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1. 发明申请

WO2009148593A1 IDENTIFICATION AND USE OF PROGNOSTIC AND PREDICTIVE MARKERS IN CANCER TREATMENT 审中-公开
标题翻译：癌症治疗中预防和预防标记的鉴定与使用
公开(公告)号：WO2009148593A1
公开(公告)日：2009-12-10
申请号：PCT/US2009/003382
申请日：2009-06-02
申请人： NSABP FOUNDATION, INC. , PAIK, Soonmyung , KIM, Chungyeul
发明人： PAIK, Soonmyung , KIM, Chungyeul
IPC分类号： C12Q1/68 , A61K39/395 , A61P35/00
CPC分类号： A61K31/704 , A61K31/337 , A61K31/675 , A61K39/39558 , C12Q1/6841 , C12Q1/6886 , C12Q2600/106 , A61K2300/00
摘要： The present invention provides a method of screening for markers useful in predicting the efficacy of a specified cancer that includes: (a) constructing a tissue microarray from a tissue bank comprising multiple tissue samples that are annotated with clinical follow up data; (b) labeling polynucleic acid probes specific for oncogenes or cancer associated genes known to be potential amplicons; (c) performing fluorescent in situ hybridization analysis on the tissue microarray; and (d) correlating the result of the fluorescent in situ hybridization with the clinical follow up data. The present disclosure also provides methods of treating breast cancer that include screening a breast cancer patient for amplification of one or more of the genes disclosed herein, and treating a patient having amplification of one or more of these genes with a therapeutically effective amount of a compound that interferes with HER2 signaling.
摘要翻译：本发明提供筛选用于预测特定癌症功效的标志物的方法，其包括：（a）从包含多个组织样本的组织库构建组织微阵列，所述多个组织样本用临床跟踪数据注释; （b）标记针对致癌基因或已知为潜在扩增子的癌症相关基因特异性的多核酸探针; （c）对组织微阵列进行荧光原位杂交分析; 和（d）将荧光原位杂交的结果与临床随访数据相关联。本公开还提供了治疗乳腺癌的方法，其包括筛选乳腺癌患者以扩增本文公开的一种或多种基因，并用治疗有效量的化合物治疗具有这些基因中的一种或多种的扩增的患者这干扰了HER2信号。

2. 发明申请

WO2008115419A2 GENE EXPRESSION MARKERS FOR PREDICTION OF PATIENT RESPONSE TO CHEMOTHERAPY 审中-公开
标题翻译：用于预防患者对化疗反应的基因表达标记
公开(公告)号：WO2008115419A2
公开(公告)日：2008-09-25
申请号：PCT/US2008/003398
申请日：2008-03-14
申请人： GENOMIC HEALTH, INC. , NSABP FOUNDATION, INC. , COWENS, Wayne , BAKER, Joffre , LANGONE, Kim , HACKETT, James , WATSON, Drew , PAIK, Soonmyung
发明人： COWENS, Wayne , BAKER, Joffre , LANGONE, Kim , HACKETT, James , WATSON, Drew , PAIK, Soonmyung
IPC分类号： C12Q1/68
CPC分类号： G01N33/57419 , C12Q1/6886 , C12Q2600/106 , C12Q2600/118 , C12Q2600/158 , G06F19/00
摘要： A method of predicting clinical outcome in a subject diagnosed with cancer and treated with chemotherapy comprising determining evidence of the expression of one or more predictive RNA transcripts or their expression products in a biological sample comprising cancer cells obtained from the subject.
摘要翻译：一种预测患有癌症并用化疗治疗的受试者的临床结果的方法，其包括确定一种或多种预测性RNA转录物或其表达产物在包含从受试者获得的癌细胞的生物样品中的表达的证据。

