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公开(公告)号：US11961593B2
公开(公告)日：2024-04-16
申请号：US17529222
申请日：2021-11-17
Applicant: ILLUMINA, INC.
Inventor： Anindita Dutta , Dorna Kashefhaghighi , Amirali Kia
IPC: G06V10/44 , G06F16/907 , G06F18/21 , G06F18/213 , G06F18/214 , G06F18/23 , G06F18/23211 , G06F18/24 , G06F18/2415 , G06F18/2431 , G06N3/04 , G06N3/08 , G06N3/084 , G06N5/046 , G06N7/01 , G06V10/26 , G06V10/75 , G06V10/762 , G06V10/764 , G06V10/77 , G06V10/778 , G06V10/82 , G06V10/98 , G06V20/40 , G06V20/69 , G16B40/00 , G16B40/20
CPC classification number: G16B40/20 , G06F16/907 , G06F18/213 , G06F18/214 , G06F18/217 , G06F18/23 , G06F18/23211 , G06F18/24 , G06F18/2415 , G06F18/2431 , G06N3/04 , G06N3/08 , G06N3/084 , G06N7/01 , G06V10/267 , G06V10/454 , G06V10/751 , G06V10/763 , G06V10/764 , G06V10/7715 , G06V10/7784 , G06V10/82 , G06V10/993 , G06V20/69 , G16B40/00 , G06N5/046 , G06V20/47
Abstract: The technology disclosed relates to artificial intelligence-based determination of analyte data for base calling. In particular, the technology disclosed uses input image data that is derived from a sequence of images. Each image in the sequence of images represents an imaged region and depicts intensity emissions indicative of one or more analytes and a surrounding background of the intensity emissions at a respective one of a plurality of sequencing cycles of a sequencing run. The input image data comprises image patches extracted from each image in the sequence of images. The input image data is processed through a neural network to generate an alternative representation of the input image data. The alternative representation is processed through an output layer to generate an output indicating properties of respective portions of the imaged region.
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公开(公告)号：US12180468B2
公开(公告)日：2024-12-31
申请号：US17010349
申请日：2020-09-02
Applicant: ILLUMINA, INC.
Inventor： Christian Gloeckner , Amirali Kia , Molly He , Trina Faye Osothprarop , Frank J. Steemers , Kevin L. Gunderson , Sasan Amini , Jerome Jendrisak
Abstract: Presented herein are methods and compositions for tagmentation of nucleic acids. The methods are useful for generating tagged DNA fragments that are qualitatively and quantitatively representative of the target nucleic acids in the sample from which they are generated.
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公开(公告)号：US12119088B2
公开(公告)日：2024-10-15
申请号：US17899539
申请日：2022-08-30
Applicant: ILLUMINA, INC.
Inventor： Kishore Jaganathan , Anindita Dutta , Dorna Kashefhaghighi , John Randall Gobbel , Amirali Kia
IPC: G06F16/907 , G06F18/21 , G06F18/214 , G06F18/23 , G06F18/23211 , G06F18/24 , G06F18/2415 , G06F18/2431 , G06N3/04 , G06N3/08 , G06N3/084 , G06N7/01 , G06V10/26 , G06V10/44 , G06V10/75 , G06V10/762 , G06V10/764 , G06V10/77 , G06V10/778 , G06V10/82 , G06V10/98 , G06V20/69 , G16B40/00 , G16B40/20 , G06N5/046 , G06V20/40
CPC classification number: G16B40/20 , G06F16/907 , G06F18/214 , G06F18/217 , G06F18/23 , G06F18/23211 , G06F18/24 , G06F18/2415 , G06F18/2431 , G06N3/04 , G06N3/08 , G06N3/084 , G06N7/01 , G06V10/267 , G06V10/454 , G06V10/751 , G06V10/763 , G06V10/764 , G06V10/7715 , G06V10/7784 , G06V10/82 , G06V10/993 , G06V20/69 , G16B40/00 , G06N5/046 , G06V20/47
Abstract: A system, a method and a non-transitory computer readable storage medium for base calling are described. The base calling method includes processing through a neural network first image data comprising images of clusters and their surrounding background captured by a sequencing system for one or more sequencing cycles of a sequencing run. The base calling method further includes producing a base call for one or more of the clusters of the one or more sequencing cycles of the sequencing run.
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公开(公告)号：US11347965B2
公开(公告)日：2022-05-31
申请号：US16825987
申请日：2020-03-20
Applicant: Illumina, Inc.
Inventor： Anindita Dutta , Dorna Kashefhaghighi , Amirali Kia
Abstract: The technology disclosed relates to generating ground truth training data to train a neural network-based template generator for cluster metadata determination task. In particular, it relates to accessing sequencing images, obtaining, from a base caller, a base call classifying each subpixel in the sequencing images as one of four bases (A, C, T, and G), generating a cluster map that identifies clusters as disjointed regions of contiguous subpixels which share a substantially matching base call sequence, determining cluster metadata based on the disjointed regions in the cluster map, and using the cluster metadata to generate the ground truth training data for training the neural network-based template generator for the cluster metadata determination task.
