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1. 发明申请

US20120072124A1 GENES ASSOCIATED WITH PROGRESSION AND RESPONSE IN CHRONIC MYELOID LEUKEMIA AND USES THEREOF 审中-公开
标题翻译：与慢性粒细胞白血病有关的进展与反应的基因及其用途
公开(公告)号：US20120072124A1
公开(公告)日：2012-03-22
申请号：US13207282
申请日：2011-08-10
申请人： Jerald P. Radich , Hongyue Dai , Mao Mao , Janell M. Schelter , Peter S. Linsley
发明人： Jerald P. Radich , Hongyue Dai , Mao Mao , Janell M. Schelter , Peter S. Linsley
IPC分类号： G06F19/20 , G01N33/50
CPC分类号： C12Q1/6886 , C12Q2600/106 , C12Q2600/112 , C12Q2600/136 , C12Q2600/158 , Y02A90/26
摘要： The invention provides molecular markers that are associated with the progression of chronic myeloid leukemia (CML), and methods and computer systems for monitoring the progression of CML in a patient based on measurements of these molecular markers. The present invention also provides CML target genes, and methods and compositions for treating CML patients by modulating the expression or activity of these CML target genes and/or their encoded proteins. The invention also provides genes that are associated with resistance to imatinib mesylate (Gleevec™) treatment in CML patients, and methods and compositions for determining the responsiveness of a CML patient to imatinib mesylate treatment based on measurements of these genes and/or their encoded proteins. The invention also provides methods and compositions for enhancing the effect of Gleevec™ by modulating the expression or activity of these genes and/or their encoded proteins.
摘要翻译：本发明提供了与慢性骨髓性白血病（CML）进展相关的分子标记，以及用于基于这些分子标记物的测量来监测患者中CML进展的方法和计算机系统。本发明还提供CML靶基因，以及通过调节这些CML靶基因和/或其编码蛋白的表达或活性来治疗CML患者的方法和组合物。本发明还提供了与CML患者中对伊马替尼甲磺酸盐（Gleevec TM）治疗有关的基因，以及基于这些基因和/或其编码蛋白质的测量来确定CML患者对甲磺酸伊马替尼治疗的反应性的方法和组合物。本发明还提供了通过调节这些基因和/或其编码的蛋白质的表达或活性来增强Gleevec TM的作用的方法和组合物。

2. 发明申请

US20100106460A1 NON-CONTIGUOUS REGIONS PROCESSING 有权
标题翻译：非连续区域处理
公开(公告)号：US20100106460A1
公开(公告)日：2010-04-29
申请号：US12421562
申请日：2009-04-09
申请人： Ernst S. Henle , Brandon T. Hunt
发明人： Ernst S. Henle , Brandon T. Hunt
IPC分类号： G06F15/00 , H01J49/26
CPC分类号： G06K9/3233 , G06K9/6203
摘要： Non-contiguous regions of interest as well as contiguous regions of interest are similarly processed. After an isotope peak detector has identified isotope peaks on LC/MS images, a microaligner microaligns bounding areas of identified isotope peaks and redefines the bounding areas to help subsequent scoring process. Forms of isotope peaks influence formation of a peak association matrix and a mass/charge association map which creates association in the mass/charge dimension. A correlation scorer produces reproducibility scores as well as quality scores to help aid scientists to discover biological features of interest.
摘要翻译：类似地处理非连续的感兴趣区域以及连续的感兴趣区域。在同位素峰检测器已经在LC / MS图像上鉴定出同位素峰之后，微标记物微分界定识别的同位素峰的区域，并重新界定了界限区域以帮助随后的评分过程。同位素峰的形式影响峰关联矩阵的形成和质量/电荷关联图，其在质量/电荷维度中产生缔合。相关记分仪产生重现性分数以及质量分数，以帮助科学家发现感兴趣的生物学特征。

