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1. 发明申请

WO2022066512A1 PREDICTION OF RESPONSE TO EPIDERMAL GROWTH FACTOR RECEPTOR-DIRECTED THERAPIES USING EPIREGULIN AND AMPHIREGULIN 审中-公开
公开(公告)号：WO2022066512A1
公开(公告)日：2022-03-31
申请号：PCT/US2021/050777
申请日：2021-09-17
申请人： VENTANA MEDICAL SYSTEMS, INC. , UNIVERSITY OF LEEDS
发明人： BAI, Isaac Yuyu , BARRETT, Jennifer Helen , ELLIOTT, Faye , LIU, Wen-Wei , QUIRKE, Philip , RICHMAN, Susan Diane , SELIGMANN, Jennifer Frances , SEYMOUR, Matthew Thomas , SHANMUGAM, Kandavel , SINGH, Shalini , WEST, Nicholas Paul , WILLIAMS, Christopher James Michael , ZHANG, Liping
IPC分类号： C07K16/28 , A61P35/00 , A61K39/395 , G01N33/574
摘要： Methods allowing prediction of a response to anti-EGFR therapies are provided, which include histochemical or cytochemical staining methods for staining amphiregulin (AREG) or epiregulin (EREG). Scoring algorithms are provided that may include but are not limited to determining a percent tumor cell positivity for each of EREG and AREG and comparing the determined percent positivity to pre-determined cut offs. The pre-determined cut offs can be either positive cut offs (in which case patients are treated with the EGFR-directed therapy if the percentage is greater than or equal to the cut off), negative cut offs (in which case patients are not treated with the EGFR-directed therapy if the percentage is less than the cut off), or both a positive and negative cut off.

2. 发明申请

WO2016107896A1 SYSTEMS AND METHODS FOR CO-EXPRESSION ANALYSIS IN IMMUNOSCORE COMPUTATION 审中-公开
标题翻译：用于免疫球蛋白计算中的协同表达分析的系统和方法
公开(公告)号：WO2016107896A1
公开(公告)日：2016-07-07
申请号：PCT/EP2015/081399
申请日：2015-12-30
申请人： VENTANA MEDICAL SYSTEMS, INC. , F. HOFFMANN-LA ROCHE AG
发明人： BARNES, Michael , SINGH, Shalini , CHEN, Ting , CHEFD´HOTEL, Christophe , TUBBS, Alisa
IPC分类号： G06T7/00
CPC分类号： G06T7/0012 , G06F19/00 , G06T7/00 , G06T2207/30024
摘要： Described herein are methods for co-expression analysis of multiple markers in a tissue sample comprising: computing a heat map of marker expression for each of a plurality of single marker channel images, wherein each of the plurality of single marker channel images comprise a single marker; identifying one or more candidate regions of interest in each heat map of marker expression; computing overlay masks comprising the identified one or more candidate regions of interest from each heat map of marker expression; determining one or more co-localized regions of interest from the overlay masks; mapping the one or more co-localized regions of interest to a same coordinate position in each of the plurality of single marker channel images; and estimating a number of cells in at least one of the determined one or more co-localized regions of interest in each of the plurality of single marker channel images.
摘要翻译：本文描述了用于组织样本中多个标记物的共表达分析的方法，包括：计算多个单个标记通道图像中的每一个的标记表达的热图，其中多个单个标记通道图像中的每一个包括单个标记 ; 识别标记表达的每个热图中的一个或多个候选区域; 从标记表达的每个热图中计算包括所识别的一个或多个候选区域的覆盖掩模; 从所述覆盖掩模确定感兴趣的一个或多个共定位区域; 将所述一个或多个共定位的感兴趣区域映射到所述多个单个标记通道图像中的每一个中的相同坐标位置; 以及估计所述多个单个标记信道图像中的每一个中确定的一个或多个共定位区域中的至少一个中的小区的数量。

