公开(公告)号：US20130017957A1

公开(公告)日：2013-01-17

申请号：US13468323

申请日：2012-05-10

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.

公开(公告)号：US20100151471A1

公开(公告)日：2010-06-17

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 ,  G06F19/00

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。

公开(公告)号：US20050100939A1

公开(公告)日：2005-05-12

申请号：US10943752

申请日：2004-09-17

申请人： Eugeni Namsaraev ,  George Karlin-Neumann ,  Malek Faham ,  Maneesh Jain ,  Paul Hardenbol ,  Thomas Willis ,  Zhiyong Wang

发明人： Eugeni Namsaraev ,  George Karlin-Neumann ,  Malek Faham ,  Maneesh Jain ,  Paul Hardenbol ,  Thomas Willis ,  Zhiyong Wang

IPC分类号： C12Q1/68 ,  G01N20060101 ,  G01N33/48 ,  G01N33/50 ,  G06F19/00

CPC分类号： C12Q1/6837 ,  C12Q2563/131

摘要： The present invention provides systems and methods for large-scale genetic measurements by generating from a sample labeled target sequences whose length, orientation, label, and degree of overlap and complementarity are tailored to corresponding end-attached probes of a solid support so that signal-to-noise ratios of measurement from specifically hybridized labeled target sequences are maximized. Systems for implementing methods of the invention include a set of sample-interacting probes to produce amplicons that either each contain a segment of a target polynucleotide or an oligonucleotide tag that corresponds to a segment of a target polynucleotide, one or more solid phase supports that contain a plurality of end-attached probes, and methods of generating from sample-interacting probe amplicons from which labeled target sequences are tailored for hybridization to the solid phase supports, such as microarrays. In one aspect, labeled target sequences and end-attached probe of the solid phase supports comprise oligonucleotide tags and tag complements, respectively, selected from a minimally cross-hybridizing set.

摘要翻译： 本发明提供了用于大规模遗传测量的系统和方法，所述系统和方法通过从样品标记的靶序列产生，所述样品标记的靶序列的长度，取向，标记，重叠度和互补度被量化到固体支持物的相应末端附接探针， 来自特异性杂交的标记靶序列的测量的信噪比最大化。 用于实施本发明方法的系统包括一组样品相互作用探针以产生扩增子，每个扩增子各含有靶多核苷酸片段或对应于靶多核苷酸片段的寡核苷酸标签，一个或多个固相载体含有 多个末端连接的探针，以及从样品相互作用的探针扩增子产生的方法，其中标记的靶序列被定制用于与固相支持物例如微阵列杂交。 在一个方面，固相载体的标记的靶序列和末端连接的探针分别包含选自最小交叉杂交组的寡核苷酸标签和标签互补物。

公开(公告)号：US08980563B2

公开(公告)日：2015-03-17

申请号：US12972208

申请日：2010-12-17

申请人： Jianbiao Zheng ,  Li Weng ,  Malek Faham

发明人： Jianbiao Zheng ,  Li Weng ,  Malek Faham

IPC分类号： C12Q1/68 ,  C12P19/34

CPC分类号： C12Q1/686 ,  C12Q1/6844 ,  C12Q1/6853 ,  C12Q2531/125

摘要： Methods for multiplex amplification of a plurality of targets of distinct sequence from a complex mixture are disclosed. In one aspect targets are circularized using a single circularization probe that is complementary to two regions in the target that flank a region to be amplified. The targets may hybridize to the circularization probe so that 5′ or 3′ flaps are generated and methods for removing flaps and circularizing the resulting product are disclosed. In another aspect targets are hybridized to dU probes so that 5′ and 3′ flaps are generated. The flaps are cleaved using 5′ or 3′ flap endonucleases or 3′ to 5′ exonucleases. The target sequences are then ligated to common primers, the dU probes digested and the ligated targets amplified.

摘要翻译： 公开了从复杂混合物多个扩增不同序列的多个靶的方法。 在一个方面，使用单个环化探针对靶标进行环化，所述单个环化探针与靶区域中将要扩增的区域侧翼的两个区域互补。 目标可以与环化探针杂交，从而产生5'或3'的瓣，并且公开了用于去除襟翼和使所得产物环化的方法。 另一方面，目标与dU探针杂交，从而产生5'和3'瓣。 使用5'或3'片段内切核酸酶或3'至5'外切核酸酶切割襟翼。 然后将靶序列连接到常见引物，消化dU探针并扩增连接的靶标。