3. 发明申请

US20100040552A1 METHODS TO EVALUATE GLUCOCORTICOID RECEPTOR AGONISTS AND ANTAGONISTS FOR EFFECTS ON NEURON-LIKE CELLS 审中-公开
标题翻译：评估GLUCOCORTICOID受体激动剂的方法和对神经元样细胞的影响的拮抗剂
公开(公告)号：US20100040552A1
公开(公告)日：2010-02-18
申请号：US12579230
申请日：2009-10-14
申请人： David J. Stone , Janet E. Clark , Edward C. Hayes, III
发明人： David J. Stone , Janet E. Clark , Edward C. Hayes, III
IPC分类号： A61K49/00 , G01N33/53 , A61P29/00
CPC分类号： G01N33/5058 , A61K49/0008 , G01N33/5044 , G01N33/5088
摘要： The present invention provides methods for identifying a modulator of glucocorticoid receptor activity. In one embodiment, the methods include the steps of (a) contacting neuron-like cells, in vitro, with a chemical agent; (b) measuring the expression of a member, or group of members, of a group of genes (as defined herein) in the neuron-like cells contacted with the chemical agent; and (c) determining whether the chemical agent significantly alters the expression of the member, or group of members, of the group of genes, thereby determining whether the chemical agent is likely to be a modulator of glucocorticoid receptor activity. In another embodiment, an in vivo method for identifying a modulator of glucocorticoid receptor activity is provided.
摘要翻译：本发明提供鉴定糖皮质激素受体活性调节剂的方法。在一个实施方案中，所述方法包括以下步骤：（a）将体外的神经元样细胞与化学试剂接触; （b）测量与化学试剂接触的神经元样细胞中一组基因（如本文所定义）的成员或成员组的表达; 和（c）确定化学试剂是否显着改变基因组成员或成员组的表达，从而确定化学试剂是否可能是糖皮质激素受体活性的调节剂。在另一个实施方案中，提供了用于鉴定糖皮质激素受体活性调节剂的体内方法。

4. 发明申请

US20080187909A1 Classification of Breast Cancer Patients Using a Combination of Clinical Criteria and Informative Genesets 失效
标题翻译：乳腺癌患者使用临床标准和信息基因组合的分类
公开(公告)号：US20080187909A1
公开(公告)日：2008-08-07
申请号：US10591800
申请日：2005-03-07
申请人： Hongyue Dai , Laura J. Van't Veer , John Lamb , Roland Stoughton , Stephen H. Friend , Yudong He
发明人： Hongyue Dai , Laura J. Van't Veer , John Lamb , Roland Stoughton , Stephen H. Friend , Yudong He
IPC分类号： C12Q1/68 , C40B40/06
CPC分类号： G01N33/57415 , C12Q1/6886 , C12Q2600/106 , C12Q2600/112 , C12Q2600/118 , Y10T436/143333
摘要： The present invention provides prognostic methods for conditions such as cancer, for example, breast cancer, comprising classifying an individual by a plurality of phenotypic, genotypic or clinical characteristics of the condition into a plurality of patient subsets, and analyzing the pattern of expression of prognosis-informative genes identified for that subset in a sample from the individual. The present invention also provides methods for constructing such patient subsets and of identifying prognosis-informative genesets for such subsets. The invention further provides methods of assigning a therapeutic regimen to an individual, microarrays useful for performing prognosis, kits comprising these microarrays, and computer systems and programs for implementing the methods of the invention.
摘要翻译：本发明提供了诸如癌症例如乳腺癌的病症的预后方法，包括将个体的多个表型，基因型或临床特征分类为多个患者子集，并分析预后表达模式在来自个体的样品中识别该子集的信息基因。本发明还提供了用于构建这样的患者子集以及鉴定这样的子集的预后信息性基因组的方法。本发明进一步提供了将个体的治疗方案分配给用于进行预后的微阵列，包括这些微阵列的试剂盒以及用于实施本发明的方法的计算机系统和程序的方法。