3. 发明申请

WO2014046730A1 METHOD OF IDENTIFYING TREATMENT RESPONSIVE NON-SMALL CELL LUNG CANCER USING ANAPLASTIC LYMPHOMA KINASE (ALK) AS A MARKER 审中-公开
标题翻译：使用溶解性LYMPHOMA激酶（ALK）作为标记物鉴定治疗反应性非小细胞肺癌的方法
公开(公告)号：WO2014046730A1
公开(公告)日：2014-03-27
申请号：PCT/US2013/031531
申请日：2013-03-14
申请人： VENTANA MEDICAL SYSTEMS, INC.
发明人： GROGAN, Thomas , NITTA, Hiro , BARNES, Michael , TOWNE, Penny , SINGH, Shalini , CLEMENTS, June, F. , SCHEMP, Crystal , ROBERTS, Esteban
IPC分类号： G01N33/574
CPC分类号： G01N33/57423 , A61K31/4545 , G01N2333/912 , G01N2800/52
摘要： Disclosed herein are methods for identifying a subject as having NSCLC that is predicted or is likely to respond to treatment with an ALK inhibitor, for example crizotinib. The methods include identifying a sample including NSCLC tumor cells as ALK-positive or ALK-negative using immunohistochemistry (IHC) and scoring methods disclosed herein. A subject is identified as having NSCLC likely to respond to treatment with an ALK inhibitor if the sample is identified as ALK-positive and is identified as having NSCLC not likely to respond to treatment with an ALK inhibitor if the sample is identified as ALK-negative. According to certain embodiments of the methods, subjects predicted to respond to an ALK inhibitor may then be treated with an ALK inhibitor such as crizotinib.
摘要翻译：本文公开了用于将受试者鉴定为具有预测或可能对ALK抑制剂（例如crizotinib）治疗反应的NSCLC的方法。所述方法包括使用本文公开的免疫组织化学（IHC）和评分方法鉴定包含NSCLC肿瘤细胞的样品为ALK阳性或ALK阴性。如果样品被鉴定为ALK阳性，并且如果样品被鉴定为ALK阴性，并且被鉴定为具有NSCLC不可能对ALK抑制剂治疗反应的受试者被鉴定为具有NSCLC可能对ALK抑制剂的治疗作出反应。根据方法的某些实施方案，预测对ALK抑制剂作出反应的受试者然后可以用ALK抑制剂如克利替尼治疗。

4. 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。

5. 发明申请

WO2018091419A1 COMPOSITIONS AND METHODS FOR PROGNOSING AND TREATING COLORECTAL CANCER 审中-公开
公开(公告)号：WO2018091419A1
公开(公告)日：2018-05-24
申请号：PCT/EP2017/079084
申请日：2017-11-13
申请人： VENTANA MEDICAL SYSTEMS, INC. , F. HOFFMANN-LA ROCHE AG , ROCHE SEQUENCING SOLUTIONS INC. , ROCHE DIAGNOSTICS GMBH , CHARITÉ - UNIVERSITÄTSMEDIZIN BERLIN GLIEDKÖRPERSCHAFT DER FREIEN UNIVERSITÄT BERLIN UND DER HUMBOLDT-UNIVERSITÄT ZU BERLIN
发明人： HERRMANN, Pia , ILM, Katharina , LEITH, Katherine F. , MURANYI, Andrea , ROHR, Ulrich-Peter , SHANMUGAM, Kandavel , SINGH, Shalini , STEIN, Ulrike
IPC分类号： C12Q1/6886 , G01N33/574
摘要： A combination of mismatch repair (MMR) and Metastasis Associated in Colon Cancer 1 (MACC1) gene expression status of the patient serve as a basis for risk stratification of early stage colon cancer patients. Patients with defective MMR (dMMR) status have improved survival and do not benefit from 5-fluorouracil (5-FU) therapies. In contrast, patients with a proficient MMR (pMMR) status have a higher risk of recurrence and worse survival. The pMMR patients are then further stratified on the basis of MACC1 gene expression. Patients with a pMMR status and a low MACC1 expression have a favorable prognosis similar to patients having a dMMR status, whereas patients having a pMMR status and high MACC1 expression have a less favorable prognosis.

