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：US20240026348A1

公开(公告)日：2024-01-25

申请号：US18476719

申请日：2023-09-28

Applicant: Illumina, Inc. ,  Illumina Cambridge Limited

Inventor： Susan C. Verity ,  Robert Scott Kuersten ,  Niall Anthony Gormley ,  Andrew B. Kennedy ,  Sarah E. Shultzaberger ,  Andrew Slatter ,  Emma Bell ,  Sebastien Georg Gabriel Ricoult ,  Grace DeSantis ,  Fiona Kaper ,  Han-Yu Chuang ,  Oliver Jon Miller ,  Jason Richard Betley ,  Stephen M. Gross ,  Mats Ekstrand

IPC: C12N15/10

CPC classification number: C12N15/1065 ,  C12N15/1068

Abstract: Materials and methods for preparing nucleic acid libraries for next-generation sequencing are described herein. A variety of approaches are described relating to the use of unique molecular identifiers with transposon-based technology in the preparation of sequencing libraries. Also described herein are sequencing materials and methods for identifying and correcting amplification and sequencing errors.

公开(公告)号：US20230392207A1

公开(公告)日：2023-12-07

申请号：US18203734

申请日：2023-05-31

Applicant: ILLUMINA, INC.

Inventor： Sarah E. Shultzaberger ,  Suzanne Rohrback ,  Carlo Randise-Hinchliff

IPC: C12Q1/6883 ,  C12Q1/6806

CPC classification number: C12Q1/6883 ,  C12Q1/6806 ,  C12Q2600/158

Abstract: The present invention includes methods and materials for use in the detection preeclampsia and/or determining an increased risk for preeclampsia in a pregnant female, the method including identifying in a biosample obtained from the pregnant women circulating RNA (C-RNA) molecules associated with preeclampsia.

公开(公告)号：US20210155987A1

公开(公告)日：2021-05-27

申请号：US16953480

申请日：2020-11-20

Applicant: ILLUMINA, INC.

Inventor： Sarah E. Shultzaberger ,  Fiona Kaper ,  Sarah Kinnings ,  Suzanne Rohrback ,  Carlo Randise-Hinchliff

IPC: C12Q1/6883 ,  C12N15/10

Abstract: The present invention includes methods and materials for use in the detection preeclampsia and/or determining an increased risk for preeclampsia in a pregnant female, the method including identifying in a biosample obtained from the pregnant women a plurality of circulating RNA (C-RNA) molecules.

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：US11753685B2

公开(公告)日：2023-09-12

申请号：US16953480

申请日：2020-11-20

Applicant: ILLUMINA, INC.

Inventor： Sarah E. Shultzaberger ,  Fiona Kaper ,  Sarah Kinnings ,  Suzanne Rohrback ,  Carlo Randise-Hinchliff

IPC: C12Q1/68 ,  C12P19/34 ,  C12Q1/6883 ,  C12N15/10

CPC classification number: C12Q1/6883 ,  C12N15/1096 ,  C12Q2600/118 ,  C12Q2600/158

Abstract: The present invention includes methods and materials for use in the detection preeclampsia and/or determining an increased risk for preeclampsia in a pregnant female, the method including identifying in a biosample obtained from the pregnant women a plurality of circulating RNA (C-RNA) molecules.

公开(公告)号：US20230183682A1

公开(公告)日：2023-06-15

申请号：US18163405

申请日：2023-02-02

Applicant: Illumina, Inc. ,  Illumina Cambridge Limited

Inventor： Niall Anthony Gormley ,  Andrew B. Kennedy ,  Robert Scott Kuersten ,  Gary Schroth ,  Carlo Randise-Hinchliff ,  Sarah E. Shultzaberger ,  Fiona Kaper ,  Yir-Shyuan Wu ,  Tarun Khurana ,  Foad Mashayekhi

IPC: C12N15/10

CPC classification number: C12N15/1065

Abstract: This application describes methods of preparing an immobilized library of tagged RNA fragments. Also described herein are a number of methods of preparing DNA and RNA sequencing libraries from a single sample. These methods can include library preparation from single cells.

公开(公告)号：US20240271126A1

公开(公告)日：2024-08-15

申请号：US18562095

申请日：2022-05-26

Applicant: ILLUMINA, INC.

Inventor： Niall Anthony Gormley ,  Carlo Randise-Hinchliff ,  Jeffrey Brodin ,  Esther Musgrave-Brown ,  Sarah E. Shultzaberger ,  Andrew Slatter ,  Jeffrey S. Fisher

IPC: C12N15/10 ,  C12N15/11 ,  C12Q1/48

CPC classification number: C12N15/1096 ,  C12N15/11 ,  C12Q1/485

Abstract: Nucleic acid techniques are disclosed. Embodiments include modified nucleotides with oligonucleotide adapters that are coupled via cleavable linkers. Incorporation of the modified nucleotide at a 3′ end of a nucleic acid permits end-adapterization via ligation of a free 5′ end of the oligonucleotide adapter to a 3′ reactive group of the modified nucleotide and cleavage at the cleavable linker to liberate a free 3′ end.

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：US20230135486A1

公开(公告)日：2023-05-04

申请号：US18091186

申请日：2022-12-29

Applicant: ILLUMINA, INC.

Inventor： Sarah E. Shultzaberger ,  Fiona Kaper ,  Sarah Kinnings ,  Suzanne Rohrback ,  Carlo Randise-Hinchliff

IPC: C12Q1/6883 ,  C12N15/10

Abstract: The present invention includes methods and materials for use in the detection preeclampsia and/or determining an increased risk for preeclampsia in a pregnant female, the method including identifying in a biosample obtained from the pregnant women a plurality of circulating RNA (C-RNA) molecules.