5. 发明申请

US20070275407A1 Methods for determining therapeutic index from gene expression profiles 失效
公开(公告)号：US20070275407A1
公开(公告)日：2007-11-29
申请号：US11879161
申请日：2007-07-16
申请人： Matthew Marton , Roland Stoughton
发明人： Matthew Marton , Roland Stoughton
IPC分类号： C12Q1/68 , C12Q1/18 , G01N33/566
CPC分类号： C12Q1/6883 , C12Q1/025 , C12Q1/18 , C12Q2600/106 , C12Q2600/158 , G01N33/5005 , G01N33/5088 , G06F19/20 , G06F19/70
摘要： This invention provides methods for determining drug specificity, therapeutic index and effective doses for individual patients. According to the methods of the invention, graded levels of drug are applied to a biological sample or a patient. A plurality of cellular constituents are measured to determine the activity of the drug on a target pathway and at least one off-target pathway. A drug specificity is determined by comparing the target and off target activities of the drug. A therapeutic concentration (or dose) is defined as a concentration (or dose) of the drug that induces certain response in the target pathway. A toxic concentration (or dose) is defined as a concentration (or dose) of the drug that induces certain response in the off target pathway. Therapeutic index is the ratio of the toxic concentration over therapeutic concentration. Methods are also provided to determine an effective dose of a drug for a patient by measuring the activity of the drug on the particular patient.

6. 发明申请

US20060292623A1 Signature genes in chronic myelogenous leukemia 审中-公开
公开(公告)号：US20060292623A1
公开(公告)日：2006-12-28
申请号：US11510798
申请日：2006-08-25
申请人： Peter Linsley , Mao Mao , Hongyue Dai , Yudong He , Jerald Radich
发明人： Peter Linsley , Mao Mao , Hongyue Dai , Yudong He , Jerald Radich
IPC分类号： C12Q1/68 , G06F19/00
CPC分类号： G01N33/57426 , C12Q1/6837 , C12Q1/6886 , C12Q2600/158 , G16B25/00
摘要： The present invention relates to genetic markers whose expression is correlated with progression of CML. Specifically, the invention provides sets of markers whose expression patterns can be used to differentiate chronic phase individuals from those in blast crisis. The invention relates to methods of using these markers to distinguish these conditions. The invention also relates to kits containing ready-to-use microarrays and computer software for data analysis using the statistical methods disclosed herein.

7. 发明申请

US20060241869A1 Computer systems and methods for inferring causality from cellullar constituent abundance data 审中-公开
标题翻译：计算机系统和方法，从细胞组成丰度数据推断因果关系
公开(公告)号：US20060241869A1
公开(公告)日：2006-10-26
申请号：US11361871
申请日：2006-02-23
申请人： Eric Schadt , John Lamb
发明人： Eric Schadt , John Lamb
IPC分类号： G06F19/00
CPC分类号： G01N33/5041 , C12Q1/6883 , C12Q1/6886 , C12Q2600/136 , C12Q2600/154 , C12Q2600/172 , G01N33/5023 , G01N2800/04 , G01N2800/042 , G01N2800/044 , G01N2800/105 , G01N2800/108 , G01N2800/122 , G01N2800/301 , G01N2800/304 , G01N2800/323 , G16B20/00
摘要： Methods for determining whether a molecule affects a disorder are provided. A cell from an organism is contacted with the molecule, or the molecule is expressed within the cell. A determination is made as to whether the RNA or protein expression in the cell of at least one open reading frame is changed relative to the expression of the reading frame in the absence of the molecule. Each such open reading frame is regulated by a promoter native to SEQ ID NOS: 5-9, 11-12, 14, 16, 18, 20-21, 23, 25, 27, 29, 31, 33 or homologs of the foregoing. A determination is made as to whether the molecule affects the disorder when the RNA or protein expression of the at least one reading frame is changed. Alternatively, a determination is made that the molecule does not affect the disorder when the RNA or protein expression of the at least one reading frame is unchanged.
摘要翻译：提供了确定分子是否影响病症的方法。来自生物体的细胞与分子接触，或者分子在细胞内表达。确定在不存在分子的情况下，至少一个开放阅读框的细胞中的RNA或蛋白质表达是否相对于阅读框的表达而改变。每个这样的开放阅读框架由SEQ ID NOS：5-9,11-12,14,16,18,20-21,23,25,27,29,31,33天然的启动子或前述同源物调节。当改变至少一个阅读框的RNA或蛋白质表达时，确定分子是否影响病症。或者，当至少一个阅读框的RNA或蛋白质表达不变时，确定分子不影响病症。

