公开(公告)号：US20250051966A1

公开(公告)日：2025-02-13

申请号：US18815653

申请日：2024-08-26

Applicant: ILLUMINA, INC.

Inventor： Frank J. Steemers ,  Fan Zhang ,  Dmitry K. Pokholok ,  Steven Norberg

IPC: C40B50/06 ,  C12Q1/6806 ,  C12Q1/6834

Abstract: Embodiments of systems, methods, and compositions provided herein relate to methods of simultaneously analyzing multiple analytes in a single sample using a single assay. Some embodiments relate to simultaneous analysis of DNA and RNA in a single sample, for example, to the simultaneous generation of DNA and RNA libraries.

公开(公告)号：US20220195504A1

公开(公告)日：2022-06-23

申请号：US17250848

申请日：2019-11-25

Applicant: ILLUMINA, INC.

Inventor： Frank J. Steemers ,  Fan Zhang ,  Dmitry K. Pokholok ,  Steve Norberg

IPC: C12Q1/6834 ,  C12Q1/6806

Abstract: Embodiments of systems, methods, and compositions provided herein relate to methods of simultaneously analyzing multiple analytes in a single sample using a single assay. Some embodiments relate to simultaneous analysis of DNA and RNA in a single sample, for example, to the simultaneous generation of DNA and RNA libraries.

公开(公告)号：US20210332349A1

公开(公告)日：2021-10-28

申请号：US17305230

申请日：2021-07-01

Applicant: Illumina, Inc.

Inventor： Steven Norberg ,  Dmitry Pokholok ,  Ramesh Ramji ,  Frank Steemers ,  Fan Zhang

IPC: C12N15/10 ,  B01L3/00 ,  C40B30/00 ,  C40B60/02 ,  C40B80/00

Abstract: Systems, methods, and compositions provided herein relate to preparation of beads encapsulating biomolecules for performing sequential reactions on the biomolecules. Some embodiments include preparation of nucleic acid reactions within the bead, wherein the bead includes pores that allow diffusion of molecules into or out of the beads while retaining other molecules of interest.

公开(公告)号：US12104281B2

公开(公告)日：2024-10-01

申请号：US17250848

申请日：2019-11-25

Applicant: ILLUMINA, INC.

Inventor： Frank J. Steemers ,  Fan Zhang ,  Dmitry K. Pokholok ,  Steven Norberg

IPC: C40B50/06 ,  C12Q1/6806 ,  C12Q1/6834

CPC classification number: C40B50/06 ,  C12Q1/6806 ,  C12Q1/6834 ,  C12Q2563/179

Abstract: Embodiments of systems, methods, and compositions provided herein relate to methods of simultaneously analyzing multiple analytes in a single sample using a single assay. Some embodiments relate to simultaneous analysis of DNA and RNA in a single sample, for example, to the simultaneous generation of DNA and RNA libraries.

公开(公告)号：US20220333157A1

公开(公告)日：2022-10-20

申请号：US17663485

申请日：2022-05-16

Applicant: ILLUMINA, INC.

Inventor： Frank J. Steemers ,  Ramesh Ramji ,  Steven Norberg ,  Lena Christiansen ,  Dmitry K. Pokholok ,  Fan Zhang

IPC: C12Q1/6806 ,  A61K47/58 ,  A61K47/69 ,  C12M1/12 ,  C12N5/00 ,  C12N5/16

Abstract: Embodiments of systems, methods, and compositions provided herein relate to hollow beads encapsulating single cells. Some embodiments include performing multiple co-assays on a single cell encapsulated within a hollow bead, including nucleic acid sequencing, preparing nucleic acid libraries, determining methylation status, identifying genomic variants, or protein analysis.

公开(公告)号：US20240404624A1

公开(公告)日：2024-12-05

申请号：US18731046

申请日：2024-05-31

Applicant: Illumina, Inc.