3. 发明申请

WO2009114836A1 GENE EXPRESSION MARKERS FOR PREDICTION OF PATIENT RESPONSE TO CHEMOTHERAPY 审中-公开
标题翻译：用于预防患者对化疗反应的基因表达标记
公开(公告)号：WO2009114836A1
公开(公告)日：2009-09-17
申请号：PCT/US2009/037203
申请日：2009-03-13
申请人： GENOMIC HEALTH, INC. , NSABP FOUNDATION INC. , BAKER, Joffre, B. , COWENS, Wayne , LANGONE, Kim , HACKETT, James , WATSON, Drew , PAIK, Soonmyung
发明人： BAKER, Joffre, B. , COWENS, Wayne , LANGONE, Kim , HACKETT, James , WATSON, Drew , PAIK, Soonmyung
IPC分类号： C12Q1/68 , G01N33/48 , G06F19/00
CPC分类号： C12Q1/6886 , C12Q2600/106 , C12Q2600/158 , G01N33/57419 , G01N2800/52
摘要： Gene sets which are useful in assessing prognosis and/or predicting the response of cancer, e.g. colorectal cancer to chemotherapy, are disclosed. Also disclosed is a clinically validated cancer test, e.g. colorectal test, for assessment of prognosis and/or prediction of patient response to chemotherapy, using expression analysis. The use of archived paraffin embedded biopsy material for assay of all markers in the relevant gene sets is accomodated for, and therefore is compatible with the most widely available type of biopsy material.
摘要翻译：可用于评估预后和/或预测癌症反应的基因组，例如。公开了结肠直肠癌化疗。还公开了临床验证的癌症测试，例如使用表达分析来评估预后和/或预测患者对化学疗法的反应。使用存档石蜡包埋的活检材料来测定相关基因组中的所有标记物，因此与最广泛可用的活检材料类型相容。

4. 发明申请

WO2007127458A3 METHODS OF WHOLE GENOME OR MICROARRAY EXPRESSION PROFILING USING NUCLEIC ACIDS 审中-公开
标题翻译：使用核酸的全基因组或微阵列表达谱的方法
公开(公告)号：WO2007127458A3
公开(公告)日：2007-12-27
申请号：PCT/US2007010392
申请日：2007-04-30
申请人： NSABP FOUNDATION INC , PAIK SOONMYUNG , POGUE-GEILE KATHERINE LEA , KIM CHUNGYEUI
发明人： PAIK SOONMYUNG , POGUE-GEILE KATHERINE LEA , KIM CHUNGYEUI
IPC分类号： C12P19/34
CPC分类号： C12Q1/6806 , C12N15/1003 , C12Q1/6837 , C12Q2565/515
摘要： The present invention provides novel methods for analyzing gene expression levels from fresh or aged (more than one year old) formalin-fixed, paraffin-embedded tissue ("FFPET") samples that comprise pre-hybridizing a labeled nucleic acid sample prepared from the formalin-fixed, paraffin-embedded tissue sample with a first microarray, hybridizing the unbound labeled nucleic acid sample with a second microarray, and detecting the labeled nucleic acid sample bound to the second microarray. The pre-hybridization step results in an increase in the specific gene signals in subsequent hybridizations with high density gene expression arrays. The first microarray used for the pre-hybridization step can be either a new or used microarray. Importantly, from a cost-savings perspective, the inventors determined that when the first microarray used for the pre-hybridization step is a previously used microarray, the results of the subsequent hybridization on a second microarray are nearly identical to the results obtained when the pre-hybridization was carried out using a new or previously unused microarray.
摘要翻译：本发明提供用于分析来自新鲜或老化（一岁以上）福尔马林固定的石蜡包埋组织（“FFPET”）样品的基因表达水平的新方法，其包括将从福尔马林制备的标记的核酸样品预先杂交固定的石蜡包埋的组织样品与第一微阵列，将未结合的标记的核酸样品与第二微阵列杂交，并检测结合到第二微阵列的标记的核酸样品。预杂交步骤导致随后与高密度基因表达阵列杂交的特异性基因信号的增加。用于预杂交步骤的第一个微阵列可以是新的或使用过的微阵列。重要的是，从成本节约的角度来看，发明人确定当用于预杂交步骤的第一微阵列是先前使用的微阵列时，第二微阵列上的随后杂交的结果几乎与当预先 - 使用新的或以前未使用的微阵列进行杂交。

5. 发明申请

WO2005008213A2 EXPRESSION PROFILE ALGORITHM AND TEST FOR CANCER PROGNOSIS 审中-公开
标题翻译：表达简档算法和癌症预防测试
公开(公告)号：WO2005008213A2
公开(公告)日：2005-01-27
申请号：PCT/US2004/021163
申请日：2004-06-30
申请人： GENOMIC HEALTH, INC. , BAKER, Joffre , BRYANT, John, L. , PAIK, Soonmyung , SHAK, Steven
发明人： BAKER, Joffre , BRYANT, John, L. , PAIK, Soonmyung , SHAK, Steven
IPC分类号： G01N
CPC分类号： C12Q1/6886 , C12Q2600/106 , C12Q2600/118 , C12Q2600/158 , G01N33/57415 , G01N33/57484 , G01N33/57492 , G06F19/20 , G06F19/24
摘要： The present invention provides a noninvasive, quantitative test for prognosis determination in cancer patients. The test relies on measurements of the tumor levels of certain messenger RNAs (mRNAs). These mRNA levels are inserted into a polynomial formula (algorithm) that yields a numerical recurrence score, which indicates recurrence risk.
摘要翻译：本发明提供了癌症患者预后测定的无创定量试验。测试依赖于某些信使RNA（mRNA）的肿瘤水平的测量。将这些mRNA水平插入到产生数字复发评分的多项式公式（算法）中，其表示复发风险。

