公开(公告)号：US20250101533A1

公开(公告)日：2025-03-27

申请号：US18910965

申请日：2024-10-09

Applicant: Ultima Genomics, Inc.

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

IPC: C12Q1/6886 ,  C12Q1/6809 ,  C12Q1/6869 ,  G06F17/18 ,  G16B20/00

Abstract: Described herein are methods, devices, and systems for measuring a level 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). Also described are methods, devices, and systems for measuring a presence, recurrence, progression, or regression of the disease in the individual. Certain methods include comparing, using nucleic acid sequencing data associated with the individual, a signal indicative of a rate at which sequenced loci selected from a personalized disease-associated small nucleotide variant (SNV) locus panel are derived from a diseased tissue to a background factor indicative of a sequencing false positive error rate, or a noise factor indicative of a sampling variance, across the selected loci.

公开(公告)号：US20240167080A1

公开(公告)日：2024-05-23

申请号：US18535267

申请日：2023-12-11

Applicant: ULTIMA GENOMICS, INC.

Inventor： Eliane TREPAGNIER ,  Mark PRATT ,  Theo NIKIFOROV ,  Gilad ALMOGY

IPC: C12Q1/6818 ,  C12Q1/6869

CPC classification number: 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：US20240027425A1

公开(公告)日：2024-01-25

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

CPC classification number: G01N33/492 ,  G01N1/02 ,  G01Q10/04 ,  G01N2001/2291

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：US20230332226A1

公开(公告)日：2023-10-19

申请号：US18176418

申请日：2023-02-28

Applicant: Ultima Genomics, Inc.

Inventor： Florian OBERSTRASS ,  Theo NIKIFOROV ,  Mark STAPLETON ,  Daniel MAZUR ,  Gilad ALMOGY ,  Ishminder MANN ,  Chandan SHEE ,  Benjamin SCHROEDER

IPC: C12Q1/6874 ,  C12Q1/6855

CPC classification number: C12Q1/6874 ,  C12Q1/6855

Abstract: The present disclosure provides compositions, methods, and systems for enrichment and analysis of template nucleic acid molecules, e.g., of a biological sample. Further provided herein are methods of using a plurality of unique bead species each comprising a unique set of identical primer molecules.

公开(公告)号：US20230279487A1

公开(公告)日：2023-09-07

申请号：US18124481

申请日：2023-03-21

Applicant: Ultima Genomics, Inc.

Inventor： Gilad ALMOGY ,  Nathan BECKETT ,  Mark PRATT ,  Anatoly A. SURDUTOVICH ,  Nathan CASWELL ,  Patrick D. KINNEY

IPC: C12Q1/6869 ,  B01L3/00 ,  G01N35/10

CPC classification number: C12Q1/6869 ,  B01L3/5085 ,  G01N35/1002 ,  B01L2200/16 ,  B01L2300/023

Abstract: Provided herein methods, systems, and apparatus for high throughput sequencing, such as at an industrial scale. A sequencing system and/or apparatus may comprise one or more stations that can be operated in parallel and/or independent of one or more other stations.

公开(公告)号：US20230183778A1

公开(公告)日：2023-06-15

申请号：US17985542

申请日：2022-11-11

Applicant: ULTIMA GENOMICS, INC.

Inventor： Eliane TREPAGNIER ,  Mark PRATT ,  Theo NIKIFOROV ,  Gilad ALMOGY

IPC: C12Q1/6818 ,  C12Q1/6869

CPC classification number: 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：US20220282309A1

公开(公告)日：2022-09-08

申请号：US17697636

申请日：2022-03-17

Applicant: Ultima Genomics, Inc.

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

IPC: 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：US20220162590A1

公开(公告)日：2022-05-26

申请号：US17546978

申请日：2021-12-09

Applicant: Ultima Genomics, Inc.

Inventor： Gilad ALMOGY ,  Eyal NEISTEIN ,  Mark PRATT

IPC: C12N15/10 ,  G16B20/20 ,  G16B40/20 ,  C12Q1/6869

Abstract: The present disclosure provides methods for accurate base calling of sequences using molecular barcodes. A method for sequencing nucleic acid molecules may comprise: (a) using barcode molecules to barcode nucleic acid molecules from a sample, to generate barcoded nucleic acid molecules comprising barcode sequences; (b) sequencing the barcoded nucleic acid molecules to generate sequencing signals comprising signals corresponding to the barcode sequences, wherein the sequencing signals are not sequencing reads; (c) using the signals corresponding to the barcode sequences to group the sequencing signals into groups, wherein sequencing signals of a given group comprise signals corresponding to a barcode sequence that is (i) identical for the given group and (ii) different from barcode sequences of other groups; (d) processing the sequencing signals within the given group to generate sets of aggregated signals which are not sequencing reads; and (e) combining the sets of aggregated signals to generate a consensus sequence.

公开(公告)号：US20210199647A1

公开(公告)日：2021-07-01

申请号：US17181378

申请日：2021-02-22

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: G01N33/53 ,  B82Y5/00

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：US20210142869A1

公开(公告)日：2021-05-13

申请号：US17090176

申请日：2020-11-05

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.