公开(公告)号：US20140255944A1

公开(公告)日：2014-09-11

申请号：US14197615

申请日：2014-03-05

申请人： Victoria Carlton ,  Malek Faham

发明人： Victoria Carlton ,  Malek Faham

IPC分类号： C12Q1/68

CPC分类号： C12Q1/686 ,  C12Q1/6886 ,  C12Q2600/106 ,  C12Q2600/156

摘要： The invention is directed to a method of monitoring or detecting treatment-resistant clones in a patient being treated for a lymphoid or myeloid neoplasm from which patient-specific correlating clonotypes have been identified. In some embodiments, such method includes the steps of obtaining a sample from the patient comprising T-cells and/or B-cells; amplifying molecules of nucleic acid from the T-cells and/or B-cells of the sample, the molecules of nucleic acid comprising recombined DNA sequences from T-cell receptor genes or immunoglobulin genes; sequencing the amplified molecules of nucleic acid to form a clonotype profile; determining from the clonotype profile a level of each correlating clonotype and clonotypes clonally evolved therefrom; and correlating a presence of a treatment-resistant clone of the neoplasm with a change in relative levels of the correlating clonotypes and clonotypes clonally evolved therefrom. In part, the invention permits one to distinguish between cases where treatment is effective but insufficiently intense and cases where a cancer clone arises that is resistant to a current treatment approach.

摘要翻译： 本发明涉及一种监测或检测被治疗的患者的治疗抗性克隆的方法，所述治疗抗性克隆被治疗用于已经鉴定了患者特异性相关克隆型的淋巴或骨髓瘤。 在一些实施方案中，这种方法包括从包括T细胞和/或B细胞的患者获得样品的步骤; 从样品的T细胞和/或B细胞扩增核酸分子，所述核酸分子包含来自T细胞受体基因或免疫球蛋白基因的重组DNA序列; 测序扩增的核酸分子以形成克隆型谱; 从克隆型分析确定每个相关克隆型和从其中克隆进化的克隆型的水平; 并将肿瘤的治疗抗性克隆的存在与从其克隆进行的相关克隆型和克隆型的相对水平的变化相关联。 部分地，本发明允许区分治疗有效但不充分的情况，以及出现对当前治疗方法有抗性的癌症克隆的情况。

公开(公告)号：US20080199916A1

公开(公告)日：2008-08-21

申请号：US12016195

申请日：2008-01-17

申请人： Jianbiao Zheng ,  Li Weng ,  Malek Faham

发明人： Jianbiao Zheng ,  Li Weng ,  Malek Faham

IPC分类号： C12P19/34

CPC分类号： C12Q1/686 ,  C12Q1/6844 ,  C12Q1/6853 ,  C12Q2531/125

摘要： Methods for multiplex amplification of a plurality of targets of distinct sequence from a complex mixture are disclosed. In one aspect targets are circularized using a single circularization probe that is complementary to two regions in the target that flank a region to be amplified. The targets may hybridize to the circularization probe so that 5′ or 3′ flaps are generated and methods for removing flaps and circularizing the resulting product are disclosed. In another aspect targets are hybridized to dU probes so that 5′ and 3′ flaps are generated. The flaps are cleaved using 5′ or 3′ flap endonucleases or 3′ to 5′ exonucleases. The target sequences are then ligated to common primers, the dU probes digested and the ligated targets amplified.

摘要翻译： 公开了从复杂混合物多个扩增不同序列的多个靶的方法。 在一个方面，使用单个环化探针对靶标进行环化，所述单个环化探针与靶区域中将要扩增的区域侧翼的两个区域互补。 目标可以与环化探针杂交，从而产生5'或3'的瓣，并且公开了用于去除襟翼和使所得产物环化的方法。 另一方面，目标与dU探针杂交，从而产生5'和3'瓣。 使用5'或3'片段内切核酸酶或3'至5'外切核酸酶切割襟翼。 然后将靶序列连接到常见引物，消化dU探针并扩增连接的靶标。

公开(公告)号：US20050239080A1

公开(公告)日：2005-10-27

申请号：US10728122

申请日：2003-12-03

申请人： David Cox ,  Malek Faham ,  Siamak Baharloo

发明人： David Cox ,  Malek Faham ,  Siamak Baharloo

IPC分类号： C12N1/21 ,  C12N15/74 ,  C12Q1/68

CPC分类号： C12Q1/6827 ,  C12Q1/6897 ,  C12Q2600/156

摘要： Mismatch Repair Detection (MRD), a novel method for DNA-variation detection, utilizes bacteria to detect mismatches by a change in expression of a marker gene. DNA fragments to be screened for variation are cloned into two MRD plasmids, and bacteria are transformed with heteroduplexes of these constructs. Resulting colonies express the marker gene in the absence of a mismatch, and lack expression in the presence of a mismatch. MRD is capable of detecting a single mismatch within 10 kb of DNA. In addition, MRD can analyze many fragments simultaneously, offering a powerful method for high-throughput genotyping and mutation detection.

