公开(公告)号：US10267790B1

公开(公告)日：2019-04-23

申请号：US15974441

申请日：2018-05-08

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: G01N33/543 ,  C12Q1/6874 ,  C12Q1/6809 ,  C12Q1/6825 ,  B01L3/00 ,  B01J19/00

Abstract: Provided are systems for biological sample processing and analysis. A system can comprise a substrate configured to rotate. The substrate can comprise an array configured to immobilize a biological analyte. A fluid flow unit comprising a fluid channel can be configured to dispense a solution comprising a plurality of probes. The solution 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 in optical communication with the array can be configured to detect one or more signals from the at least one probe coupled to the biological analyte.

公开(公告)号：US20250027154A1

公开(公告)日：2025-01-23

申请号：US18803028

申请日：2024-08-13

Applicant: ULTIMA GENOMICS, INC.

Inventor： Zohar SHIPONY ,  Florian OBERSTRASS ,  Doron LIPSON ,  Eti MEIRI ,  Tommie Lloyd LINCECUM, JR. ,  Daniel MAZUR ,  Omer BARAD

IPC: C12Q1/6876 ,  C12Q1/6869

Abstract: Nucleic acid molecule constructs, methods of making such construct, and methods of sequencing using such constructs are described herein. The nucleic acid molecule constructs can include a template sequence and a copy of the template sequence, along with a sequencing primer region associated with the template sequence and a copy of the sequencing primer region associated with the copy of the template sequence, which allows the template sequence and the copy of the template sequence to be simultaneously sequenced. Also described are methods of using the nucleic acid molecule constructs for methylation sequencing.

公开(公告)号：US20240417718A1

公开(公告)日：2024-12-19

申请号：US18745437

申请日：2024-06-17

Applicant: Ultima Genomics, Inc.

Inventor： Tyson CLARK ,  Tommie Lloyd LINCECUM, JR. ,  Daniel MAZUR

IPC: C12N15/10

Abstract: Provided herein are systems, methods, compositions, and kits for library preparation. In some cases, multiple distinct types of adapter molecules may be provided to a template nucleic acid molecule. In some cases, a single type of adapter molecule may be provided to a template molecule. In some cases, multiple distinct types of adapter molecules may be sequentially provided to a template molecule to form multi-adapter template complexes.

公开(公告)号：US20240401130A1

公开(公告)日：2024-12-05

申请号：US18738596

申请日：2024-06-10

Applicant: Ultima Genomics, Inc.

Inventor： Florian OBERSTRASS ,  Daniel MAZUR

IPC: C12Q1/6874 ,  C12Q1/44 ,  C12Q1/6876

Abstract: Provided herein are systems, methods, compositions, and kits for sequencing with multi-priming. In some cases, multiple distinct primer molecules may be provided to a template nucleic acid to hybridize to distinct regions of the template nucleic acid. In some cases, a connected primer molecule may be provided to a template nucleic acid to have multiple distinct primer regions hybridize to distinct regions of the template nucleic acid. Non-adjacent regions of the template nucleic acid may be sequenced in distinct sequencing operations.

公开(公告)号：US12152277B2

公开(公告)日：2024-11-26

申请号：US18132693

申请日：2023-04-10

Applicant: ULTIMA GENOMICS, INC.

Inventor： Gilad Almogy ,  Mark Pratt ,  Florian Oberstrass

IPC: C12Q1/68 ,  C12Q1/6806 ,  C12Q1/6869

Abstract: Recognized herein is the need for methods and processes for increasing the efficiency and accuracy of paired end sequencing.

公开(公告)号：US12119087B2

公开(公告)日：2024-10-15

申请号：US17574260

申请日：2022-01-12

Applicant: ULTIMA GENOMICS, INC.

Inventor： Mark Pratt ,  Gilad Almogy ,  Avishai Bartov

IPC: G16B40/10 ,  C12Q1/6806 ,  C12Q1/6869 ,  G16B30/10 ,  G16B45/00

CPC classification number: G16B40/10 ,  C12Q1/6806 ,  C12Q1/6869 ,  G16B30/10 ,  G16B45/00

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：US20240326090A1

公开(公告)日：2024-10-03

申请号：US18608317

申请日：2024-03-18

Applicant: Ultima Genomics, Inc.

Inventor： William SCHULKINS ,  Angela STERN ,  Florian OBERSTRASS

IPC: B05D1/00 ,  B05D1/32

CPC classification number: B05D1/60 ,  B05D1/32

Abstract: Provided herein are systems and methods for functionalizing a substrate. The method may comprise providing a substrate surface, wherein the substrate surface comprises a plurality of individually addressable locations, and exposing the substrate surface to a dose of organosilane vapor to generate a plurality of organosilane-functionalized locations on the substrate surface, wherein the plurality of organosilane-functionalized locations corresponds to at least a subset of the plurality of individually addressable locations. The dose of organosilane vapor may be provided at relatively low dose, in an example, at most about 1×1024 molecules per m2.

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.

公开(公告)号：US20240274237A1

公开(公告)日：2024-08-15

申请号：US18410051

申请日：2024-01-11

Applicant: ULTIMA GENOMICS, INC.

Inventor： Yoav ETZIONI ,  Omer BARAD ,  Florian OBERSTRASS ,  Edward PERELMAN ,  Mark GESHEL

IPC: G16B30/00 ,  G16B45/00

CPC classification number: G16B30/00 ,  C12Q1/6876 ,  G16B45/00 ,  C12Q1/6869 ,  G16B35/00

Abstract: Provided herein are methods, systems, and compositions for generating and selecting barcode sequences. A method for selecting barcode sequences may comprise generating a set of sequence data for the barcode sequences and filtering the data using one or more criteria or filters to provide a filtered set of barcode sequences. The resultant filtered set of barcode sequences may satisfy one or more selection criteria and may be sufficiently diverse from one another.

公开(公告)号：US20240257906A1

公开(公告)日：2024-08-01

申请号：US18617448

申请日：2024-03-26

Applicant: Ultima Genomics, Inc.

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

IPC: G16B20/20 ,  C12Q1/6874 ,  G06F17/00 ,  G16B20/00 ,  G16B30/00 ,  G16B30/10 ,  G01N21/64

CPC classification number: G16B20/20 ,  C12Q1/6874 ,  G06F17/00 ,  G16B20/00 ,  G16B30/00 ,  G16B30/10 ,  C12Q2600/156 ,  C12Q2600/158 ,  G01N2021/6439

Abstract: Methods for detecting a short genetic variant in a test sample are described herein. In some exemplary methods, the short genetic variant is called using one or match scores, which are determined using one or more sequencing data sets obtained from a test nucleic acid molecule, wherein the test sequencing data sets are determined by sequencing the test nucleic acid molecule using non-terminating nucleotides provided in separate nucleotide flows according to a flow-cycle order. Also described herein are methods of sequencing a test nucleic acid molecule using two or more different flow-cycle orders and/or extended flow cycle orders having five or more nucleotide flows per flow cycle.