公开(公告)号：US11143638B2

公开(公告)日：2021-10-12

申请号：US17254466

申请日：2020-05-26

Applicant: ILLUMINA, INC.

Inventor： Tarun Khurana ,  Ali Agah ,  Aathavan Karunakaran ,  Stanley Hong ,  Merek Siu ,  Arvin Emadi ,  Craig Ciesla

IPC: G01N30/74 ,  C12Q1/6874

Abstract: An apparatus includes a flow cell body, a plurality of electrodes, an imaging assembly, and one or more barrier features. The flow cell body defines one or more flow channels and a plurality of wells defined as recesses in the floor of each flow channel. Each well is fluidically coupled with the corresponding flow channel. The flow cell body further defines interstitial surfaces between adjacent wells. Each well defines a corresponding depth. Each electrode is positioned in a corresponding well of the plurality of wells. The electrodes are to effect writing of polynucleotides in the wells. The imaging assembly is to capture images of polynucleotides written in the wells. The one or more barrier features are positioned in the wells, between the wells, or above the wells. The one or more barrier features contain reactions in each well, reduce diffusion between the wells, or reduce optical cross-talk between the wells.

公开(公告)号：US20210151129A1

公开(公告)日：2021-05-20

申请号：US17254459

申请日：2020-05-26

Applicant: ILLUMINA, INC.

Inventor： Craig Ciesla ,  Ali Agah ,  Stanley Hong ,  Tarun Khurana ,  Aathavan Karunakaran ,  Arvin Emadi ,  Merek Siu

IPC: G16B50/30 ,  G06F3/06 ,  G16B30/10 ,  C12Q1/6869

Abstract: A system writes input data to a storage device as machine-written polynucleotides; and reads machine written polynucleotides from the storage device as output data. The storage device includes a flow cell including a plurality of storage wells in which machine written polynucleotides may be stored. The storage device may include a set of electrodes corresponding to the storage wells that allow for selective interactions with wells across the surface of a flow cell. Operation of the storage device may include receiving a read request associated with a particular location in the storage device, creating a copy of a nucleotide sequence located at the particular location in the storage device, transferring the copy of the nucleotide sequence to a read location, and reading the copy of the nucleotide sequence at the read location.

公开(公告)号：US20210147833A1

公开(公告)日：2021-05-20

申请号：US17254470

申请日：2020-05-26

Applicant: ILLUMINA, INC.

Inventor： Yir-Shyuan Wu ,  Amirali Kia ,  Tarun Khurana ,  Ali Agah ,  Aathavan Karunakaran ,  Xi-Jun Chen

IPC: C12N15/10 ,  C12Q1/6874

Abstract: A method includes grafting oligonucleotides to a flow cell and preparing a library of polynucleotides. Each polynucleotide has been written to contain retrievable information and includes a region complementary to one of the sequencing initiation primers grafted to the flow cell. Each polynucleotide is indexed to permit discrete identification of that polynucleotide and the information it contains over other polynucleotides in the library. Another method includes writing two polynucleotides including two sequences with reverse complementary joining sequences onto a flow cell. One of the polynucleotides is extended to generate a third polynucleotide comprising a sequence that is the combination of the first and second sequences. A fourth polynucleotide is written with a third joining sequence of a fourth sequence. The third joining sequence is a reverse complement of a portion of the third polynucleotide comprising the third sequence and forming a second joining bridge between the third and fourth polynucleotides.

公开(公告)号：US20240301464A1

公开(公告)日：2024-09-12

申请号：US18414085

申请日：2024-01-16

Applicant: Illumina, Inc.

Inventor： Aathavan Karunakaran ,  Shagesh Sridharan ,  Jonathan Mark Boutell ,  Gery M. Vessere

IPC: C12Q1/6806 ,  C12Q1/6869

CPC classification number: C12Q1/6806 ,  C12Q1/6869

Abstract: The invention relates to methods of detecting modified cytosines in nucleic acid sequences.

公开(公告)号：US12062419B2

公开(公告)日：2024-08-13

申请号：US17683426

申请日：2022-03-01

Applicant: ILLUMINA, INC.

Inventor： Craig Ciesla ,  Ali Agah ,  Stanley Hong ,  Tarun Khurana ,  Aathavan Karunakaran ,  Arvin Emadi ,  Merek Siu

IPC: G16B50/30 ,  B01L3/00 ,  G11C13/02 ,  G16B30/10 ,  C12Q1/6874

CPC classification number: G16B50/30 ,  B01L3/5027 ,  G11C13/02 ,  G16B30/10 ,  C12Q1/6874

Abstract: A system writes input data to a storage device as machine-written polynucleotides; and reads machine written polynucleotides from the storage device as output data. The storage device includes a flow cell including a plurality of storage wells in which machine written polynucleotides may be stored. The storage device may include a set of electrodes corresponding to the storage wells that allow for selective interactions with wells across the surface of a flow cell. Operation of the storage device may include receiving a read request associated with a particular location in the storage device, creating a copy of a nucleotide sequence located at the particular location in the storage device, transferring the copy of the nucleotide sequence to a read location, and reading the copy of the nucleotide sequence at the read location.

公开(公告)号：US20240177807A1

公开(公告)日：2024-05-30

申请号：US18468333

申请日：2023-09-15

Applicant: Illumina, Inc.

