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1. 发明授权

US08748103B2 Monitoring health and disease status using clonotype profiles 有权
公开(公告)号：US08748103B2
公开(公告)日：2014-06-10
申请号：US13100365
申请日：2011-05-04
申请人： Malek Faham , Thomas Willis
发明人： Malek Faham , Thomas Willis
IPC分类号： C12Q1/68 , C12P19/34
CPC分类号： C12Q1/6886 , C12Q1/6874 , C12Q1/6881 , C12Q1/6883 , C12Q2600/112 , C12Q2600/118 , C12Q2600/156 , C12Q2600/158 , C12Q2600/16
摘要： There is a need for improved methods for determining the diagnosis and prognosis of patients with conditions, including autoimmune disease and cancer, especially lymphoid neoplasms, such as lymphomas and leukemias. Provided herein are methods for using DNA sequencing to identify personalized, or patient-specific biomarkers in patients with lymphoid neoplasms, autoimmune disease and other conditions. Identified biomarkers can be used to determine and/or monitor the disease state for a subject with an associated lymphoid disorder or autoimmune disease or other condition. In particular, the invention provides a sensitive method for monitoring lymphoid neoplasms that undergo clonal evolutions without the need to development alternative assays for the evolved or mutated clones serving as patient-specific biomarkers.

2. 发明授权

US08628927B2 Monitoring health and disease status using clonotype profiles 有权
标题翻译：使用克隆型概况监测健康和疾病状态
公开(公告)号：US08628927B2
公开(公告)日：2014-01-14
申请号：US13763978
申请日：2013-02-11
申请人： Malek Faham , Thomas Willis
发明人： Malek Faham , Thomas Willis
IPC分类号： C12P19/34 , C12Q1/68
CPC分类号： C12Q1/6886 , C12Q1/6881 , C12Q1/6883 , C12Q2600/118 , C12Q2600/156 , C12Q2600/158 , C12Q2600/16
摘要： There is a need for improved methods for determining the diagnosis and prognosis of patients with conditions, including autoimmune disease and cancer, especially lymphoid neoplasms, such as lymphomas and leukemias. Provided herein are methods for using DNA sequencing to identify personalized, or patient-specific biomarkers in patients with lymphoid neoplasms, autoimmune disease and other conditions. Identified biomarkers can be used to determine and/or monitor the disease state for a subject with an associated lymphoid disorder or autoimmune disease or other condition. In particular, the invention provides a sensitive method for monitoring lymphoid neoplasms that undergo clonal evolutions without the need to development alternative assays for the evolved or mutated clones serving as patient-specific biomarkers.
摘要翻译：需要一种改进的方法来确定包括自身免疫性疾病和癌症在内的患者的诊断和预后，特别是淋巴瘤和白血病等淋巴样肿瘤。本文提供了使用DNA测序鉴定患有淋巴样肿瘤，自身免疫疾病和其他病症的个体化或患者特异性生物标志物的方法。识别的生物标志物可以用于确定和/或监测具有相关淋巴样病症或自身免疫疾病或其他病症的受试者的疾病状态。特别地，本发明提供了用于监测经历克隆进化的淋巴样肿瘤的敏感方法，而不需要用作用作患者特异性生物标志物的进化或突变克隆的替代性测定。

3. 发明授权

US08236503B2 Methods of monitoring conditions by sequence analysis 有权
标题翻译：通过序列分析监测条件的方法
公开(公告)号：US08236503B2
公开(公告)日：2012-08-07
申请号：US12615263
申请日：2009-11-09
申请人： Malek Faham , Thomas Willis
发明人： Malek Faham , Thomas Willis
IPC分类号： C12Q1/68 , C12P19/34
CPC分类号： C12Q1/6886 , C12N15/1072 , C12Q1/6809 , C12Q1/6827 , C12Q1/6869 , C12Q1/6881 , C12Q1/6883 , C12Q2600/106 , C12Q2600/118 , C12Q2600/156 , C12Q2600/158 , C12Q2600/16 , Y02A90/26
摘要： There is a need for improved methods for determining the diagnosis and prognosis of patients with conditions, including autoimmune disease and cancer. Provided herein are methods for using DNA sequencing to identify personalized biomarkers in patients with autoimmune disease and other conditions. Identified biomarkers can be used to determine the disease state for a subject with an autoimmune disease or other condition.
摘要翻译：需要改进的方法来确定包括自身免疫性疾病和癌症在内的患者的诊断和预后。本文提供了使用DNA测序鉴定患有自身免疫疾病和其他病症的个体化生物标志物的方法。识别的生物标志物可用于确定具有自身免疫疾病或其他病症的受试者的疾病状态。

