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1. 发明申请

US20060286580A1 MULTIPLEXED POLYMERASE CHAIN REACTION FOR GENETIC SEQUENCE ANALYSIS 失效
标题翻译：用于遗传序列分析的多重聚合酶链反应
公开(公告)号：US20060286580A1
公开(公告)日：2006-12-21
申请号：US11422425
申请日：2006-06-06
申请人： Baochuan Lin , Kate Blaney , Anthony Malanoski , Joel Schnur , David Stenger
发明人： Baochuan Lin , Kate Blaney , Anthony Malanoski , Joel Schnur , David Stenger
IPC分类号： C12Q1/68 , C12P19/34
CPC分类号： C12Q1/689 , C12Q2600/16
摘要： A PCR method involving: providing a biological sample suspected of containing one or more pathogen nucleic acids; adding a plurality of PCR primers corresponding to genes found in the pathogens; and performing a polymerase chain reaction on the sample to amplify a subset of the nucleic acids that correspond to the genes. The primers include at least one primer pair for each pathogen, and the primers contain a tail sequence that is not homologous any pathogen DNA or to any background DNA in the sample. The concentration of at least one primer in the polymerase chain reaction is no more than about 100 nM.
摘要翻译：一种PCR方法，涉及：提供怀疑含有一种或多种病原体核酸的生物样品; 添加对应于病原体中发现的基因的多个PCR引物; 以及对所述样品进行聚合酶链反应以扩增与所述基因相对应的核酸的子集。引物包括每个病原体的至少一个引物对，并且引物含有与样品中任何病原体DNA或任何背景DNA不同源的尾部序列。聚合酶链反应中至少一个引物的浓度不超过约100nM。

2. 发明申请

US20070059728A1 COMPUTER-IMPLEMENTED BIOLOGICAL SEQUENCE IDENTIFIER SYSTEM AND METHOD 失效
标题翻译：计算机实现生物学序列识别系统和方法
公开(公告)号：US20070059728A1
公开(公告)日：2007-03-15
申请号：US11422431
申请日：2006-06-06
申请人： Anthony Malanoski , Baochuan Lin , Joel Schnur , David Stenger
发明人： Anthony Malanoski , Baochuan Lin , Joel Schnur , David Stenger
IPC分类号： C12Q1/68 , G06F19/00 , C12M1/34
CPC分类号： G06F19/22 , G06F19/18 , G06F19/20 , Y10S707/99936
摘要： A method of: submitting reference sequences to a taxonomic database to produce taxonomic results; and reporting a taxonomic identification based on the taxonomic results. The reference sequences are the output of genetic database queries that return a score for each reference sequence. A method for processing a biological sequence obtained from an assay by: converting base calls located in a predetermined list of positions within the biological sequence to N; and determining the ratio of single nucleotide polymorphisms in the biological sequence relative to a reference sequence. Each entry in the predetermined list of positions represents the capability of a substance hybridizing to a microarray used to generate the biological sequence. The substance is not the nucleic acid of a target pathogen.
摘要翻译：一种方法：将参考序列提交给分类数据库以产生分类结果; 并根据分类结果报告分类鉴定。参考序列是返回每个参考序列分数的遗传数据库查询的输出。一种用于处理通过以下方式获得的生物学序列的方法：将位于所述生物学序列内的预定位置列表中的基本呼叫转换为N; 并确定生物序列中单核苷酸多态性相对于参考序列的比例。预定位置列表中的每个条目表示与用于产生生物序列的微阵列杂交的物质的能力。该物质不是目标病原体的核酸。

