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公开(公告)号：US11319593B2
公开(公告)日：2022-05-03
申请号：US15380348
申请日：2016-12-15
Applicant: Illumina, Inc.
Inventor： Jonathan Toung , Li Liu , Min-Jui Richard Shen , Ruoyu Zhang
Abstract: Provided herein is a method for distinguishing an aberrant methylation level for DNA from a first cell type, including steps of (a) providing a test data set that includes (i) methylation states for a plurality of sites from test genomic DNA from at least one test organism, and (ii) coverage at each of the sites for detection of the methylation states; (b) providing methylation states for the plurality of sites in reference genomic DNA from one or more reference individual organisms, (c) determining, for each of the sites, the methylation difference between the test genomic DNA and the reference genomic DNA, thereby providing a normalized methylation difference for each site; and (d) weighting the normalized methylation difference for each site by the coverage at each of the sites, thereby determining an aggregate coverage-weighted normalized methylation difference score. Also provided herein are sensitive methods for using genomic DNA methylation levels to distinguish cancer cells from normal cells and to classify different cancer types according to their tissues of origin.
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Patent Agency Ranking
公开(公告)号：US20210130885A1
公开(公告)日：2021-05-06
申请号：US17145846
申请日：2021-01-11
Applicant: ILLUMINA, INC.
Inventor： Alex So , Li Liu , Min-Jui Richard Shen , Neeraj Salathia , Kathryn M. Stephens , Anne Jager , Timothy Wilson , Justin Fullerton , Sean M. Ramirez , Shannon Kaplan , Rigo Pantoja , Bala Murali Venkatesan , Steven Modiano
IPC: C12Q1/6837 , C12Q1/6874 , C12Q1/6816 , C12Q1/6855
Abstract: Presented are methods and compositions for spatial detection and analysis of nucleic acids in a tissue sample. The methods can enable the characterization of transcriptomes and/or genomic variations in tissues while preserving spatial information about the tissue.
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公开(公告)号：US20220170113A1
公开(公告)日：2022-06-02
申请号：US17665849
申请日：2022-02-07
Applicant: Illumina, Inc.
Inventor： Jonathan Toung , Li Liu , Min-Jui Shen , Ruoyu Zhang
Abstract: Provided herein is a method for distinguishing an aberrant methylation level for DNA from a first cell type, including steps of (a) providing a test data set that includes (i) methylation states for a plurality of sites from test genomic DNA from at least one test organism, and (ii) coverage at each of the sites for detection of the methylation states; (b) providing methylation states for the plurality of sites in reference genomic DNA from one or more reference individual organisms, (c) determining, for each of the sites, the methylation difference between the test genomic DNA and the reference genomic DNA, thereby providing a normalized methylation difference for each site; and (d) weighting the normalized methylation difference for each site by the coverage at each of the sites, thereby determining an aggregate coverage-weighted normalized methylation difference score. Also provided herein are sensitive methods for using genomic DNA methylation levels to distinguish cancer cells from normal cells and to classify different cancer types according to their tissues of origin.
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公开(公告)号：US20210254170A1
公开(公告)日：2021-08-19
申请号：US17172380
申请日：2021-02-10
Applicant: ILLUMINA, INC.
Inventor： Mahdi Golkaram , Shile Zhang , Li Liu , Aaron Wise , Joyee Yao , Shannon Kaplan , Alex So , Michael Salmans , Raakhee Vijayaraghavan
IPC: C12Q1/6886
Abstract: A potential prognostic biomarker is based on a combination of a composite score generated by sequence analysis of global human endogenous retrovirus (hERV)/retro-transposon transactivation and a cell signature generated using deconvolution of immune cells within a tumor sample for predicting the efficacy of chemotherapeutic agents and immune checkpoint inhibitors. Correlation analysis of the composite score with cell signature within a tumor sample enables survival analysis in individuals receiving chemotherapeutic agents and immune checkpoint inhibitors.
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公开(公告)号：US10913975B2
公开(公告)日：2021-02-09
申请号：US15747670
申请日：2016-07-21
Applicant: ILLUMINA, INC.
Inventor： Alex So , Li Liu , Min-Jui Richard Shen , Neeraj Salathia , Kathryn M. Stephens , Anne Jager , Timothy Wilson , Justin Fullerton , Sean M. Ramirez , Shannon Kaplan , Rigo Pantoja , Bala Murali Venkatesan , Steven Modiano
IPC: C12Q1/68 , C12Q1/6837 , C12Q1/6874 , C12Q1/6816 , C12Q1/6855
Abstract: Presented are methods and compositions for spatial detection and analysis of nucleic acids in a tissue sample. The methods can enable the characterization of transcriptomes and/or genomic variations in tissues while preserving spatial information about the tissue.
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公开(公告)号：US20170175205A1
公开(公告)日：2017-06-22
申请号：US15380348
申请日：2016-12-15
Applicant: Illumina, Inc.
Inventor： Jonathan Toung , Li Liu , Min-Jui Richard Shen , Ruoyu Zhang
CPC classification number: C12Q1/6886 , C12Q1/6881 , C12Q2600/154 , G16B40/00 , G16B99/00
Abstract: Provided herein is a method for distinguishing an aberrant methylation level for DNA from a first cell type, including steps of (a) providing a test data set that includes (i) methylation states for a plurality of sites from test genomic DNA from at least one test organism, and (ii) coverage at each of the sites for detection of the methylation states; (b) providing methylation states for the plurality of sites in reference genomic DNA from one or more reference individual organisms, (c) determining, for each of the sites, the methylation difference between the test genomic DNA and the reference genomic DNA, thereby providing a normalized methylation difference for each site; and (d) weighting the normalized methylation difference for each site by the coverage at each of the sites, thereby determining an aggregate coverage-weighted normalized methylation difference score. Also provided herein are sensitive methods for using genomic DNA methylation levels to distinguish cancer cells from normal cells and to classify different cancer types according to their tissues of origin.
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