4. 发明申请

US20130005584A1 METHODS OF MONITORING CONDITIONS BY SEQUENCE ANALYSIS 有权
标题翻译：通过序列分析监测条件的方法
公开(公告)号：US20130005584A1
公开(公告)日：2013-01-03
申请号：US13459701
申请日：2012-04-30
申请人： Malek Faham , Thomas Willis
发明人： Malek Faham , Thomas Willis
IPC分类号： C40B20/00
CPC分类号： C12Q1/6886 , C12N15/1072 , C12Q1/6809 , C12Q1/6827 , C12Q1/6869 , C12Q1/6881 , C12Q1/6883 , C12Q2600/106 , C12Q2600/118 , C12Q2600/156 , C12Q2600/158 , C12Q2600/16 , Y02A90/26
摘要： There is a need for improved methods for determining the diagnosis and prognosis of patients with conditions, including autoimmune disease and cancer. Provided herein are methods for using DNA sequencing to identify personalized biomarkers in patients with autoimmune disease and other conditions. Identified biomarkers can be used to determine the disease state for a subject with an autoimmune disease or other condition.
摘要翻译：需要改进的方法来确定包括自身免疫性疾病和癌症在内的患者的诊断和预后。本文提供了使用DNA测序鉴定患有自身免疫疾病和其他病症的个体化生物标志物的方法。识别的生物标志物可用于确定具有自身免疫疾病或其他病症的受试者的疾病状态。

5. 发明申请

US20110207617A1 SINGLE CELL ANALYSIS BY POLYMERASE CYCLING ASSEMBLY 有权
标题翻译：通过聚合物循环组装进行单细胞分析
公开(公告)号：US20110207617A1
公开(公告)日：2011-08-25
申请号：US13100395
申请日：2011-05-04
申请人： Malek Faham , Thomas Willis
发明人： Malek Faham , Thomas Willis
IPC分类号： C40B30/00
CPC分类号： C12Q1/6886 , C12N15/1072 , C12Q1/6809 , C12Q1/6827 , C12Q1/6869 , C12Q1/6881 , C12Q1/6883 , C12Q2600/106 , C12Q2600/118 , C12Q2600/156 , C12Q2600/158 , C12Q2600/16 , Y02A90/26
摘要： The invention provides a method of making measurements on individual cells of a population, particularly cells that have identifying nucleic acid sequences, such as lymphoid cells. In one aspect, the invention provides a method of making multiparameter measurements on individual cells of such a population by carrying out a polymerase cycling assembly (PCA) reaction to link their identifying nucleic acid sequences to other cellular nucleic acids of interest. The fusion products of such PCA reaction are then sequenced and tabulated to generate multiparameter data for cells of the population.
摘要翻译：本发明提供了对群体的单个细胞进行测量的方法，特别是具有鉴定核酸序列的细胞，例如淋巴样细胞。一方面，本发明提供了一种通过进行聚合酶循环组件（PCA）反应以将其鉴定的核酸序列与感兴趣的其它细胞核酸连接的方法来对这样的群体的个体细胞进行多参数测量。然后对这种PCA反应的融合产物进行测序并列表，以产生群体细胞的多参数数据。

6. 发明授权

US10385475B2 Random array sequencing of low-complexity libraries 有权
公开(公告)号：US10385475B2
公开(公告)日：2019-08-20
申请号：US13596581
申请日：2012-08-28
申请人： Jianbiao Zheng , Thomas Willis , Malek Faham
发明人： Jianbiao Zheng , Thomas Willis , Malek Faham
IPC分类号： C40B20/00 , C12Q1/6874 , C40B50/14
摘要： The invention is directed to a method of sequencing low-complexity amplicons randomly arrayed at high density on a surface. Methods of the invention include preparing amplicons for sequencing by a sets of primers that ensure initial signals front different amplicons on the surface will be evenly distributed among the different nucleotides being added in a sequencing by synthesis operation.

7. 发明授权

US08771954B2 Methods of monitoring conditions by sequence analysis 有权
公开(公告)号：US08771954B2
公开(公告)日：2014-07-08
申请号：US13214111
申请日：2011-08-19
申请人： Malek Faham , Thomas Willis
发明人： Malek Faham , Thomas Willis
IPC分类号： C12Q1/68 , C12P19/34
摘要： There is a need for improved methods for determining the diagnosis and prognosis of patients with conditions, including autoimmune disease and cancer. Provided herein are methods for using DNA sequencing to identify personalized biomarkers in patients with autoimmune disease and other conditions. Identified biomarkers can be used to determine the disease state for a subject with an autoimmune disease or other condition.