3. 发明申请

US20080033706A1 DESIGN AND SELECTION OF GENETIC TARGETS FOR SEQUENCE RESOLVED ORGANISM DETECTION AND IDENTIFICATION 失效
标题翻译：设计和选择用于序列分解的有机体检测和鉴定的遗传学目标
公开(公告)号：US20080033706A1
公开(公告)日：2008-02-07
申请号：US11843126
申请日：2007-08-22
申请人： Anthony Malanoski , Zheng Wang , Baochuan Lin , David Stenger , Joel Schnur
发明人： Anthony Malanoski , Zheng Wang , Baochuan Lin , David Stenger , Joel Schnur
IPC分类号： G06G7/48 , C40B40/08 , C40B50/02
CPC分类号： C40B40/08 , G06F19/20
摘要： A computer-implemented method as follows. Providing a list of target sequences associated with one or more organisms in a list of organisms. Providing a list of candidate prototype sequences suspected of hybridizing to one or more of the target sequences. Generating a collection of probes corresponding to each candidate prototype sequence, each collection of probes having a set of probes for every subsequence having a predetermined, fixed subsequence length of the corresponding candidate prototype sequence. The sets consist of the corresponding subsequence and every variation of the corresponding subsequence formed by varying a center nucleotide of the corresponding subsequence. Generating a set of fragments corresponding to each target sequence, each set of fragments having every fragment having a predetermined, fixed fragment length of the corresponding target sequence. Calculating the binding free energy of each fragment with a perfect complimentary sequence of the fragment. If any binding free energy is above a predetermined, fixed threshold, the fragment is extended one nucleotide at a time until the binding free energy is below the threshold or the fragment is the same length as the probe, generating a set of extended fragments. Determining which extended fragments are perfect matches to any of the probes. Assembling a base call sequence corresponding to each candidate prototype sequence. The base call sequence has a base call corresponding to the center nucleotide of each probe of the corresponding prototype sequence that is a perfect match to any extended fragment, but for which the other members of the set of probes containing the perfect match probe are not perfect matches to any extended fragment and a non-base call in all other circumstances.
摘要翻译：计算机实现的方法如下。提供与生物体列表中的一种或多种生物相关的靶序列的列表。提供疑似与一个或多个靶序列杂交的候选原型序列的列表。产生与每个候选原型序列相对应的探针的集合，每个探针集合具有用于每个子序列的探针组，其具有相应候选原型序列的预定的固定子序列长度。这些集由相应的子序列和通过改变相应子序列的中心核苷酸形成的相应子序列的每个变化组成。产生对应于每个靶序列的一组片段，每组片段具有每个片段具有相应靶序列的预定的固定片段长度。用片段的完美互补序列计算每个片段的结合自由能。如果任何结合自由能高于预定的固定阈值，则片段一次延伸一个核苷酸，直到结合自由能低于阈值或片段与探针的长度相同，产生一组扩展片段。确定哪些扩展片段与任何探针完美匹配。组装对应于每个候选原型序列的基本调用序列。基本调用序列具有对应于相应原型序列的每个探针的中心核苷酸的碱基调用，其与任何扩展片段完美匹配，但是包含完美匹配探针的探针组的其它成员对于其不是完美的在任何其他情况下匹配任何扩展片段和非基本调用。

4. 发明申请

US20060210967A1 Re-sequencing pathogen microarray 审中-公开
标题翻译：重新测序病原体微阵列
公开(公告)号：US20060210967A1
公开(公告)日：2006-09-21
申请号：US11177646
申请日：2005-07-02
申请人： Brian Agan , Eric Hanson , Russell Kruzelock , Baochuan Lin , Robb Rowley , Donald Seto , David Stenger , Jennifer Johnson , Clark Tibbetts , Dzung Thach , Gary Vora , Elizabeth Walter , Zheng Wang
发明人： Brian Agan , Eric Hanson , Russell Kruzelock , Baochuan Lin , Robb Rowley , Donald Seto , David Stenger , Jennifer Johnson , Clark Tibbetts , Dzung Thach , Gary Vora , Elizabeth Walter , Zheng Wang
IPC分类号： C12Q1/70 , C12Q1/68 , C12M1/34
CPC分类号： G16B30/00 , C12Q1/6874 , C12Q1/6888 , C12Q1/689 , C12Q1/6893 , C12Q1/701
摘要： The present invention relates to pathogen detection and identification by use of DNA resequencing microarrays. The present invention also provides resequencing microarray chips for differential diagnosis and serotyping of pathogens present in a biological sample. The present invention further provides methods of detecting the presence and identity of pathogens present in a biological sample.
摘要翻译：本发明涉及使用DNA重排序微阵列进行病原体检测和鉴定。本发明还提供用于鉴别诊断和生物样品中存在的病原体血清分型的重新测序微阵列芯片。本发明还提供了检测存在于生物样品中的病原体的存在和身份的方法。