Inventor： John S. Vieceli ,  Eric Jon Ojard ,  Aathavan Karunakaran ,  David Olmstead Bracher ,  Gery Vessere

IPC: G16B40/00 ,  G16B30/00

CPC classification number: G16B40/00 ,  G16B30/00

Abstract: The technology disclosed is directed to cluster segmentation and base calling. The technology disclosed describes a computer-implemented method including segmenting a population of clusters into a plurality of subpopulations of clusters based on one or more prior bases called at one or more prior sequencing cycles of a sequencing run. At a current sequencing cycle of the sequencing run, the method includes applying a mixture of four distributions to current sequenced data of each subpopulation of clusters in the plurality of subpopulations of clusters, the four distributions corresponding to four bases adenine (A), cytosine (C), guanine (G), and thymine (T), and the current sequenced data being generated at the current sequencing cycle. The method further includes base calling clusters in a particular subpopulation of clusters using a corresponding mixture of four distributions.

公开(公告)号：US20230260096A1

公开(公告)日：2023-08-17

申请号：US18111281

申请日：2023-02-17

Applicant: Illumina, Inc. ,  Illumina Software, Inc.

Inventor： Simon Prince ,  Stanley Hong ,  Michael Gallaspy ,  Merek Siu ,  Jeffrey Gau ,  Anindita Dutta ,  Aathavan Karunakaran ,  Yina Wang ,  Rishi Verma

IPC: G06T5/50 ,  G06T5/20 ,  G06T5/00 ,  G06T7/00 ,  G16B30/00 ,  G16B40/20 ,  G16B40/10

CPC classification number: G06T5/50 ,  G06T5/20 ,  G06T5/003 ,  G06T7/0002 ,  G16B30/00 ,  G16B40/20 ,  G16B40/10 ,  G06T2207/20081 ,  G06T2207/20084 ,  G06T2207/30168 ,  G06T2207/30004 ,  G06T2207/10016 ,  G06T2207/10064

Abstract: Artificial intelligence driven enhancement of motion blurred sequencing images enables enhanced sequencing that determines a sequence of bases in genetic material with any one or more of: improved performance, improved accuracy, and/or reduced cost. A training set of images taken after unreduced and reduced movement settling times during sequencing is used to train a neural network to enable the neural network to recover enhanced images, as if taken after the unreduced movement settling time, from unenhanced images taken after the reduced movement settling time.

公开(公告)号：US20230183799A1

公开(公告)日：2023-06-15

申请号：US18063581

申请日：2022-12-08

Applicant: Illumina, Inc.

Inventor： Shaun E. Hunter ,  Paul Sangiorgio ,  Aathavan Karunakaran ,  David Bracher

IPC: C12Q1/6874

CPC classification number: C12Q1/6874 ,  C12Q1/6806

Abstract: Systems and methods of identifying nucleobases in a template polynucleotide are disclosed. In one embodiment, such a method may include providing a substrate comprising a plurality of the template polynucleotides in a cluster. The method may further include generating light to stimulate fluorescent emissions from the cluster. The method may further include receiving a first signal emitted at a first intensity from a first plurality of nucleotide analogs hybridized to the plurality of template polynucleotides at a first site. The method may further include receiving a second signal emitted at a second intensity from a second plurality of nucleotide analogs hybridized to the plurality of template polynucleotides at a second site. The method may further include identifying the nucleobases hybridized at the first and second sites of the template polynucleotide based on a combination of the first and second signals.

公开(公告)号：US20220254452A1

公开(公告)日：2022-08-11

申请号：US17683426

申请日：2022-03-01

Applicant: ILLUMINA, INC.

Inventor： Craig Ciesla ,  Ali Agah ,  Stanley Hong ,  Tarun Khurana ,  Aathavan Karunakaran ,  Arvin Emadi ,  Merek Siu

IPC: G16B50/30 ,  G16B30/10 ,  G11C13/02 ,  B01L3/00

Abstract: A system writes input data to a storage device as machine-written polynucleotides; and reads machine written polynucleotides from the storage device as output data. The storage device includes a flow cell including a plurality of storage wells in which machine written polynucleotides may be stored. The storage device may include a set of electrodes corresponding to the storage wells that allow for selective interactions with wells across the surface of a flow cell. Operation of the storage device may include receiving a read request associated with a particular location in the storage device, creating a copy of a nucleotide sequence located at the particular location in the storage device, transferring the copy of the nucleotide sequence to a read location, and reading the copy of the nucleotide sequence at the read location.

公开(公告)号：US20220097060A1

公开(公告)日：2022-03-31

申请号：US17550063

申请日：2021-12-14

Applicant: ILLUMINA, INC.

Inventor： Ali Agah ,  Aathavan Karunakaran ,  Tarun Khurana ,  Stanley Hong ,  Merek Siu ,  Arvin Emadi ,  Craig Ciesla

IPC: B01L3/00 ,  G11C13/02 ,  B01J19/00

Abstract: An apparatus includes a flow cell body, a plurality of electrodes, an integrated circuit, and an imaging assembly. The flow cell body defines one or more flow channels and a plurality of wells. Each flow channel is configured to receive a flow of fluid. Each well is fluidically coupled with the corresponding flow channel. Each well is configured to contain at least one polynucleotide. Each electrode is positioned in a corresponding well of the plurality of wells. The electrodes are operable to effect writing of polynucleotides in the corresponding wells. The integrated circuit is operable to drive selective deposition or activation of selected nucleotides to attach to polynucleotides in the wells to thereby generate polynucleotides representing machine-written data in the wells. The imaging assembly is operable to capture images indicative of one or more nucleotides in a polynucleotide.