8. 发明申请

US20130324422A1 DETECTING DISEASE-CORRELATED CLONOTYPES FROM FIXED SAMPLES 审中-公开
标题翻译：从固定样品中检测疾病相关的克隆
公开(公告)号：US20130324422A1
公开(公告)日：2013-12-05
申请号：US13487980
申请日：2012-06-04
申请人： Malek Faham , Thomas Willis
发明人： Malek Faham , Thomas Willis
IPC分类号： C40B20/04 , C12Q1/68
CPC分类号： C07K16/00
摘要： The invention is directed to a method for determining immunophenotypes of tissue-infiltrating lymphocytes in a solid tissue of a patient by (a) generating clonotype profiles from a sample of nucleic acid extracted from a fixed tissue sample from a solid tissue of the patient, where such tissue contains tissue-infiltrating lymphocytes; and (b) determining immunophenotypes of the tissue-infiltrating lymphocytes by (i) obtaining a sample of lymphocytes from peripheral blood of the patient; (ii) sorting the lymphocytes from peripheral blood into at least one subset based on different immunophenotypes of the lymphocytes; (iii) generating a clonotype profile for each of the at least one subset of lymphocytes; and (iv) determining immunophenotypes of lymphocytes in the fixed tissue sample by a correspondence between clonotypes of the fixed tissue sample and clonotypes of the at least one subset.
摘要翻译：本发明涉及一种用于通过（a）从来自患者的固体组织的固定组织样品提取的核酸样品产生克隆型谱的方法，用于确定患者的固体组织中组织浸润淋巴细胞的免疫表型，其中这种组织含有组织浸润淋巴细胞; （b）通过（i）从患者的外周血中获得淋巴细胞的样品来确定组织浸润淋巴细胞的免疫表型; （ii）基于淋巴细胞的不同免疫表型将淋巴细胞从外周血分离成至少一个亚组; （iii）产生淋巴细胞的至少一个子集中的每一个的克隆型谱; 和（iv）通过所述固定组织样品的克隆型与所述至少一个亚组的克隆型之间的对应关系确定所述固定组织样品中淋巴细胞的免疫表型。

9. 发明授权

US08507205B2 Single cell analysis by polymerase cycling assembly 有权
标题翻译：通过聚合酶循环装置的单细胞分析
公开(公告)号：US08507205B2
公开(公告)日：2013-08-13
申请号：US13100395
申请日：2011-05-04
申请人： Malek Faham , Thomas Willis
发明人： Malek Faham , Thomas Willis
IPC分类号： C12Q1/68 , C12P19/34
CPC分类号： C12Q1/6886 , C12N15/1072 , C12Q1/6809 , C12Q1/6827 , C12Q1/6869 , C12Q1/6881 , C12Q1/6883 , C12Q2600/106 , C12Q2600/118 , C12Q2600/156 , C12Q2600/158 , C12Q2600/16 , Y02A90/26
摘要： The invention provides a method of making measurements on individual cells of a population, particularly cells that have identifying nucleic acid sequences, such as lymphoid cells. In one aspect, the invention provides a method of making multiparameter measurements on individual cells of such a population by carrying out a polymerase cycling assembly (PCA) reaction to link their identifying nucleic acid sequences to other cellular nucleic acids of interest. The fusion products of such PCA reaction are then sequenced and tabulated to generate multiparameter data for cells of the population.
摘要翻译：本发明提供了对群体的单个细胞进行测量的方法，特别是具有鉴定核酸序列的细胞，例如淋巴样细胞。一方面，本发明提供了一种通过进行聚合酶循环组件（PCA）反应以将其鉴定的核酸序列与感兴趣的其它细胞核酸连接的方法来对这样的群体的个体细胞进行多参数测量。然后对这种PCA反应的融合产物进行测序并列表，以产生群体细胞的多参数数据。

10. 发明申请

US20110207134A1 MONITORING HEALTH AND DISEASE STATUS USING CLONOTYPE PROFILES 有权
标题翻译：使用CLONOTYPE配置文件监测健康和疾病状态
公开(公告)号：US20110207134A1
公开(公告)日：2011-08-25
申请号：US13100365
申请日：2011-05-04
申请人： Malek Faham , Thomas Willis
发明人： Malek Faham , Thomas Willis
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6886 , C12Q1/6874 , C12Q1/6881 , C12Q1/6883 , C12Q2600/112 , C12Q2600/118 , C12Q2600/156 , C12Q2600/158 , C12Q2600/16
摘要： There is a need for improved methods for determining the diagnosis and prognosis of patients with conditions, including autoimmune disease and cancer, especially lymphoid neoplasms, such as lymphomas and leukemias. Provided herein are methods for using DNA sequencing to identify personalized, or patient-specific biomarkers in patients with lymphoid neoplasms, autoimmune disease and other conditions. Identified biomarkers can be used to determine and/or monitor the disease state for a subject with an associated lymphoid disorder or autoimmune disease or other condition. In particular, the invention provides a sensitive method for monitoring lymphoid neoplasms that undergo clonal evolutions without the need to development alternative assays for the evolved or mutated clones serving as patient-specific biomarkers.
摘要翻译：需要一种改进的方法来确定包括自身免疫性疾病和癌症在内的患者的诊断和预后，特别是淋巴瘤和白血病等淋巴样肿瘤。本文提供了使用DNA测序鉴定患有淋巴样肿瘤，自身免疫疾病和其他病症的个体化或患者特异性生物标志物的方法。识别的生物标志物可以用于确定和/或监测具有相关淋巴样病症或自身免疫疾病或其他病症的受试者的疾病状态。特别地，本发明提供了用于监测经历克隆进化的淋巴样肿瘤的敏感方法，而不需要用作用作患者特异性生物标志物的进化或突变克隆的替代性测定。

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