8. 发明申请

US20060166199A1 Methods to assess quality of microarrays 有权
公开(公告)号：US20060166199A1
公开(公告)日：2006-07-27
申请号：US10520031
申请日：2003-06-27
申请人： Matthew Marton , Michael Meyer , Allan Jones
发明人： Matthew Marton , Michael Meyer , Allan Jones
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6837 , B01J19/0046 , B01J2219/0036 , B01J2219/00378 , B01J2219/00432 , B01J2219/00497 , B01J2219/00527 , B01J2219/00574 , B01J2219/00576 , B01J2219/00585 , B01J2219/00596 , B01J2219/00605 , B01J2219/00608 , B01J2219/0061 , B01J2219/00612 , B01J2219/00617 , B01J2219/00626 , B01J2219/00641 , B01J2219/00659 , B01J2219/00675 , B01J2219/00689 , B01J2219/00693 , B01J2219/00695 , B01J2219/00722 , B01J2219/00725 , B01J2219/00727 , B01J2219/00731 , B82Y30/00 , C07H21/04 , G06F19/20
摘要： The present invention relates to methods and compositions for assessing the quality of microarrays. In particular, the invention relates to the use of quality control probes that are synthesized on the microarray monomer by monomer in a step-by-step synthesis. By assessing the degree of signal from the quality control probes and determining their deviation from expected signal intensities, the quality of microarray synthesis can be ascertained. The invention further relates to a method of detecting defects occurring during storage or processing of the microarray. The invention further relates to a method of using a computer to identify microarrays that have had a defect or defects during synthesis, storage, or processing.

9. 发明申请

US20060141501A1 Iterative probe design and detailed expression profiling with flexible in-situ synthesis arrays 审中-公开
标题翻译：迭代探针设计和具有灵活原位合成阵列的详细表达谱
公开(公告)号：US20060141501A1
公开(公告)日：2006-06-29
申请号：US11282025
申请日：2005-11-16
申请人： Stephen Friend , Roland Stoughton , Peter Linsley , Julia Burchard
发明人： Stephen Friend , Roland Stoughton , Peter Linsley , Julia Burchard
IPC分类号： C12Q1/68
CPC分类号： G16B25/00
摘要： Methods and compositions are provided that are useful for detecting and reporting a plurality of different target polynucleotide sequences in a sample, such as polynucleotides corresponding to a plurality of different genes expressed by a cell or cells. In particular, the invention provides methods for screening a plurality of candidate polynucleotide probes to evaluate both the sensitivity and the specificity with which each candidate probe hybridizes to a target polynucleoide sequence. Candidate polynucleotide probes can then be ranked according to both their sensitivity and specificity, and probes that have optimal sensitivity and specificity for a target polynucleotide sequence can be selected. In one embodiment, polynucleotide probes can be selected according to the methods described herein to prepare “screening chips” wherein a large number of target polynucleotide sequences are detected using a single microarray have a few (e.g., 1-5) probes for each target polynucleotide sequence. In a particularly preferred embodiment, the invention provides a screening chip that can detect genetic transcripts from the entire genome of an organism. In an alternative embodiment, polynucleotide probes can be selected according to the methods described herein to prepare “signature chips” to more accurately detect certain selected “signature genes” using several polynucleotide probes (e:g., 10-20) for each signature gene. The invention additionally provides microarrays containing polynucleotide probes for a large number of genes expressed by a cell or organism. Further, methods for detecting a plurality of polynucleotide molecules, including a large number of genes expressed by a cell or organism, are also provided.
摘要翻译：提供了可用于检测和报告样品中多个不同靶多核苷酸序列的方法和组合物，例如对应于由细胞或细胞表达的多种不同基因的多核苷酸。特别地，本发明提供了筛选多个候选多核苷酸探针以评估每个候选探针与目标多核苷酸序列杂交的灵敏度和特异性的方法。然后可以根据其灵敏度和特异性对候选多核苷酸探针进行排序，并且可以选择对靶多核苷酸序列具有最佳敏感性和特异性的探针。在一个实施方案中，可以根据本文所述的方法选择多核苷酸探针以制备“筛选芯片”，其中使用单个微阵列检测大量目标多核苷酸序列，其中每个靶多核苷酸具有少量（例如1-5）探针序列。在一个特别优选的实施方案中，本发明提供了可以检测来自生物体的整个基因组的遗传转录物的筛选芯片。在替代实施方案中，可以根据本文所述的方法选择多核苷酸探针，以制备“签名芯片”，以使用每个签名基因的多个多核苷酸探针（例如，10-20）更准确地检测某些所选择的“签名基因” 。本发明另外提供含有由细胞或生物表达的大量基因的多核苷酸探针的微阵列。此外，还提供了用于检测多个多核苷酸分子的方法，包括由细胞或生物体表达的大量基因。

