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1. 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.

2. 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。

3. 发明申请

WO2015126766A1 METHODS AND COMPOSITIONS FOR DNA PROFILING 审中-公开
标题翻译： DNA分析的方法和组合
公开(公告)号：WO2015126766A1
公开(公告)日：2015-08-27
申请号：PCT/US2015/015939
申请日：2015-02-13
申请人： ILLUMINA, INC.
发明人： STEPHENS, Kathryn, M. , HOLT, Cydne , DAVIS, Carey , JAGER, Anne , WAICHHIEWICZ, Paulina , HAN, Yonmee , SILVA, David , SHEN, Min-jui, Richard , AMINI, Sasan , STEEMERS, Frank
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6827 , C12Q1/6858
摘要： Embodiments disclosed herein provide methods for constructing a DNA profile comprising: providing a nucleic acid sample, amplifying the nucleic acid sample with a plurality of primers that specifically hybridize to at least one target sequence comprising a SNP and at least one target sequence comprising a tandem repeat, and determining the genotypes of the at least one SNP and at least one tandem repeat in the amplification products, thereby constructing the DNA profile of the nucleic acid sample. Embodiments disclosed herein further provide a plurality of primers that specifically hybridize to at least one short target sequence and at least one long target sequence in a nucleic acid sample, wherein amplifying the nucleic acid sample using the plurality of primers in a single reaction results in a short amplification product and a long amplification product, wherein each of the plurality of primers comprises one or more tag sequences.
摘要翻译：本文公开的实施方案提供了用于构建DNA谱的方法，其包括：提供核酸样品，用多个引物扩增核酸样品，多个引物与至少一个包含SNP的靶序列和至少一个包含串联重复序列的靶序列特异性杂交，并确定扩增产物中至少一个SNP的基因型和至少一个串联重复序列，由此构建核酸样品的DNA谱。本文公开的实施方案还提供了与核酸样品中的至少一个短靶序列和至少一个长靶序列特异性杂交的多个引物，其中在单个反应中使用多个引物扩增核酸样品导致短扩增产物和长扩增产物，其中多个引物中的每一个包含一个或多个标签序列。

4. 发明申请

WO2011025477A1 METHODS FOR SELECTING AND AMPLIFYING POLYNUCLEOTIDES 审中-公开
标题翻译：选择和放大多核苷酸的方法
公开(公告)号：WO2011025477A1
公开(公告)日：2011-03-03
申请号：PCT/US2009/054945
申请日：2009-08-25
申请人： ILLUMINA, INC. , SABOT, Andrea , RIGATTI, Roberto , SHEN, Min-jui, Richard
发明人： SABOT, Andrea , RIGATTI, Roberto , SHEN, Min-jui, Richard
IPC分类号： C12P19/34
CPC分类号： C12N15/1068 , C12Q1/6806 , C12Q1/6837 , C12Q1/6874 , C12Q2565/543 , C12Q2565/507 , C12Q2531/107
摘要： The invention provides methods for controlling the density of different molecular species on the surface of a solid support. A first mixture of different molecular species is attached to a solid support under conditions to attach each species at a desired density, thereby producing a derivatized support having attached capture molecules. The derivatized support is treated with a second mixture of different molecular species, wherein different molecular species in the second mixture bind specifically to the different capture molecules attached to the solid support. One or more of the capture molecules can be reversibly modified such that the capture molecules have a different activity before and after the second mixture of molecular species are attached. In particular embodiments, the different molecular species are nucleic acids that are reversibly modified to have different activity in an amplification reaction.
摘要翻译：本发明提供了控制固体支持物表面上不同分子种类的密度的方法。将不同分子种类的第一混合物连接到固体支持物上，以便以期望的密度附着每种物质，从而产生具有附着捕获分子的衍生化载体。衍生的载体用不同分子种类的第二混合物处理，其中第二混合物中的不同分子物质特异性地结合到固相载体上的不同捕获分子。一个或多个捕获分子可以被可逆地修饰，使得捕获分子在分子物质的第二混合物附着之前和之后具有不同的活性。在具体实施方案中，不同的分子种类是可逆修饰以在扩增反应中具有不同活性的核酸。

5. 发明申请

WO2010068702A3 METHODS AND COMPOSITIONS FOR HYBRIDIZING NUCLEIC ACIDS 审中-公开
公开(公告)号：WO2010068702A3
公开(公告)日：2010-06-17
申请号：PCT/US2009/067392
申请日：2009-12-09
申请人： ILLUMINA, INC. , YEAKLEY, Joanne, M. , LENTA, Ross, Edward , SHEN, Min-jui, Richard
发明人： YEAKLEY, Joanne, M. , LENTA, Ross, Edward , SHEN, Min-jui, Richard
IPC分类号： C12Q1/68 , C12N15/10
摘要： Methods and compositions for hybridizing nucleic acids are disclosed herein. Also disclosed herein are methods and compositions to detect a nucleic acid provided to an array.

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