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1. 发明申请

WO2021163204A1 SYSTEM AND METHOD FOR CANCER PROGNOSIS 审中-公开
公开(公告)号：WO2021163204A1
公开(公告)日：2021-08-19
申请号：PCT/US2021/017472
申请日：2021-02-10
申请人： ILLUMINA, INC.
发明人： GOLKARAM, Mahdi , ZHANG, Shile , LIU, Li , WISE, Aaron , YAO, Joyee , KAPLAN, Shannon , SO, Alex , SALMANS, Michael , VIJAYARAGHAVAN, Raakhee
IPC分类号： C12Q1/6886
摘要： 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.

2. 发明申请

WO2017106481A9 DISTINGUISHING METHYLATION LEVELS IN COMPLEX BIOLOGICAL SAMPLES 审中-公开
公开(公告)号：WO2017106481A9
公开(公告)日：2017-06-22
申请号：PCT/US2016/066901
申请日：2016-12-15
申请人： ILLUMINA, INC.
发明人： TOUNG, Jonathan , LIU, Li , SHEN, Min-jui, Richard , ZHANG, Ruoyu
IPC分类号： C12Q1/68
摘要： 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.

3. 发明申请

WO2017019456A2 SPATIAL MAPPING OF NUCLEIC ACID SEQUENCE INFORMATION 审中-公开
标题翻译：核酸序列信息的空间映射
公开(公告)号：WO2017019456A2
公开(公告)日：2017-02-02
申请号：PCT/US2016/043385
申请日：2016-07-21
申请人： ILLUMINA, INC.
发明人： SO, Alex , LIU, Li , SHEN, Min-Jui Richard , SALATHIA, Neeraj , STEPHENS, Kathryn M. , JAGER, Anne , WILSON, Timothy , FULLERTON, Justin , RAMIREZ, Sean M. , KAPLAN, Shannon , PANTOJA, Rigo , VENKATESAN, Bala Murali , MODIANO, Steven
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6874 , C12Q1/6837 , C12Q2565/514 , C12Q2565/543 , C12Q2565/125 , C12Q2563/143 , C12Q2563/155 , C12Q2543/10
摘要： 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.
摘要翻译：提出了用于组织样品中核酸的空间检测和分析的方法和组合物。所述方法可以使得能够表征组织中的转录组和/或基因组变异，同时保留关于组织的空间信息。

4. 发明申请

WO2017106481A1 DISTINGUISHING METHYLATION LEVELS IN COMPLEX BIOLOGICAL SAMPLES 审中-公开
标题翻译：在复杂的生物样品中鉴别甲基化水平
公开(公告)号：WO2017106481A1
公开(公告)日：2017-06-22
申请号：PCT/US2016/066901
申请日：2016-12-15
申请人： ILLUMINA, INC.
发明人： TOUNG, Jonathan , LIU, Li , SHEN, Min-jui, Richard , ZHANG, Ruoyu
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6886 , C12Q1/6881 , C12Q2600/154 , G06F19/10 , G06F19/24
摘要： 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.
摘要翻译：本文提供了用于区别来自第一细胞类型的DNA的异常甲基化水平的方法，所述方法包括以下步骤：（a）提供测试数据集，所述测试数据集包括（i）多个位点的甲基化状态来自至少一种测试生物的测试基因组DNA，和（ii）覆盖每个位点以检测甲基化状态; （b）为来自一个或多个参考个体生物体的参考基因组DNA中的多个位点提供甲基化状态，（c）针对每个位点确定测试基因组DNA与参考基因组DNA之间的甲基化差异，由此提供每个位点的归一化甲基化差异; （d）通过每个位点的覆盖度对每个位点的归一化甲基化差异进行加权，从而确定总覆盖加权归一化甲基化差异分数。本文还提供了使用基因组DNA甲基化水平来区分癌细胞与正常细胞并根据其来源组织区分不同癌症类型的敏感方法。

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