6. 发明申请

WO2007082099A2 GENE EXPRESSION MARKERS FOR COLORECTAL CANCER PROGNOSIS 审中-公开
标题翻译：基因表达标记用于彩色癌症预防
公开(公告)号：WO2007082099A2
公开(公告)日：2007-07-19
申请号：PCT/US2007/000995
申请日：2007-01-11
申请人： GENOMIC HEALTH, INC. , NASBP FOUNDATION, INC. , COWENS, Wayne , BAKER, Joffre, B. , CLARK, Kim , HACKETT, James , WATSON, Drew , PAIK, Soonmyung
发明人： COWENS, Wayne , BAKER, Joffre, B. , CLARK, Kim , HACKETT, James , WATSON, Drew , PAIK, Soonmyung
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6886 , C12Q2600/106 , C12Q2600/118 , G01N33/57419 , G01N33/57446
摘要： A method of predicting clinical outcome in a subject diagnosed with colorectal cancer comprising determining evidence of the expression of one or more predictive RNA transcripts or their expression products in a biological sample of cancer cells obtained from the subject.
摘要翻译：一种预测患有结肠直肠癌的受试者的临床结果的方法，包括确定从受试者获得的癌细胞的生物样品中一种或多种预测性RNA转录物或其表达产物的表达的证据。

7. 发明申请

WO2006065940A2 IDENTIFICATION AND USE OF PROGNOSTIC AND PREDICTIVE MARKERS IN CANCER TREATMENT 审中-公开
标题翻译：在癌症治疗中识别和使用预测性和预测性标志物
公开(公告)号：WO2006065940A2
公开(公告)日：2006-06-22
申请号：PCT/US2005/045322
申请日：2005-12-15
申请人： NSABP FOUNDATION, INC. , PAIK, Soonmyung , KIM, Chungyeul
发明人： PAIK, Soonmyung , KIM, Chungyeul
IPC分类号： C12Q1/68 , G01N33/574
CPC分类号： G01N33/5082 , C12Q1/6886 , C12Q2600/106 , C12Q2600/158 , G01N33/574 , G01N33/57415 , G01N33/57492 , G01N33/6845 , G01N2500/00
摘要： The present invention provides a method of screening for markers useful in predicting the efficacy of a specified cancer that includes: (a) constructing a tissue microarray from a tissue bank comprising multiple tissue samples that are annotated with clinical follow up data; (b) labeling polynucleic acid probes specific for oncogenes or cancer associated genes known to be potential amplicons; (c) performing fluorescent in situ hybridization analysis on the tissue microarray; and (d) correlating the result of the fluorescent in situ hybridization with the clinical follow up data. In addition, the present invention provides a method of treating breast cancer that includes measuring the expression levels or amplification of HTPAP in a patient having breast cancer and then providing a patient having increased levels of HTPAP expression or HTPAP amplification with therapeutic quantities of at least one compound that interferes with the phosphatidic acid phosphatase activity of HTPAP. The present invention also encompasses a method of treating breast cancer that includes screening a breast cancer patient for amplification of the cMYC gene and then treating a patient having amplification of the cMYC gene with therapeutic quantities of a compound that interferes with HER2 signaling.
摘要翻译：本发明提供筛选可用于预测特定癌症功效的标志物的方法，所述方法包括：（a）从包含多个组织样本的组织库构建组织样本，所述组织样本用临床跟进数据; （b）标记对已知为潜在扩增子的致癌基因或癌症相关基因特异性的多核苷酸探针; （c）对组织微阵列进行荧光原位杂交分析; 和（d）将荧光原位杂交的结果与临床随访数据相关联。此外，本发明提供了治疗乳腺癌的方法，其包括测量患有乳腺癌的患者中的HTPAP的表达水平或扩增，然后提供具有增加水平的HTPAP表达或HTPAP扩增的患者，其治疗量为至少一种干扰HTPAP的磷脂酸磷酸酶活性的化合物。本发明还包括治疗乳腺癌的方法，包括筛选乳腺癌患者扩增cMYC基因，然后用治疗量的干扰HER2信号传导的化合物治疗患有cMYC基因扩增的患者。

