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1. 发明申请

WO2010138912A1 METHODS OF SCORING GENE COPY NUMBER IN A BIOLOGICAL SAMPLE USING IN SITU HYBRIDIZATION 审中-公开
标题翻译：使用原位杂交在生物样品中测定基因拷贝数的方法
公开(公告)号：WO2010138912A1
公开(公告)日：2010-12-02
申请号：PCT/US2010/036725
申请日：2010-05-28
申请人： VENTANA MEDICAL SYSTEMS, INC. , SINGH, Shalini , GAIRE, Fabien , RANGER-MOORE, James
发明人： SINGH, Shalini , GAIRE, Fabien , RANGER-MOORE, James
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6841 , C12Q2545/101 , C12Q2537/157
摘要： Disclosed herein are methods of predicting prognosis of a neoplastic disease (such as lung cancer, for example NSCLC), including determining the IGF1R gene copy number in a biological sample from a patient having a neoplastic disease; wherein an increase in IGF1R copy number predicts a good prognosis of the neoplastic disease in the patient. Also disclosed herein are methods of scoring copy number of a gene of interest in a biological sample. The method includes identifying individual cells in the sample having highest number of signals for the gene of interest detected by in situ hybridization, counting the number of signals for the gene of interest in the identified individual cells and determining an average number of signals per cell.
摘要翻译：本文公开了预测肿瘤疾病（例如肺癌，例如NSCLC）的预后的方法，包括确定来自患有肿瘤疾病的患者的生物样品中的IGF1R基因拷贝数; 其中IGF1R拷贝数的增加预示了患者肿瘤疾病的良好预后。本文还公开了在生物样品中评价感兴趣的基因的拷贝数的方法。该方法包括鉴定通过原位杂交检测到的感兴趣基因的具有最高数目信号的样品中的单个细胞，计数所识别的个体细胞中感兴趣的基因的信号数，并确定每个细胞的平均信号数。

2. 发明申请

WO2011082307A1 SIMULTANEOUS DETECTION OF MUTATIONAL STATUS AND GENE COPY NUMBER 审中-公开
标题翻译：同时检测突变状态和基因拷贝数
公开(公告)号：WO2011082307A1
公开(公告)日：2011-07-07
申请号：PCT/US2010/062514
申请日：2010-12-30
申请人： VENTANA MEDICAL SYSTEMS, INC. , SINGH, Shalini , NITTA, Hiro , GAIRE, Fabien , DEL VALLE, Edmundo David
发明人： SINGH, Shalini , NITTA, Hiro , GAIRE, Fabien , DEL VALLE, Edmundo David
IPC分类号： G01N33/574 , C07H21/04
CPC分类号： C12Q1/6886 , C12Q2600/106 , C12Q2600/118 , C12Q2600/156 , C12Q2600/158 , G01N33/57492 , G01N33/74 , G01N2333/71 , G01N2333/91205
摘要： The present invention provides compositions and methods for simultaneously detecting mutational status and gene copy number. In particular, the present invention provides simultaneous measurement of gene copy number and detection of the L858R and Exon 19 del mutations in a tissue sample.
摘要翻译：本发明提供同时检测突变状态和基因拷贝数的组合物和方法。特别地，本发明提供了基因拷贝数的同时测量以及组织样本中L858R和外显子19 del突变的检测。

3. 发明申请

WO2010022332A1 METHOD FOR CHROMOGENIC DETECTION OF TWO OR MORE TARGET MOLECULES IN A SINGLE SAMPLE 审中-公开
标题翻译：用于在单个样品中检测两种或更多种目标分子的方法
公开(公告)号：WO2010022332A1
公开(公告)日：2010-02-25
申请号：PCT/US2009/054614
申请日：2009-08-21
申请人： VENTANA MEDICAL SYSTEMS, INC. , GNIEWEK, Richard , FARRELL, Michael , NITTA, Hiroaki , LEHRKAMP, Megan , KOSMEDER, Jerome , BIENIARZ, Christopher , KELLY, Brian, Daniel , GROGAN, Thomas , GAIRE, Fabien , PADILLA, Mary
发明人： GNIEWEK, Richard , FARRELL, Michael , NITTA, Hiroaki , LEHRKAMP, Megan , KOSMEDER, Jerome , BIENIARZ, Christopher , KELLY, Brian, Daniel , GROGAN, Thomas , GAIRE, Fabien , PADILLA, Mary
IPC分类号： C12Q1/68 , G01N33/58
CPC分类号： C12Q1/6841 , G01N33/53 , G01N33/581 , G01N33/583
摘要： The present invention provides a method and kit for detection of two or more target molecules in a single tissue sample, such as for gene and protein dual detection in a single tissue sample. Methods comprise treating a tissue sample with a first binding moiety that specifically binds a first target molecule. Methods further comprise treating the tissue sample with a solution containing a soluble electron-rich aromatic compound prior to or concomitantly with contacting the tissue sample with a hapten-labeled binding moiety and detecting a second target molecule. In one example, the first target molecule is a protein and the second is a nucleic acid sequence, the first target molecule being detected by immunohistochemistry and the second by in situ hybridization. The disclosed method reduces background due to non-specific binding of the hapten-labeled specific binding moiety to an insoluble electron rich compound deposited near the first target molecule.
摘要翻译：本发明提供了用于检测单个组织样品中两种或更多种靶分子的方法和试剂盒，例如用于单个组织样品中的基因和蛋白质双重检测。方法包括用特异性结合第一靶分子的第一结合部分处理组织样品。方法还包括在使组织样品与半抗原标记的结合部分接触或同时检测第二靶分子之前或同时使用含有可溶于富电子的芳族化合物的溶液处理组织样品。在一个实例中，第一靶分子是蛋白质，第二个是核酸序列，第一个靶分子通过免疫组织化学检测，第二个是原位杂交。所公开的方法由于半抗原标记的特异性结合部分与沉积在第一靶分子附近的不溶性富电子化合物的非特异性结合而减少背景。

