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1. 发明申请

US20110020831A1 GENETIC DETECTION OF HIV-1 STRAINS THAT USE THE CXCR4 CO-RECEPTOR 审中-公开
标题翻译：遗传性检测使用CXCR4 CO受体的HIV-1菌株
公开(公告)号：US20110020831A1
公开(公告)日：2011-01-27
申请号：US12933836
申请日：2009-03-20
申请人： Chris Marlene Verhofstede , Linos Peter Roger Vandekerckhove , Lieven Jozef Stiuver
发明人： Chris Marlene Verhofstede , Linos Peter Roger Vandekerckhove , Lieven Jozef Stiuver
IPC分类号： C12Q1/68
CPC分类号： C12Q1/703 , G01N2333/16 , C12Q2545/114 , C12Q2537/165
摘要： The invention relates to a method for obtaining clonal HIV-1 sequence information from a clinical isolate derived from an HIV-1 infected individual to guide highly active anti-retroviral therapy (HAART) comprising the following steps; a) extracting cell-associated viral nucleic acid b) amplifying said nucleic acid c) obtaining clonal sequence information d) interpreting the clonal sequence information and determining the ratio of the minority viral species by bio-informatics means whereby the ratio obtained is used to guide HAART.
摘要翻译：本发明涉及从源自HIV-1感染个体的临床分离株获得克隆HIV-1序列信息以引导高活性抗逆转录病毒治疗（HAART）的方法，包括以下步骤： a）提取细胞相关病毒核酸b）扩增所述核酸c）获得克隆序列信息d）解释克隆序列信息并通过生物信息学方法确定少数病毒种类的比例，由此获得的比例用于指导 HAART。

2. 发明授权

US07058616B1 Method and system for predicting resistance of a disease to a therapeutic agent using a neural network 失效
标题翻译：使用神经网络预测疾病对治疗剂的抵抗力的方法和系统
公开(公告)号：US07058616B1
公开(公告)日：2006-06-06
申请号：US09589167
申请日：2000-06-08
申请人： Brendan Larder , Dechao Wang
发明人： Brendan Larder , Dechao Wang
IPC分类号： G06N3/02 , C12Q1/70
CPC分类号： G06F19/24 , G06F19/18
摘要： A method and system for predicting the resistance of a disease to a therapeutic agent is provided. Further provided is a method and system for designing a therapeutic treatment agent for a patient afflicted with a disease. Specifically, the methods use a trained neural network to interpret genotypic information obtained from the disease. The trained neural network is trained using a database of known or determined genotypic mutations that are correlated with phenotypic therapeutic agent resistance. The present invention also provides methods and systems for predicting the probability of a patient developing a genetic disease. A trained neural network for making such predictions is also provided.
摘要翻译：提供了一种用于预测疾病对治疗剂的抵抗力的方法和系统。还提供了设计用于患有疾病的患者的治疗剂的方法和系统。具体来说，该方法使用训练有素的神经网络来解释从疾病获得的基因型信息。训练有素的神经网络使用与表型治疗剂抗性相关的已知或确定的基因型突变的数据库进行训练。本发明还提供了用于预测患者发展遗传性疾病的可能性的方法和系统。还提供了用于进行这种预测的经过训练的神经网络。

3. 发明授权

US08338101B2 Method for designing a drug regime for HIV-infected patients 有权
标题翻译：为HIV感染患者设计药物制度的方法
公开(公告)号：US08338101B2
公开(公告)日：2012-12-25
申请号：US12524120
申请日：2008-01-23
申请人： Kurt Van Baelen , Lieven Jozef Stuyver , Kevin Karel Florentina Ariën
发明人： Kurt Van Baelen , Lieven Jozef Stuyver , Kevin Karel Florentina Ariën
IPC分类号： C12Q1/00 , C12Q1/70 , C12Q1/68
CPC分类号： C12Q1/025 , C07H21/04 , C12N7/00 , C12N2740/16021 , C12N2740/16031 , C12N2740/16043 , C12N2740/16051 , C12Q1/703 , G01N2333/16 , G01N2500/02 , G01N2500/10
摘要： The instant disclosure describes a novel genotype and phenotype assay to elucidate and/or evaluate new potential HIV integrase inhibitors, but also currently approved and experimental compounds that target protease, reverse transcriptase, and RNaseH. This assay allows studying linked mutations and mutational patterns that occur under HAART and experimental therapies.
摘要翻译：本公开描述了一种新颖的基因型和表型测定法，用于阐明和/或评估新的潜在的HIV整合酶抑制剂，但也是靶向蛋白酶，逆转录酶和RNA酶H的当前批准和实验化合物。该测定允许研究在HAART和实验疗法下发生的连锁突变和突变模式。

