic acid molecules during the nucleic acid extension reaction. The detectable signals may be used to generate a sequence of the target nucleic acid molecule at a length of at least about 500 bases and an accuracy of at least about 97%.

公开(公告)号：US20250084475A1

公开(公告)日：2025-03-13

申请号：US18828961

申请日：2024-09-09

Applicant: ULTIMA GENOMICS, INC.

Inventor： Florian OBERSTRASS ,  Gilad ALMOGY ,  Ron Saar DOVER ,  Na Kyung LEE ,  Jillynne QUINN

IPC: C12Q1/6874

Abstract: Methods of sequencing and resequencing nucleic acids using incorporation and binding of nucleotides, including terminated nucleotides, are provided. Also provided herein are methods using combinations of terminated nucleotides and non-terminated nucleotides or combinations of terminated nucleotides and non-incorporable nucleotides. These methods allow for determination of the length of homopolymer sequences and increased accuracy of the sequencing reads. The compositions, reagents, and kits for practicing the methods are also provided.

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.