公开(公告)号：US12188924B2

公开(公告)日：2025-01-07

申请号：US18224378

申请日：2023-07-20

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 ,  G01Q10/04 ,  G01N1/22

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：US20240376525A1

公开(公告)日：2024-11-14

申请号：US18763834

申请日：2024-07-03

Applicant: Ultima Genomics, Inc.

Inventor： Xi LONG ,  Florian OBERSTRASS

IPC: C12Q1/6806 ,  C12Q1/6844 ,  C12Q1/6869 ,  C12Q1/6876

Abstract: Provided herein are methods and are methods for preparing nucleic acid molecules for sequencing on a surface using ethylene carbonate. Further described are methods for sequencing said nucleic acid molecules on a surface, using flow sequencing methods.

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：US20240318243A1

公开(公告)日：2024-09-26

申请号：US18435829

申请日：2024-02-07

Applicant: Ultima Genomics, Inc.

Inventor： Florian OBERSTRASS ,  Tyson CLARK ,  Caterina SCHWEIDENBACK ,  Daniel MAZUR

IPC: C12Q1/6869 ,  C12Q1/6844

CPC classification number: C12Q1/6869 ,  C12Q1/6844

Abstract: The present disclosure provides compositions, methods, and systems for preparing nucleic acid samples for sequencing, including attaching adapters to template inserts, attaching template nucleic acid molecules to a support, enrichment. Further provided herein are methods of error correction by preserving both strands of a template nucleic acid molecule during amplification.

公开(公告)号：US20240318169A1

公开(公告)日：2024-09-26

申请号：US18737499

申请日：2024-06-07

Applicant: Ultima Genomics, Inc.

Inventor： Ron Saar Dover ,  Zohar Shipony

IPC: C12N15/10

CPC classification number: C12N15/1065 ,  C12N15/1068

Abstract: Disclosed herein are method for labeling analytes using spatial barcodes, illumination, and/or photolabile cross-linkers. The methods may generate a set of unique spatial barcodes using limited sets differential nucleotide sequences. The labeling may identify a spatial location of an analyte. Also provided herein are compositions, kits, or system for carrying out the methods.

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：US20240249797A1

公开(公告)日：2024-07-25

申请号：US18424587

申请日：2024-01-26

Applicant: Ultima Genomics, Inc.

Inventor： Yoav ETZIONI ,  Edward PERELMAN ,  Asaf HALLE

IPC: G16B30/00 ,  C12Q1/6874 ,  G16B40/20

CPC classification number: G16B30/00 ,  C12Q1/6874 ,  G16B40/20

Abstract: Methods for updating a system comprising a sequencer are described herein. In some exemplary methods, the system is updated through generating sequencing data for a plurality of nucleic acid molecule colonies, selecting sequencing data for a subset of the nucleic acid molecule colonies, calling preliminary sequences for the subset of the nucleic acid colonies, mapping the called preliminary sequences to a known reference sequence, and updating the pre-trained sequencer-specific machine-learning model. Also described herein are systems for carrying out such methods and computer readable memory for storing such methods.

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：US20240018599A1

公开(公告)日：2024-01-18

申请号：US18035075

申请日：2021-11-17

Applicant: Ultima Genomics, Inc.

Inventor： Omer BARAD ,  Itai RUSINEK ,  Ilya SOIFER

IPC: C12Q1/6886 ,  C12Q1/6827

CPC classification number: C12Q1/6886 ,  C12Q1/6827 ,  C12Q2600/112

Abstract: Described herein are methods, devices, and systems for measuring a level, presence, recurrence, progression, or regression of a disease (such as cancer), for example a fraction of nucleic acid molecules (such as cell-free DNA) in a sample from an individual that relate to diseased tissue (such as cancer tissue). The methods include generating, using the sequencing data comprising sequencing reads associated with loci selected from a personalized disease-associated small nucleotide variant panel, a plurality of variant motif-specific models that each associate sequencing data corresponding to a respective variant motif, a background factor indicative of a false positive error rate for the respective variant motif, and an estimated fraction of the nucleic acid molecules associated with the disease. From the plurality of variant motif-specific models, a fraction of the nucleic acid molecules associated with the disease for the individual can be determined.

公开(公告)号：US20230348969A1

公开(公告)日：2023-11-02

申请号：US18132703

申请日：2023-04-10

Applicant: ULTIMA GENOMICS, INC.

Inventor： Mark PRATT ,  Florian OBERSTRASS ,  Linda LEE ,  Steven MENCHEN

IPC: C12Q1/6874

CPC classification number: C12Q1/6874 ,  C12Y207/07007 ,  C12Q2537/157 ,  C12Q2549/10 ,  C12Q2537/155 ,  C12Q2535/113

Abstract: The present disclosure provides methods and systems for processing a nucleotide mixture. A nucleotide mixture can be purified. A nucleotide mixture can be processed for use in nucleic acid synthesis. A nucleotide mixture can be processed for use in nucleic acid sequencing.