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：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：US20240191288A1

公开(公告)日：2024-06-13

申请号：US18285222

申请日：2022-03-30

Applicant: Illumina, Inc.

Inventor： Colin Brown ,  Sarah Shultzaberger ,  Stephen M. Gross ,  Angelica Barr ,  Samantha Snow

IPC: C12Q1/6848 ,  C12Q1/48 ,  C12Q1/6855

CPC classification number: C12Q1/6848 ,  C12Q1/485 ,  C12Q1/6855

Abstract: The disclosure relates to methods, compositions, and kits for the selective depletion of non-desirable fragments from amplified libraries using blocking oligonucleotides.

公开(公告)号：US20240127906A1

公开(公告)日：2024-04-18

申请号：US18484268

申请日：2023-10-10

Applicant: Illumina, Inc. ,  Illumina Cambridge Limited ,  Illumina Singapore PTE. LTD.

Inventor： Qi Wang ,  Suzanne Rohrback ,  Sarah Shultzaberger ,  Rebekah Karadeema ,  Leslie Beh Yee Ming ,  James Baye ,  Colin Brown

IPC: G16B30/10 ,  G16B20/20

CPC classification number: G16B30/10 ,  G16B20/20

Abstract: This disclosure describes methods, non-transitory computer readable media, and systems that can use a computationally efficient model to determine a corrected methylation-level value for a specific sample nucleotide sequence. For instance, the disclosed systems determine a false positive rate and a false negative rate at which a given methylation sequencing assay converts cytosine bases. Based on the determined false positive rate and false negative rate, the disclosed systems determine a corrected methylation-level value that corrects for a bias of the given methylation sequencing assay.

公开(公告)号：US20230313271A1

公开(公告)日：2023-10-05

申请号：US18172821

申请日：2023-02-22

Applicant: Illumina, Inc. ,  Illumina Cambridge Limited

Inventor： Steven Norberg ,  Luis Fernando Camarillo Guerrero ,  Colin Brown ,  Andrea Manzo ,  Sarah E. Shultzaberger ,  Michael Eberle ,  Sepideh Almasi ,  Suzanne Rohrback ,  Pascale Mathonet ,  Egor Dolzhenko

IPC: C12Q1/6809 ,  G16C20/70

CPC classification number: C12Q1/6809 ,  G16C20/70

Abstract: This disclosure describes methods, non-transitory computer readable media, and systems that can use a machine-learning to determine factors or scores indicating an error level with which a given methylation assay detects methylation of cytosine bases. For instance, the disclosed systems use a machine-learning model to generate a bias score indicating a degree to which a given methylation assay errs in detecting cytosine methylation when specific sequence contexts surround such cytosines compared to other sequence contexts. The machine-learning model may take various forms of models, including a decision-tree model, a neural network, or a combination of a decision-tree model and a neural network. In some cases, the disclosed system combines or uses bias scores from multiple machine-learning models to generate a consensus bias score.

公开(公告)号：US20240287505A1

公开(公告)日：2024-08-29

申请号：US18567697

申请日：2022-06-23

Applicant: Illumina, Inc.

Inventor： Andrea Manzo ,  Colin Brown ,  Steven Norberg ,  Timothy Harrington

IPC: C12N15/10 ,  C12Q1/6834

CPC classification number: C12N15/1065 ,  C12Q1/6834

Abstract: Some embodiments relate to methods and compositions for preparing combinatorially indexed beads. Some embodiments include sequential addition of different indexes to polynucleotides attached to beads. In some embodiments, indexes are added by chemical ligation, polymerase extension, ligation of partially double-stranded adaptors, or short splint ligation.