Inventor： Fan Zhang ,  Daniel Lee Cameron ,  Michael Ruehle ,  Sean Truong ,  Sujai Chari ,  Arun Subramaniyan ,  John Cooper Roddey

IPC: G16B20/00 ,  G16B30/10 ,  G16B40/20

Abstract: This disclosure describes methods, non-transitory computer-readable media, and systems that can (i) identify reads that align with at least some portion of alternative contiguous sequences representing structural variant haplotypes within a structural variant reference genome and (ii) generate a structural-variant-alignment tag within an alignment file for such read alignments to guide identifying candidate structural-variant locations. In addition to employing structural-variant-alignment tags, the disclosed systems identify read fragments that align or overlap with portions of alternate contiguous sequences representing an insertion (or other structural variant) and further masks such insertion-overlapping read fragments as part of an alignment file. When a read aligns completely within an insertion-representing alternate contiguous sequence, the disclosed system can mark the genomic coordinate corresponding to a primary contiguous sequence at which the insertion alternate contiguous sequence is lifted over and generates an unaligned read base indicator indicating that such an insertion-aligned nucleotide read is masked.

公开(公告)号：US11359226B2

公开(公告)日：2022-06-14

申请号：US16384741

申请日：2019-04-15

Applicant: ILLUMINA, INC.

Inventor： Frank J. Steemers ,  Ramesh Ramji ,  Steven Norberg ,  Lena Christiansen ,  Dmitry K. Pokholok ,  Fan Zhang

IPC: C12Q1/6806 ,  A61K47/58 ,  A61K47/69 ,  C12M1/12 ,  C12N5/00 ,  C12N5/16

Abstract: Embodiments of systems, methods, and compositions provided herein relate to hollow beads encapsulating single cells. Some embodiments include performing multiple co-assays on a single cell encapsulated within a hollow bead, including nucleic acid sequencing, preparing nucleic acid libraries, determining methylation status, identifying genomic variants, or protein analysis.

公开(公告)号：US20190352591A1

公开(公告)日：2019-11-21

申请号：US16384741

申请日：2019-04-15

Applicant: ILLUMINA, INC.

Inventor： Frank J. Steemers ,  Ramesh Ramji ,  Steven Norberg ,  Lena Christiansen ,  Dmitry K. Pokholok ,  Fan Zhang

IPC: C12M1/12 ,  C12N5/16 ,  C12N5/00 ,  A61K47/58 ,  A61K47/69

Abstract: Embodiments of systems, methods, and compositions provided herein relate to hollow beads encapsulating single cells. Some embodiments include performing multiple co-assays on a single cell encapsulated within a hollow bead, including nucleic acid sequencing, preparing nucleic acid libraries, determining methylation status, identifying genomic variants, or protein analysis.

公开(公告)号：US11999945B2

公开(公告)日：2024-06-04

申请号：US17305230

申请日：2021-07-01

Applicant: Illumina, Inc.

Inventor： Steven Norberg ,  Dmitry K. Pokholok ,  Ramesh Ramji ,  Frank J. Steemers ,  Fan Zhang

IPC: C12N15/10 ,  B01L3/00 ,  C40B30/00 ,  C40B60/02 ,  C40B80/00

CPC classification number: C12N15/1006 ,  B01L3/502761 ,  C12N15/1065 ,  C40B30/00 ,  C40B60/02 ,  C40B80/00

Abstract: Systems, methods, and compositions provided herein relate to preparation of beads encapsulating biomolecules for performing sequential reactions on the biomolecules. Some embodiments include preparation of nucleic acid reactions within the bead, wherein the bead includes pores that allow diffusion of molecules into or out of the beads while retaining other molecules of interest.

公开(公告)号：US20210380972A1

公开(公告)日：2021-12-09

申请号：US17344030

申请日：2021-06-10

Applicant: Illumina, Inc. ,  Illumina Cambridge Limited ,  Oregon Health and Science University

Inventor： Andrew C. Adey ,  Ryan Mulqueen ,  Frank Steemers ,  Dmitry K Pokholok ,  Fan Zhang ,  Esther Musgrave-Brown

IPC: C12N15/10 ,  C12Q1/6869 ,  C12Q1/6855

Abstract: The present disclosure is concerned with compositions, methods, and kits for preparing a sequencing library. In one embodiment, methods include producing a library of target nucleic acids having the same adapter at each end and then switching the identity of one adapter to result in target nucleic acids flanked by distinct adapters.