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5.发明授权
公开(公告)号：US10815478B2
公开(公告)日：2020-10-27
申请号：US15523765
申请日：2015-11-05
Applicant: Illumina, Inc.
Inventor： Christian Gloeckner , Amirali Kia , Molly He , Trina Faye Osothprarop , Frank J. Steemers , Kevin L. Gunderson , Sasan Amini , Jerome Jendrisak
Abstract: Presented herein are methods and compositions for tagmentation of nucleic acids. The methods are useful for generating tagged DNA fragments that are qualitatively and quantitatively representative of the target nucleic acids in the sample from which they are generated.
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6.发明申请
公开(公告)号：US20180298356A1
公开(公告)日：2018-10-18
申请号：US16021417
申请日：2018-06-28
Applicant: ILLUMINA, INC.
Inventor： Christian Gloeckner , Amirali Kia , Erin Bomati , Molly He , Haiying Li Grunenwald , Scott Kuersten , Trina Faye Osothprarop , Darin Haskins , Joshua Burgess , Anupama Khanna , Daniel Schlingman , Ramesh Vaidyanathan
IPC: C12N9/12 , C12N9/22 , C12Q1/6869 , C12N15/10
CPC classification number: C12N9/1241 , C12N9/22 , C12N15/1068 , C12Q1/6869 , C12Q2521/507 , C12Q2565/514
Abstract: Presented herein are transposase enzymes and reaction conditions for improved fragmentation and tagging of nucleic acid samples, in particular altered transposases and reaction conditions which exhibit improved insertion sequence bias, as well as methods and kits using the same.
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公开(公告)号：US11590505B2
公开(公告)日：2023-02-28
申请号：US17254462
申请日：2020-05-26
Applicant: ILLUMINA, INC.
Inventor： Merek Siu , Ali Agah , Stanley Hong , Tarun Khurana , Aathavan Karunakaran , Craig Ciesla , Amirali Kia
Abstract: Devices, systems, and methods for non-volatile storage include a well activation device operable to modify one or more wells from a plurality of wells of a flow cell to provide a set of readable wells. Readable wells are configured to allow exposure of a well to substances from nucleotide sequencing fluids, and prevent exposure to other substances and fluids, such as nucleotide synthesizing fluids. The well activation device may also modify wells to provide a set of writeable wells. This set of wells is configured to allow exposure to the nucleotide synthesizing fluids and substances; and prevent exposure to the nucleotide sequencing fluids and substances. There may also be provisions made for risk mitigation for data errors such as generating commands to write specified data to a nucleotide sequence associated with a particular location in a storage device, reading the nucleotide sequence and performing a comparison.
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公开(公告)号：US11210554B2
公开(公告)日：2021-12-28
申请号：US16825991
申请日：2020-03-20
Applicant: Illumina, Inc.
Inventor： Anindita Dutta , Dorna Kashefhaghighi , Amirali Kia
Abstract: The technology disclosed uses neural networks to determine analyte metadata by (i) processing input image data derived from a sequence of image sets through a neural network and generating an alternative representation of the input image data, the input image data has an array of units that depicts analytes and their surrounding background, (ii) processing the alternative representation through an output layer and generating an output value for each unit in the array, (iii) thresholding output values of the units and classifying a first subset of the units as background units depicting the surrounding background, and (iv) locating peaks in the output values of the units and classifying a second subset of the units as center units containing centers of the analytes.
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9.发明授权
公开(公告)号：US10035992B2
公开(公告)日：2018-07-31
申请号：US15782757
申请日：2017-10-12
Applicant: ILLUMINA, INC.
Inventor： Christian Gloeckner , Amirali Kia , Erin Bomati , Molly He , Haiying Li Grunenwald , Scott Kuersten , Trina Faye Osothprarop , Darin Haskins , Joshua Burgess , Anupama Khanna , Daniel Schlingman , Ramesh Vaidyanathan
IPC: C12N9/12 , C12N9/22 , C12N15/10 , C12Q1/6869
CPC classification number: C12N9/1241 , C12N9/22 , C12N15/1068 , C12Q1/6869 , C12Q2521/507 , C12Q2565/514
Abstract: Presented herein are transposase enzymes and reaction conditions for improved fragmentation and tagging of nucleic acid samples, in particular altered transposases and reaction conditions which exhibit improved insertion sequence bias, as well as methods and kits using the same.
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公开(公告)号：US20180016571A1
公开(公告)日：2018-01-18
申请号：US15523765
申请日：2015-11-05
Applicant: Illumina, Inc.
Inventor： Christian Gloeckner , Amirali Kia , Molly He , Trina Faye Osothprarop , Frank J. Steemers , Kevin L. Gunderson , Sasan Amini , Jerome Jendrisak
Abstract: Presented herein are methods and compositions for tagmentation of nucleic acids. The methods are useful for generating tagged DNA fragments that are qualitatively and quantitatively representative of the target nucleic acids in the sample from which they are generated.