6. 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。

7. 发明申请

WO2010138908A1 IGFIR GENE COPY NUMBER AS A PROGNOSTIC MARKER IN A NON-SMALL CELL LUNG CANCER 审中-公开
标题翻译： IGFIR基因拷贝数作为非小细胞肺癌中的预防标记
公开(公告)号：WO2010138908A1
公开(公告)日：2010-12-02
申请号：PCT/US2010/036721
申请日：2010-05-28
申请人： VENTANA MEDICAL SYSTEMS, INC. , THE REGENTS OF THE UNIVERSITY OF COLORADO, A BODY CORPORATE , HIRSCH, Fred, R. , WYNES, Murry, W. , SINGH, Shalini , RANGER-MOORE, James , MEDICAL UNIVERSITY OF GDANSK , DZIADZIUSZKO, Rafal , JASSEM, Jacek
发明人： HIRSCH, Fred, R. , WYNES, Murry, W. , SINGH, Shalini , RANGER-MOORE, James , DZIADZIUSZKO, Rafal , JASSEM, Jacek
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6883 , C12Q1/6841 , C12Q2600/118 , C12Q2600/158
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 gene 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基因拷贝数的增加预示了患者中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。

8. 发明申请

WO2017001350A1 MATERIALS AND METHODS FOR PERFORMING HISTOCHEMICAL ASSAYS FOR HUMAN PRO-EPIREGULIN AND AMPHIREGULIN 审中-公开
标题翻译：用于人类EPIREGULIN和AMPHIREGULIN的组织化学测定的材料和方法
公开(公告)号：WO2017001350A1
公开(公告)日：2017-01-05
申请号：PCT/EP2016/064883
申请日：2016-06-27
申请人： VENTANA MEDICAL SYSTEMS, INC. , F. HOFFMANN-LA ROCHE AG
发明人： SINGH, Shalini , ZHU, Yifei , LIAO, Zhiming , MURANYI, Andrea , SHANMUGAM, Kandavel , COUTO, Fernando
IPC分类号： C07K16/22 , C07K16/30
CPC分类号： G01N33/57496 , C07K16/22 , C07K16/30 , C07K2317/20 , C07K2317/34 , C07K2317/92 , G01N2333/485
摘要： The invention provides anti-human pro-epiregulin and anti-human amphiregulin antibodies and methods of using the same. Anti-EREG antibodies raised against amino acids 148-169 and 156-169 of the human EREG protein, and anti-AREG antibodies raised against amino acids 238-252 of the human AREG protein are disclosed. Methods of using these antibodies to detect EREG and AREG and kits and other products for performing such methods are also disclosed.
摘要翻译：本发明提供了抗人前 - 外调蛋白和抗人双调蛋白抗体及其使用方法。公开了针对人EREG蛋白的氨基酸148-169和156-169产生的抗EREG抗体，以及针对人AREG蛋白的氨基酸238-252产生的抗AREG抗体。还公开了使用这些抗体来检测EREG和AREG以及用于进行这些方法的试剂盒和其它产品的方法。