4. 发明授权

US07977053B2 Circular probe amplification (CPA) using energy-transfer primers 有权
标题翻译：使用能量转移引物的圆形探针扩增（CPA）
公开(公告)号：US07977053B2
公开(公告)日：2011-07-12
申请号：US11609436
申请日：2006-12-12
申请人： David C. Thomas
发明人： David C. Thomas
IPC分类号： C12Q1/68 , C12P19/34 , C07H21/02 , C07H21/04
CPC分类号： C12Q1/6844 , C12Q2537/143 , C12Q2525/307 , C12Q2521/101
摘要： The present invention provides methods and kits for the rapid exponential amplification of nucleic acid molecules using a padlock probe. The present invention improves upon the existing methods for amplifying padlock probes by eliminating or delaying the appearance of artifact products that cause false positive results, and also increase the sensitivity and speed of the assay. Further provided are nucleic acid amplification primers containing non-informative base analogs.
摘要翻译：本发明提供了使用挂锁探针快速指数扩增核酸分子的方法和试剂盒。本发明通过消除或延迟造成假阳性结果的伪影产品的外观来改进现有的挂锁探针的方法，并且还提高了测定的灵敏度和速度。还提供含有非信息性碱基类似物的核酸扩增引物。

5. 发明授权

US07292944B2 Establishment of biological cut-off values for predicting resistance to therapy 失效
标题翻译：建立预防耐药性的生物学临界值
公开(公告)号：US07292944B2
公开(公告)日：2007-11-06
申请号：US10399412
申请日：2001-10-22
申请人： Brendan Larder , Richard P. Harrigan , Kurt Hertogs
发明人： Brendan Larder , Richard P. Harrigan , Kurt Hertogs
IPC分类号： G06F19/00
CPC分类号： G01N33/5091 , G01N2800/52
摘要： The present invention concerns methods and systems for improving the accuracy of predicting resistance of a disease to a therapy. In one embodiment of the invention, mean and standard deviation (SD) values of fold change in normalized sensitivity, relative to a laboratory wild type standard pathogen or malignant cell are calculated to demonstrate that the patient samples display inherently different degrees of variation in susceptibility to each therapy. In another embodiment, the 2×SD value for each therapy is used as the cut-off between sensitive (within normal susceptible range) and resistant (above normal susceptible range).
摘要翻译：本发明涉及用于提高预测疾病对治疗的抵抗力的准确性的方法和系统。在本发明的一个实施方案中，计算相对于实验室野生型标准病原体或恶性细胞的归一化灵敏度的折叠变化的平均值和标准偏差（SD）值，以证明患者样品显示出对每次治疗在另一个实施方案中，每次治疗的2xSD值用作敏感（在正常敏感范围内）和抗性（高于正常敏感范围）之间的截止值。

6. 发明授权

US08790870B2 Quantitative HIV phenotype or tropism assay 失效
标题翻译：定量HIV表型或趋向性检测
公开(公告)号：US08790870B2
公开(公告)日：2014-07-29
申请号：US12159813
申请日：2007-02-02
申请人： Lieven Jozef Stuyver , Kurt Van Baelen , Ina Isabel Vandenbroucke
发明人： Lieven Jozef Stuyver , Kurt Van Baelen , Ina Isabel Vandenbroucke
IPC分类号： C12Q1/70 , C12N15/00
CPC分类号： C12Q1/703
摘要： The present invention concerns a method for predicting quantitative phenotype, e.g. gag-phenotype, integrase phenotype or tropism in a patient infected by Human Immunodeficiency Virus (HIV).
摘要翻译：本发明涉及用于预测定量表型的方法。 gag表型，整合酶表型或嗜性感染人类免疫缺陷病毒（HIV）患者。

7. 发明申请

US20130079506A1 METHOD FOR DESIGNING A DRUG REGIME FOR HIV-INFECTED PATIENTS 审中-公开
公开(公告)号：US20130079506A1
公开(公告)日：2013-03-28
申请号：US13668906
申请日：2012-11-05
申请人： VIRCO BVBA
发明人： Kurt Van Baelen , Lieven Jozef Stuyver , Kevin Karel Florentina Arien
IPC分类号： C07H21/04
CPC分类号： C12Q1/025 , C07H21/04 , C12N7/00 , C12N2740/16021 , C12N2740/16031 , C12N2740/16043 , C12N2740/16051 , C12Q1/703 , G01N2333/16 , G01N2500/02 , G01N2500/10
摘要： The instant disclosure describes a novel genotype and phenotype assay to elucidate and/or evaluate new potential HIV integrase inhibitors, but also currently approved and experimental compounds that target protease, reverse transcriptase, and RNaseH. This assay allows studying linked mutations and mutational patterns that occur under HAART and experimental therapies.