4. 发明申请

WO2012024185A1 SUBSTRATES FOR CHROMOGENIC DETECTION AND METHODS OF USE IN DETECTION ASSAYS AND KITS 审中-公开
标题翻译：用于染色体检测的基质和检测方法和试剂盒
公开(公告)号：WO2012024185A1
公开(公告)日：2012-02-23
申请号：PCT/US2011/047613
申请日：2011-08-12
申请人： VENTANA MEDICAL SYSTEMS, INC. , KELLY, Brian, Daniel , BIENIARZ, Christopher , NITTA, Hiroaki , GAIRE, Fabien
发明人： KELLY, Brian, Daniel , BIENIARZ, Christopher , NITTA, Hiroaki , GAIRE, Fabien
IPC分类号： C07F9/6503
CPC分类号： C07F9/65035 , G01N21/78
摘要： Embodiments of substrates and processes for chromogenic detection, and in particular pyrazolyl dihydrogen phosphate compounds, are disclosed.
摘要翻译：公开了用于显色检测的底物和方法，特别是吡唑基二氢磷酸酯化合物的实施方案。

5. 发明申请

WO2011149943A1 METHOD FOR DIFFERENTIATION OF NON-SMALL CELLUNG CARCINOMA 审中-公开
标题翻译：非小细胞肺癌的鉴别方法
公开(公告)号：WO2011149943A1
公开(公告)日：2011-12-01
申请号：PCT/US2011/037750
申请日：2011-05-24
申请人： VENTANA MIDICAL SYSTEMS, INC. , GAIRE, Fabien , SINGH, Shalini , SEBASTIAO, Noemi , FISCHETTE, Maria, R.
发明人： GAIRE, Fabien , SINGH, Shalini , SEBASTIAO, Noemi , FISCHETTE, Maria, R.
IPC分类号： G01N33/574
CPC分类号： G01N33/57423
摘要： Disclosed herein are methods for diagnosing lung carcinoma type in a subject by differentiating subtypes of non-small cell lung carcinoma (NSCLC), for example, diagnosing a squamous cell type lung carcinoma or a non-squamous type lung carcinoma in the subject. In some embodiments, the methods include determining a first amount of serpin B13 protein in the sample, determining a second amount of cytokeratin 5 and/or cytokeratin 6 protein in the sample, determining a third amount of thyroid transcription factor- 1 protein in the sample, and determining a fourth amount of napsin A protein in an NSCLC sample. In some embodiments, the methods further include determining a fifth amount of p63 protein in an NSCLC sample. In other embodiments, the methods include determining a first amount of cytokeratin 5 and/or cytokeratin 6 protein in the sample, determining a second amount of thyroid transcription factor- 1 protein in the sample, and determining a third amount of napsin A protein in an NSCLC sample.
摘要翻译：本文公开了通过区分非小细胞肺癌（NSCLC）亚型（例如诊断受试者中鳞状细胞型肺癌或非鳞状肺癌）来诊断受试者的肺癌类型的方法。在一些实施方案中，所述方法包括确定样品中第一量的丝氨酸蛋白酶抑制剂B13蛋白，确定样品中第二量的细胞角蛋白5和/或细胞角蛋白6蛋白，确定样品中第三量的甲状腺转录因子-1蛋白，并且确定NSCLC样品中第四数量的napsin A蛋白。在一些实施方案中，所述方法还包括确定NSCLC样品中第五量的p63蛋白。在其它实施方案中，所述方法包括确定样品中的第一量的细胞角蛋白5和/或细胞角蛋白6蛋白，确定样品中第二量的甲状腺转录因子-1蛋白，以及确定第 NSCLC样本。

