公开(公告)号：US12209266B2

公开(公告)日：2025-01-28

申请号：US17317700

申请日：2021-05-11

Applicant: Illumina, Inc. ,  Illumina Singapore Pte. Ltd.

Inventor： Saurabh Rajendra Nirantar ,  Sergio Peisajovich ,  Eric Brustad

IPC: C12N9/12 ,  C12P19/34

Abstract: Disclosed herein include methods of generating a single stranded deoxyribonucleic acid (ssDNA) scaffold comprising nucleotides with modified bases using a recombinant terminal deoxynucleotidyl transferase (TdT). The recombinant TdT can comprise an amino acid sequence that is at least 80% identical to a Bos taurus TdT, or a fragment thereof, and for example comprise one or more amino acid substitution mutations at one or more positions functionally equivalent to Glu191, Lys193, Glu194, Asp242, Lys287, Phe296, Met299, Thr342, and His420 in the Bos taurus TdT.

公开(公告)号：US20250101505A1

公开(公告)日：2025-03-27

申请号：US18894517

申请日：2024-09-24

Applicant: Illumina, Inc.

Inventor： Nam Trong Nguyen ,  Xavier von Hatten ,  Xiangyuan Yang ,  Eric Brustad ,  Will Tovey ,  Matthew Worsdale ,  Gianluca Artioli ,  Teodora Gal

IPC: C12Q1/6853

Abstract: In some examples, a dendritic molecule may include a dendritic core; a seeding primer coupled to the dendritic core; and a plurality of dendrons, each of the dendrons comprising an inert, elongated polymer comprising a first end coupled to the dendritic core and a second end coupled to a first functional group, wherein the first functional group is to react with a second functional group to form a covalent bond. In other examples, a dendritic molecule may include a dendritic core; a single-stranded polynucleotide covalently bonded to the dendritic core; and a plurality of dendrons, each of the dendrons comprising an inert, elongated polymer comprising a first end coupled to the dendritic core and a second end.

公开(公告)号：US20240279733A1

公开(公告)日：2024-08-22

申请号：US18567989

申请日：2022-12-15

Applicant: Illumina, Inc.

Inventor： Fei Shen ,  Mathieu Lessard-Viger ,  Eric Brustad ,  Allison Meade ,  Esteban Armijo ,  Michael Howard ,  Jeffrey Fisher ,  Jonathan Boutell ,  Ramon Saracho ,  Olivia Ghazinejad ,  Seth McDonald ,  Lena Storms ,  Jeffrey Brodin

IPC: C12Q1/6874

CPC classification number: C12Q1/6874

Abstract: The present disclosure is directed to decoupling library capture (template seeding) from cluster generation to optimise both processes. This is achieved by introducing orthogonality between the seeding and clustering primer.

公开(公告)号：US20240182881A1

公开(公告)日：2024-06-06

申请号：US18538262

申请日：2023-12-13

Applicant: ILLUMINA, INC.

Inventor： Dewei Joel Toh ,  Leslie Yee Ming Beh ,  Shu Ting Tan ,  Anna Traczyk ,  Saurabh Nirantar ,  Eric Brustad ,  Hamed Tabatabaei Ghomi ,  Zahra Fahmi ,  Lekha Ravichandraprabhu ,  Colin Brown ,  Kayla Busby ,  Stephen Gross ,  Rebekah Karadeema ,  Huy Lam ,  Pascale Mathonet ,  Sarah E. Shultzaberger ,  Kathleen Tzeng ,  Allison Kathleen Yunghans

IPC: C12N9/78

CPC classification number: C12N9/78 ,  C12Y305/04005

Abstract: The present disclosure is concerned with proteins, methods, compositions, and kits for mapping of methylation status of nucleic acids, including 5-methylcytosine and 5-hydroxymethyl cytosine (5 hmC). In one embodiment, proteins are provided that selectively act on certain modified cytosines of target nucleic acids and converts them to thymidine or modified thymidine analogues. In another embodiment, proteins are provided that selectively act on certain modified cytosines of target nucleic acids and converts them to uracil or thymidine and selectively do not act on other certain modified cytosines of target nucleic acids. Also provided are compositions and kits that include one or more of the proteins and methods for using one or more of the proteins.