摘要翻译： 用于DNA变异检测的新方法的不匹配修复检测（MRD）利用细菌通过标记基因的表达变化来检测错配。 将待筛选的DNA片段克隆到两个MRD质粒中，并用这些构建体的异源双链体转化细菌。 得到的菌落在不存在错配的情况下表达标记基因，并且在存在失配的情况下缺乏表达。 MRD能够检测DNA的10 kb内的单一错配。 此外，MRD可以同时分析许多片段，为高通量基因分型和突变检测提供了强大的方法。

公开(公告)号：US06406847B1

公开(公告)日：2002-06-18

申请号：US09271055

申请日：1999-03-17

申请人： David R. Cox ,  Malek Faham ,  Siamak Baharloo

发明人： David R. Cox ,  Malek Faham ,  Siamak Baharloo

IPC分类号： C12Q168

CPC分类号： C12Q1/6827 ,  C12Q1/6897 ,  C12Q2600/156

摘要： Mismatch Repair Detection (MRD), a novel method for DNA-variation detection, utilizes bacteria to detect mismatches by a change in expression of a marker gene. DNA fragments to be screened for variation are cloned into two MRD plasmids, and bacteria are transformed with heteroduplexes of these constructs. Resulting colonies express the marker gene in the absence of a mismatch, and lack expression in the presence of a mismatch. MRD is capable of detecting a single mismatch within 10 kb of DNA. In addition, MRD can analyze many fragments simultaneously, offering a powerful method for high-throughput genotyping and mutation detection.

公开(公告)号：US20090004701A1

公开(公告)日：2009-01-01

申请号：US11739654

申请日：2007-04-24

申请人： Malek Faham ,  Jianbiao Zheng

发明人： Malek Faham ,  Jianbiao Zheng

IPC分类号： C12P19/34

CPC分类号： C12Q1/6853 ,  C12Q1/6855 ,  C12Q2537/143 ,  C12Q2525/161 ,  C12Q2521/325 ,  C12Q2521/307

摘要： Methods for appending oligonucleotides directly to nucleic acid templates, particularly to defined sites internal to single-stranded templates, are described. Appending first and second common priming sites to each of a plurality of templates of distinct sequence allows the subsequent stoichiometric amplification of a plurality of templates of distinct sequence.

摘要翻译： 描述了将寡核苷酸直接附加到核酸模板，特别是单链模板内部的定义位点的方法。 将不同序列的多个模板中的每一个附加第一和第二共同引发位点允许对不同序列的多个模板的后续化学计量放大。

公开(公告)号：US20080108073A1

公开(公告)日：2008-05-08

申请号：US11923649

申请日：2007-10-24

申请人： Shivani Nautiyal ,  Malek Faham

发明人： Shivani Nautiyal ,  Malek Faham

IPC分类号： C12Q1/68

CPC分类号： C12Q1/683 ,  C12Q1/6806 ,  C12Q1/6813

摘要： Methods for determining the methylation status of a plurality of cytosines are disclosed. In some aspects genomic DNA target sequences containing CpGs are targeted for analysis by multiplex amplification using target specific probes that can be specifically degraded prior to amplification. The targets may be modified with bisulfite prior to amplification. In another aspect targets are cut with methylation sensitive or insensitive restriction enzymes and marked with a tag using the target specific probes. The presence or absence of methylation may be determined using methylation sensitive restriction enzyme or bisulfite treatment. Detection in many embodiments employs hybridization to tag arrays, genotyping arrays or resequencing arrays.

摘要翻译： 公开了确定多种胞嘧啶的甲基化状态的方法。 在某些方面，含有CpG的基因组DNA靶序列靶向用于通过多重扩增进行分析，使用可在扩增前特异性降解的靶特异性探针。 在扩增前可以用亚硫酸氢盐修饰靶标。 在另一方面，用甲基化敏感或不敏感限制酶切割靶标，并使用靶标特异性探针用标签标记。 甲基化的存在或不存在可以使用甲基化敏感的限制酶或亚硫酸氢盐处理来确定。 在许多实施方案中的检测采用与标签阵列，基因分型阵列或重排序阵列的杂交。