公开(公告)号：US20240360505A1

公开(公告)日：2024-10-31

申请号：US18650407

申请日：2024-04-30

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

CPC classification number: C12Q1/6874 ,  G01N35/1002

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：US20240263216A1

公开(公告)日：2024-08-08

申请号：US18410793

申请日：2024-01-11

Applicant: Ultima Genomics, Inc.

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

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

CPC classification number: C12Q1/6823 ,  C12Q1/6869 ,  C12Q1/6876

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：US20240226900A1

公开(公告)日：2024-07-11

申请号：US18391291

申请日：2023-12-20

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 ,  C12Q1/686

CPC classification number: B01L7/52 ,  B01L3/508 ,  B01L2200/0647 ,  B01L2300/1805 ,  B01L2400/0415 ,  C12Q1/686

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：US20230313289A1

公开(公告)日：2023-10-05

申请号：US18076214

申请日：2022-12-06

Applicant: Ultima Genomics, Inc.

Inventor： Florian OBERSTRASS ,  Gilad ALMOGY

IPC: C12Q1/6869 ,  C12Q1/6874 ,  C12N15/10

CPC classification number: C12Q1/6869 ,  C12N15/1096 ,  C12Q1/6874 ,  C12Q2525/161 ,  C12Q2525/173 ,  C12Q2525/191 ,  C12Q2563/179 ,  C12Q2563/185 ,  C12Q2600/178 ,  C12Y207/07049

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：US20230022124A1

公开(公告)日：2023-01-26

申请号：US17713934

申请日：2022-04-05

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：US20210147931A1

公开(公告)日：2021-05-20

申请号：US17158960

申请日：2021-01-26

Applicant: Ultima Genomics, Inc.

Inventor： Florian OBERSTRASS ,  Gilad ALMOGY

IPC: C12Q1/6874 ,  C12N15/10

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：US20210079464A1

公开(公告)日：2021-03-18

申请号：US16953071

申请日：2020-11-19

Applicant: Ultima Genomics, Inc.

Inventor： Nathan BECKETT ,  Gilad ALMOGY ,  Nathan CASWELL ,  Jacob A. WOLF ,  Kristopher BARBEE ,  Denis PRINTINSKI ,  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：US20200318170A1

公开(公告)日：2020-10-08

申请号：US16822121

申请日：2020-03-18

Applicant: Ultima Genomics, Inc.

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

IPC: C12Q1/6823 ,  C12Q1/6869 ,  C12Q1/6806 ,  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：US20200291469A1

公开(公告)日：2020-09-17

申请号：US16445798

申请日：2019-06-19

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：US20240309445A1

公开(公告)日：2024-09-19

申请号：US18281930

申请日：2022-03-22

Applicant: Ultima Genomics, Inc.

Inventor： Florian OBERSTRASS ,  Gilad ALMOGY

IPC: C12Q1/6874 ,  C12N15/10

CPC classification number: C12Q1/6874 ,  C12N15/1065

Abstract: Methods for determining a sequence of a polynucleotide comprising two or more barcode regions and an intervening region thereof are described herein. Flow sequencing methods can be used to sequence the barcode regions by extending a sequencing primer in a plurality of discrete flow steps, which include combining a primer/polynucleotide hybrid with a nucleotide that is incorporated into the extending primer if a complementary base in the poly nucleotide is present at the primer terminus. For one or more regions in the polynucleotide (e.g., barcode regions, a region of interest in the polynucleotide), the presence or absence of an incorporated nucleotide is detected (e.g., the sequence is determined for the said regions). For one or more regions in the polynucleotide (e.g., intervening regions), the primer can be extended without detecting the presence or absence of an incorporated nucleotide (e.g., the sequence is not determined), thereby increasing efficiency of the primer extension.