公开(公告)号：US20220290234A1

公开(公告)日：2022-09-15

申请号：US17694404

申请日：2022-03-14

Applicant: ILLUMINA, INC. ,  ILLUMINA CAMBRIDGE LIMITED

Inventor： Sarah Shultzaberger ,  Xiaolin Wu ,  Eric Brustad ,  Niall Gormley

IPC: C12Q1/6876 ,  C12Q1/6806 ,  C07H19/16

Abstract: Examples provided herein are related to detecting methylcytosine and its derivatives using S-adenosyl-L-methionine analogs (xSAMs). Compositions and methods for performing such detection are disclosed. A target polynucleotide may include cytosine (C) and methylcytosine (mC). The method may include (a) protecting the C in the target polynucleotide from deamination; and (b) after step (a), deaminating the mC in the target polynucleotide to form thymine (T). Protecting the C from deamination may include adding a protective group to the 5 position of the C, e.g., using a methyltransferase enzyme that adds the first protective group from an xSAM.

公开(公告)号：US20240117426A1

公开(公告)日：2024-04-11

申请号：US18469440

申请日：2023-09-18

Applicant: Illumina, Inc. ,  Illumina Cambridge Limited

Inventor： Nam Nguyen ,  Xavier von Hatten ,  Will Tovey ,  Andrew Brown ,  Wayne George ,  Eric Brustad ,  Gianluca Artioli

IPC: C12Q1/6874 ,  C08F120/06 ,  C08F120/56 ,  C08F120/60 ,  C08F122/38 ,  C08F138/02

CPC classification number: C12Q1/6874 ,  C08F120/06 ,  C08F120/56 ,  C08F120/60 ,  C08F122/385 ,  C08F138/02

Abstract: In some examples, novel nanogel particles are described having dual functionality, temperature responsiveness and pH responsiveness. For nucleic acid sequencing, amplification primers are grafted to nanogel particles to form primer-grafted nanogel particles, and the primer-grafted nanogel particles are captured onto surfaces within a flow cell. Within flow cells such as used in SBS nucleic acid sequencing, each primer-grafted nanogel particle functions as a nano-well in the flow cell, thus eliminating the need for nano-wells in some examples.

公开(公告)号：US20250109428A1

公开(公告)日：2025-04-03

申请号：US18899460

申请日：2024-09-27

Applicant: Illumina, Inc.

Inventor： Olivia Ghazinejad ,  Fei Shen ,  Kyle Bentz ,  Rohit Subramanian ,  Eric Brustad ,  Lena Storms ,  Xiaoyu Ma ,  Mathieu Lessard-Viger ,  Jeffrey Brodin

IPC: C12Q1/6806 ,  B01L3/00 ,  C12Q1/6844

Abstract: In some examples, a hybrid particle for use in capturing a polynucleotide may include a scaffold molecule including a seeding primer and a plurality of first moieties, and a nanoparticle including a plurality of second moieties. The scaffold molecule is coupled to the nanoparticle via interactions between the plurality of first moieties and the plurality of second moieties.

公开(公告)号：US20240271185A1

公开(公告)日：2024-08-15

申请号：US18569192

申请日：2022-08-16

Applicant: Illumina, Inc.

Inventor： Colin Brown ,  Xiaohai Liu ,  Xiaolin Wu ,  Eric Brustad ,  Sarah E. Shultzaberger

IPC: C12Q1/6806 ,  C12Q1/26 ,  C12Q1/6869

CPC classification number: C12Q1/6806 ,  C12Q1/26 ,  C12Q1/6869

Abstract: Disclosed herein include methods, compositions, reaction mixtures, kits and systems for identification of methylated cytosines in nucleic acids using a bisulfite-free, one-step chemoenzymatic modification of methylated cytosines.

公开(公告)号：US20210355518A1

公开(公告)日：2021-11-18

申请号：US17317700

申请日：2021-05-11

Applicant: Illumina, Inc. ,  Illumina Singapore Pte. Ltd.

Inventor： Saurabh Rajendra Nirantar ,  Sergio Peisajovich ,  Eric Brustad

IPC: C12P19/34

Abstract: Disclosed herein include methods of generating a single stranded deoxyribonucleic acid (ssDNA) scaffold comprising nucleotides with modified bases using a recombinant terminal deoxynucleotidyl transferase (TdT). The recombinant TdT can comprise an amino acid sequence that is at least 80% identical to a Bos taurus TdT, or a fragment thereof, and for example comprise one or more amino acid substitution mutations at one or more positions functionally equivalent to Glu191, Lys193, Glu194, Asp242, Lys287, Phe296, Met299, Thr342, and His420 in the Bos taurus TdT.