6. 发明申请

WO2022094629A1 ATTENTION-BASED MULTIPLE INSTANCE LEARNING 审中-公开
公开(公告)号：WO2022094629A1
公开(公告)日：2022-05-05
申请号：PCT/US2021/072166
申请日：2021-11-01
申请人： GENENTECH, INC. , F. HOFFMANN-LA ROCHE AG , HOFFMAN-LA ROCHE INC. , VENTANA MEDICAL SYSTEMS, INC. , NIE, Yao
发明人： LI, Xiao , NGUYEN, Trung Kien , GAIRE, Fabien , KLAIMAN, Eldad , BEN-SHAUL, Ido , GILDENBLAT, Jacob , HADAR, Ofir Etz
IPC分类号： G06V10/82 , G06V20/69 , G06T7/00
摘要： Systems and methods relate to predicting disease progression by processing digital pathology images using neural networks. A digital pathology image that depicts a specimen stained with one or more stains is accessed. The specimen may have been collected from a subject. A set of patches are defined for the digital pathology image. Each patch of the set of patches depicts a portion of the digital pathology image. For each patch of the set of patches and using an attention-score neural network, an attention score is generated. The attention-score neural network may have been trained using a loss function that penalized attention-score variability across patches in training digital pathology images labeled to indicate no or low subsequent disease progression. Using a result-prediction neural network and the attention scores, a result is generated that represents a prediction of whether or an extent to which a disease of the subject will progress.

7. 发明授权

EP2606055B1 SUBSTRATES FOR CHROMOGENIC DETECTION AND METHODS OF USE IN DETECTION ASSAYS AND KITS 有权
标题翻译： FOR显色反应检测和方法底物，使用检测测定和试剂盒
公开(公告)号：EP2606055B1
公开(公告)日：2015-06-03
申请号：EP11751996.7
申请日：2011-08-12
申请人： Ventana Medical Systems, Inc.
发明人： KELLY, Brian, Daniel , BIENIARZ, Christopher , NITTA, Hiro , GAIRE, Fabien
IPC分类号： C07F9/6503
CPC分类号： C07F9/65035 , G01N21/78

8. 发明授权

EP2519825B1 SIMULTANEOUS DETECTION OF MUTATIONAL STATUS AND GENE COPY NUMBER 有权
标题翻译：突变状态和基因拷贝数可同时检测
公开(公告)号：EP2519825B1
公开(公告)日：2015-01-14
申请号：EP10841723.9
申请日：2010-12-30
申请人： Ventana Medical Systems, Inc.
发明人： SINGH, Shalini , NITTA, Hiro , GAIRE, Fabien , DEL VALLE, Edmundo David
IPC分类号： G01N33/574 , C07H21/04
CPC分类号： C12Q1/6886 , C12Q2600/106 , C12Q2600/118 , C12Q2600/156 , C12Q2600/158 , G01N33/57492 , G01N33/74 , G01N2333/71 , G01N2333/91205

9. 发明公开

EP2446053A1 METHODS OF SCORING GENE COPY NUMBER IN A BIOLOGICAL SAMPLE USING IN SITU HYBRIDIZATION 审中-公开
标题翻译：方法用于计算基因拷贝的生物样品利用原位HYBRDISIERUNG
公开(公告)号：EP2446053A1
公开(公告)日：2012-05-02
申请号：EP10723456.9
申请日：2010-05-28
申请人： Ventana Medical Systems, Inc.
发明人： SINGH, Shalini , GAIRE, Fabien , RANGER-MOORE, James
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6841 , C12Q2545/101 , C12Q2537/157
摘要： Disclosed herein are methods of predicting prognosis of a neoplastic disease (such as lung cancer, for example NSCLC), including determining the IGF1R gene copy number in a biological sample from a patient having a neoplastic disease; wherein an increase in IGF1R copy number predicts a good prognosis of the neoplastic disease in the patient. Also disclosed herein are methods of scoring copy number of a gene of interest in a biological sample. The method includes identifying individual cells in the sample having highest number of signals for the gene of interest detected by in situ hybridization, counting the number of signals for the gene of interest in the identified individual cells and determining an average number of signals per cell.

10. 发明公开

EP2519825A1 SIMULTANEOUS DETECTION OF MUTATIONAL STATUS AND GENE COPY NUMBER 有权
标题翻译：突变状态和基因拷贝数可同时检测
公开(公告)号：EP2519825A1
公开(公告)日：2012-11-07
申请号：EP10841723.9
申请日：2010-12-30
申请人： Ventana Medical Systems, Inc.
发明人： SINGH, Shalini , NITTA, Hiro , GAIRE, Fabien , DEL VALLE, Edmundo David
IPC分类号： G01N33/574 , C07H21/04
CPC分类号： C12Q1/6886 , C12Q2600/106 , C12Q2600/118 , C12Q2600/156 , C12Q2600/158 , G01N33/57492 , G01N33/74 , G01N2333/71 , G01N2333/91205
摘要： The present invention provides compositions and methods for simultaneously detecting mutational status and gene copy number. In particular, the present invention provides simultaneous measurement of gene copy number and detection of the L858R and Exon 19 del mutations in a tissue sample.

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