8. 发明申请

US20120064514A1 HIV-1-C RESISTANCE MONITORING 审中-公开
标题翻译： HIV-1-C电阻监测
公开(公告)号：US20120064514A1
公开(公告)日：2012-03-15
申请号：US13266973
申请日：2010-05-11
申请人： David Nauwelaers , Lieven Jozef Stuyver
发明人： David Nauwelaers , Lieven Jozef Stuyver
IPC分类号： C12Q1/70 , C12N15/63
CPC分类号： C12Q1/703 , C12N2740/16011 , C12Q2600/106
摘要： The present invention relates to methods for the evaluation of HIV-1 Subtype C (HIV-1-C) treatment. The methods are based on evaluating molecular events at the HIV-1-C gag-protease-reverse transcriptase (GPRT) resulting in altered therapeutic efficacy of investigated anti-retroviral compounds. The methods rely on providing HIV-1-C GPRT RNA and evaluating a treatment either through genotyping or phenotyping methods. Said methods may find a use in the field of diagnostics, drug screening, pharmacogenetics and drug development.
摘要翻译：本发明涉及用于评估HIV-1亚型C（HIV-1-C）治疗的方法。该方法基于评估HIV-1-C gag-蛋白酶 - 逆转录酶（GPRT）上的分子事件，导致所研究的抗逆转录病毒化合物的治疗功效改变。该方法依靠提供HIV-1-C GPRT RNA并通过基因分型或表型分析方法评价治疗。所述方法可用于诊断，药物筛选，药物遗传学和药物开发领域。

9. 发明授权

US08099262B2 Estimation of clinical cut-offs 失效
标题翻译：临床截止的估计
公开(公告)号：US08099262B2
公开(公告)日：2012-01-17
申请号：US10598479
申请日：2005-03-01
申请人： Lee Terry Bacheler , Bart Reginald Alfons Winters
发明人： Lee Terry Bacheler , Bart Reginald Alfons Winters
IPC分类号： G06F17/10
CPC分类号： G06F19/3456 , G06F19/00 , G06F19/18 , G06F19/28 , G06F19/326 , G16H50/50
摘要： Methods and systems for improving the accuracy of predicting resistance of a disease to a drug are described. More specifically, methods for assessing the impact of pre-existing variations in drug susceptibility, whether naturally occurring or selected by previous drug exposure, on treatment response in order to establish clinically relevant cut-off values for phenotypic or genotypic resistance tests are described.
摘要翻译：描述了用于提高预测疾病对药物的抵抗力的准确性的方法和系统。更具体地，描述了用于评估药物敏感性中先前存在的变化（无论是天然存在的或由先前的药物暴露选择）对治疗反应的影响的方法，以便建立用于表型或基因型耐药性试验的临床相关临界值。

10. 发明授权

US07235387B2 Method for mutation detection in HIV-1 using pol sequencing 有权
标题翻译：使用pol测序的HIV-1突变检测方法
公开(公告)号：US07235387B2
公开(公告)日：2007-06-26
申请号：US10258151
申请日：2001-04-20
申请人： Brendan Larder , Sharon Kemp , Stuart Bloor , Ann Brophy
发明人： Brendan Larder , Sharon Kemp , Stuart Bloor , Ann Brophy
IPC分类号： C12Q1/68 , C12Q1/70
CPC分类号： C12Q1/6837 , C12Q1/6858 , C12Q1/6869 , C12Q1/703 , C12Q2537/125 , C12Q2523/101 , C12Q2549/113
摘要： The present invention relates to a method for mutation analysis of the HIV pol gene of HIV virions comprising amplifying virion RNA or DNA via nested PCR using outer primers as represented in SEQ ID No. 1 and 2, amplifying said PCR product via nested PCR using a 5′ and 3′ primer chosen from the inner primers SEQ ID No. 3, 4, 5, and 6, and sequencing this secondary obtained PCR product using at least one sequencing primer chosen from any of SEQ ID No. 7 to 12 or variants thereof. In the alternative, at least one secondary sequencing primer may be used chosen from any of SEQ ID No. 13 to 24. The benefit of the sequences present in the invention resides in the fact that, with the aid of the oligonucleotides, the sequences of all presently known HIV subtypes and all mutations of the pol gene presently known to yield resistance towards antiretroviral therapy can be determined. The present invention also relates to kits for performing such a method as well as primers for performing the same.
摘要翻译：本发明涉及HIV病毒体的HIV pol基因的突变分析方法，其包括使用SEQ ID No.1和2所示的外部引物通过巢式PCR扩增病毒体RNA或DNA，通过巢式PCR扩增所述PCR产物，使用选自内引物SEQ ID No.3,4,5和6的5'和3'引物，并使用至少一种选自SEQ ID No.7至12或任何变体的测序引物对该次级获得的PCR产物进行测序其中。在替代方案中，可以使用从SEQ ID No.13至24中任一个中选择的至少一个二次测序引物。存在于本发明中的序列的益处在于：借助于寡核苷酸，目前已知所有目前已知的HIV亚型和目前已知对抗逆转录病毒治疗产生抗性的pol基因的所有突变可以被确定。本发明还涉及用于进行这种方法的试剂盒以及用于进行该方法的引物。

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