8. 发明申请

WO2006052731A3 MOLECULAR INDICATORS OF BREAST CANCER PROGNOSIS AND PREDICTION OF TREATMENT RESPONSE 审中-公开
公开(公告)号：WO2006052731A3
公开(公告)日：2006-05-18
申请号：PCT/US2005/039970
申请日：2005-11-04
申请人： GENOMIC HEALTH, INC. , NSABP FOUNDATION, INC. , BAKER, Joffre, B. , BRYANT, John, L. , PAIK, Soonmyung , SHAK, Steven
发明人： BAKER, Joffre, B. , BRYANT, John, L. , PAIK, Soonmyung , SHAK, Steven
IPC分类号： C12Q1/68 , G01N33/574 , C12N15/10
摘要： The present invention relates to quantitative molecular indicators that can guide clinical decisions in breast cancer, such as estrogen receptor (ESR1)-positive, lymph node-negative breast cancer. In particular, the invention concerns certain genes, the varied expression of which indicates the likelihood of recurrence of surgically resected breast cancer in patients who are not treated with a therapeutic agent in the adjuvant setting. In addition, the invention concerns the use of quantitative measurement of the expression of certain genes, including the ESR1 gene, that measures as a continuous variable, to determine (a) the likelihood of a beneficial response to the anti-estrogen therapeutic agent, such as tamoxifen; and (b) the potential magnitude of beneficial response to chemotheraphy.

9. 发明申请

WO2014190311A2 DEFECTIVE MISMATCH REPAIR AND BENEFIT FROM BEVACIZUMAB FOR COLON CANCER 审中-公开
标题翻译：来自BEVACIZUMAB针对结肠癌的缺陷性障碍修复和益处
公开(公告)号：WO2014190311A2
公开(公告)日：2014-11-27
申请号：PCT/US2014039429
申请日：2014-05-23
申请人： NSABP FOUNDATION INC , POGUE-GEILE KATHERINE LEA , PAIK SOONMYUNG
发明人： POGUE-GEILE KATHERINE LEA , PAIK SOONMYUNG
IPC分类号： A61K39/395
CPC分类号： C07K16/22 , A61K39/39558 , A61K45/06 , C12Q1/6886 , C12Q2600/106 , C12Q2600/154 , C12Q2600/156 , G01N33/57419 , G01N2333/922 , G01N2800/52 , A61K2300/00
摘要： Methods of testing to identify and to treat a subset of colon cancer patients exhibiting dMMR tumor tissue, who derive significant clinical benefit from the addition of bevacizumab to standard adjuvant chemotherapy. The presence of a V600E BRAF munition is also of significance.
摘要翻译：鉴定和治疗显示dMMR肿瘤组织的结肠癌患者亚组的测试方法，其从标准辅助化学疗法中加入贝伐珠单抗获得显着的临床益处。 V600E BRAF弹药的存在也是重要的。

10. 发明申请

WO2011133979A1 METHODS TO EXPAND THE ELIGIBLE PATIENT POPULATION FOR HER2-DIRECTED TARGETED THERAPIES 审中-公开
标题翻译：扩大符合HER2指导目标治疗资格的患者人口的方法
公开(公告)号：WO2011133979A1
公开(公告)日：2011-10-27
申请号：PCT/US2011/033807
申请日：2011-04-25
申请人： NSABP FOUNDATION, INC. , PAIK, Soonmyung , POGUE-GEILE, Katherine , GAVIN, Patrick
发明人： PAIK, Soonmyung , POGUE-GEILE, Katherine , GAVIN, Patrick
IPC分类号： G01N33/574
CPC分类号： G01N33/57415 , C12Q1/6886 , C12Q2600/106 , C12Q2600/158 , G01N2800/52
摘要： The present disclosure provides improved methods for identifying breast cancer patients that receive an increased benefit from the addition of a HER2-targeted therapy, for example adjuvant trastuzumab, to chemotherapy.
摘要翻译：本公开提供了用于鉴定从添加HER2靶向治疗（例如曲妥珠单抗佐剂）到化疗的增加益处的乳腺癌患者的改进方法。

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