10. 发明授权

US07013221B1 Iterative probe design and detailed expression profiling with flexible in-situ synthesis arrays 有权
标题翻译：迭代探针设计和具有灵活原位合成阵列的详细表达谱
公开(公告)号：US07013221B1
公开(公告)日：2006-03-14
申请号：US09561487
申请日：2000-04-28
申请人： Stephen H. Friend , Roland Stoughton , Peter S. Linsley , Julja Burchard
发明人： Stephen H. Friend , Roland Stoughton , Peter S. Linsley , Julja Burchard
IPC分类号： G01N33/48 , C12Q1/68
CPC分类号： G06F19/20
摘要： Methods and compositions are provided that are useful for detecting and reporting a plurality of different target polynucleotide sequences in a sample, such as polynucleotides corresponding to a plurality of different genes expressed by a cell or cells. In particular, the invention provides methods for screening a plurality of candidate polynucleotide probes to evaluate both the sensitivity and the specificity with which each candidate probe hybridizes to a target polynucleoide sequence. Candidate polynucleotide probes can then be ranked according to both their sensitivity and specificity, and probes that have optimal sensitivity and specificity for a target polynucleotide sequence can be selected. In one embodiment, polynucleotide probes can be selected according to the methods described herein to prepare “screening chips” wherein a large number of target polynucleotide sequences are detected using a single microarray have a few (e.g., 1–5) probes for each target polynucleotide sequence. In a particularly preferred embodiment, the invention provides a screening chip that can detect genetic transcripts from the entire genome of an organism. In an alternative embodiment, polynucleotide probes can be selected according to the methods described herein to prepare “signature chips” to more accurately detect certain selected “signature genes” using several polynucleotide probes (e.g., 10–20) for each signature gene. The invention additionally provides microarrays containing polynucleotide probes for a large number of genes expressed by a cell or organism. Further, methods for detecting a plurality of polynucleotide molecules, including a large number of genes expressed by a cell or organism, are also provided.
摘要翻译：提供了可用于检测和报告样品中多个不同靶多核苷酸序列的方法和组合物，例如对应于由细胞或细胞表达的多种不同基因的多核苷酸。特别地，本发明提供了筛选多个候选多核苷酸探针以评估每个候选探针与目标多核苷酸序列杂交的灵敏度和特异性的方法。然后可以根据其灵敏度和特异性对候选多核苷酸探针进行排序，并且可以选择对靶多核苷酸序列具有最佳敏感性和特异性的探针。在一个实施方案中，可以根据本文所述的方法选择多核苷酸探针以制备“筛选芯片”，其中使用单个微阵列检测大量目标多核苷酸序列，其中每个靶多核苷酸具有少量（例如1-5）探针序列。在一个特别优选的实施方案中，本发明提供了可以检测来自生物体的整个基因组的遗传转录物的筛选芯片。在替代实施方案中，可以根据本文所述的方法选择多核苷酸探针以通过使用每个特征基因的多个多核苷酸探针（例如10-20）来制备“签名芯片”以更精确地检测某些所选择的“特征基因”。本发明另外提供含有由细胞或生物表达的大量基因的多核苷酸探针的微阵列。此外，还提供了用于检测多个多核苷酸分子的方法，包括由细胞或生物体表达的大量基因。

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