9. 发明申请

WO2015121465A1 G-ALPHA, INTERACTING VESICLE ASSOCIATED PROTEIN (GIV) AS A PREDICTIVE MARKER IN STAGE II COLORECTAL CANCER 审中-公开
标题翻译： G-ALPHA，相互作用的VESICLE相关蛋白（GIV）作为II期彩色癌中的预测标记
公开(公告)号：WO2015121465A1
公开(公告)日：2015-08-20
申请号：PCT/EP2015/053196
申请日：2015-02-16
申请人： VENTANA MEDICAL SYSTEMS, INC. , THE REGENTS OF THE UNIVERSITY OF CALIFORNIA , THE UNITED STATES OF AMERICA AS REPRESENTED BY THE DEPARTMENT OF VETERANS AFFAIRS , ROCHE MOLECULAR SYSTEMS, INC. , F. HOFFMANN-LA ROCHE AG
发明人： LEITH, Katherine , ROHR, Ulrich-Peter , SINGH, Shalini , GHOSH, Pradipta , HU, Song , LAFLEUR, Bonnie , MURANYI, Andrea , SHANMUGAM, Kandavel
IPC分类号： G01N33/574
CPC分类号： G01N33/57419 , C12Q1/6886 , C12Q2600/112 , C12Q2600/158 , G01N2800/56
摘要： Provided herein are methods of analyzing stage II colorectal cancer (CRC) samples (such as those that are mis-match repair proficient, pMMR), by scoring G- alpha interacting vesicle associated protein (GIV, also known as girdin) full-length (GlV-fl) expression in combination with lymphovascular invasion (LVI) status or clinical variables. The disclosed methods can be used to identify GIV-fl expressing tumors that are likely to recur (high risk) and those that are not likely to recur (high risk). Subjects identified as having a high risk CRC can be selected to receive chemotherapy or biotherapy for the CRC. Thus, in some examples, the disclosed methods can be used to identify CRC tumors that are likely to respond to chemotherapy or biotherapy. Also provided are computer implemented methods, systems, and kits that can be used with these methods.
摘要翻译：本文提供了通过对G-α相互作用的囊泡相关蛋白（GIV，也称为girdin）全长（GIV）进行评分的方法来分析II期结直肠癌（CRC）样品（例如那些与精子错误匹配的pMMR） GlV-fl）表达与淋巴血管侵袭（LVI）状态或临床变量组合。所公开的方法可用于鉴定可能复发（高风险）的GIV-fl表达的肿瘤和不可能再发生的（高风险）的GIV-fl表达的肿瘤。被确定为具有高风险CRC的受试者可以选择接受化学疗法或生物疗法用于CRC。因此，在一些实例中，所公开的方法可用于鉴定可能对化学疗法或生物疗法作出反应的CRC肿瘤。还提供了可以与这些方法一起使用的计算机实现的方法，系统和工具包。

10. 发明申请

WO2014102130A1 IMAGE ANALYSIS FOR BREAST CANCER PROGNOSIS 审中-公开
标题翻译：乳腺癌预后的图像分析
公开(公告)号：WO2014102130A1
公开(公告)日：2014-07-03
申请号：PCT/EP2013/077295
申请日：2013-12-19
申请人： VENTANA MEDICAL SYSTEMS, INC. , CLEVELAND CLINIC FOUNDATION , THE UNIVERSITY OF MELBOURNE , F. HOFFMANN-LA ROCHE AG
发明人： CHUKKA, Srinivas , SARKAR, Anindya , SCHEMP, Crystal , SERTEL, Olcay , SINGH, Shalini , TUBBS, Raymond , WARING, Paul Michael , WICK, Nikolaus
IPC分类号： G01N33/574 , G06F19/00
CPC分类号： G06F19/3431 , G01N33/57415 , G01N2800/52 , G01N2800/54 , G06F19/00 , G06F19/22 , G06F19/321 , G16H50/30
摘要： Heterogeneity for biomarkers in a tissue sample can be calculated. A heterogeneity score can be combined with an immunohistochemistry combination score to provide breast cancer recurrence prognosis. Heterogeneity can be based on percent positivity determinations for a plurality of biomarkers according to how many cells in the sample stain positive. An immunohistochemistry combination score can be calculated. An imaging tool can support a digital pathologist workflow that includes designating fields of view in an image of the tissue sample. Based on the fields of view, a heterogeneity metric can be calculated and combined with an immunohistochemistry combination score to generate a breast cancer recurrence prognosis score.
摘要翻译：可以计算组织样品中生物标志物的异质性。异质性评分可与免疫组织化学组合评分相结合，以提供乳腺癌复发预后。异质性可以基于多个生物标志物的百分比阳性测定，根据样品中多少个细胞染色阳性。可以计算免疫组织化学组合评分。成像工具可以支持包括在组织样本的图像中指定视野的数字病理学家工作流程。基于视野，可以计算异质性度量，并与免疫组织化学组合评分相结合，产生乳腺癌复发预后评分。

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