5. 发明申请

US20080020379A1 Diagnosis and prognosis of infectious diseases clinical phenotypes and other physiologic states using host gene expression biomarkers in blood 审中-公开
标题翻译：使用宿主基因表达生物标志物在血液中的传染病临床表型和其他生理状态的诊断和预后
公开(公告)号：US20080020379A1
公开(公告)日：2008-01-24
申请号：US11268373
申请日：2005-11-07
申请人： Brian Agan , Eric Hanson , Michael Jenkins , Baochuan Lin , Chris Olsen , Robb Rowley , David Stenger , Dzung Thach , Clark Tibbetts , Elizabeth Walter , Jinny Liu
发明人： Brian Agan , Eric Hanson , Michael Jenkins , Baochuan Lin , Chris Olsen , Robb Rowley , David Stenger , Dzung Thach , Clark Tibbetts , Elizabeth Walter , Jinny Liu
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6883 , C12Q1/6806 , C12Q2600/158
摘要： The present invention provides a specific set of gene expression markers from peripheral blood leukocytes that are indicative of a host response to exposure, response, and recovery infectious pathogen infections. The present invention further provides methods for identifying the specific set of gene expression markers, methods of monitoring disease progression and treatment of infectious pathogen infections, methods of prognosing the onset of an infectious pathogen infection, and methods of diagnosing an infectious pathogen infection and identifying the pathogen involved.
摘要翻译：本发明提供来自外周血白细胞的特异性基因表达标志物，其指示宿主对暴露，应答和恢复感染性病原体感染的反应。本发明还提供了用于鉴定特定基因表达标志物组的方法，监测疾病进展和感染性病原体感染治疗的方法，预测感染性病原体感染发病的方法，诊断感染性病原体感染的方法以及鉴定涉及病原体。

6. 发明申请

US20050019884A1 Immobilization of oligonucleotides and proteins in sugar-containing hydrogels 有权
标题翻译：寡糖和蛋白质在含糖水凝胶中的固定
公开(公告)号：US20050019884A1
公开(公告)日：2005-01-27
申请号：US10627143
申请日：2003-07-25
申请人： Mark Spector , David Stenger , Charles Patterson , Brett Martin , Paul Charles
发明人： Mark Spector , David Stenger , Charles Patterson , Brett Martin , Paul Charles
IPC分类号： A61K9/00 , C07H1/00 , C07H15/00 , C08J3/00 , C12M1/34 , C12N11/00 , C12Q20060101 , C12Q1/00 , C12Q1/68 , G01N33/543 , G01N33/548
CPC分类号： G01N33/548 , G01N33/54353
摘要： We describe the novel use of a sugar-containing hydrogels as very highly porous, aqueous support material for the immobilization of oligonucleotides, peptides, proteins, antigens, antibodies, polysaccharides, and other biomolecules for sensor applications. The unusually large sizes of the interconnected pores allow large target molecules to pass rapidly into and through the gel and bind to immobilized biomolecules. An additional advantage of the sugar-containing hydrogels are their extremely low non-specific absorption of labeled target molecules, providing low background levels. State-of-the-art hydrogel materials do not have this type of homogeneous interconnected macroporosity, thus large target molecules cannot readily diffuse through them. In addition, they nearly always experience non-specific (background) absorption of labeled target molecules, limiting their usefulness in sensor applications. This invention provides a method for preparing a sugar polyacrylate hydrogel with functional chemical groups which covalently bond oligonucleotides and peptides. A method for copolymerizing acrylate-terminated oligonucleotides with sugar acrylate monomers and diacrylate cross-linking agents is also provided.
摘要翻译：我们描述了含糖水凝胶作为用于固定寡核苷酸，肽，蛋白质，抗原，抗体，多糖和其他用于传感器应用的生物分子的非常高度多孔的水性载体材料的新用途。互连孔的异常大尺寸允许大的目标分子快速通过并穿过凝胶并结合固定的生物分子。含糖水凝胶的另外的优点是它们非常低的标记靶分子的非特异性吸收，提供低的背景水平。最先进的水凝胶材料不具有这种类型的均匀相互连接的大孔隙度，因此大的靶分子不能容易地通过它们扩散。此外，它们几乎总是经历非特异性（背景）吸收标记的靶分子，限制了它们在传感器应用中的用途。本发明提供了制备具有共价键合寡核苷酸和肽的功能化学基团的糖聚丙烯酸酯水凝胶的方法。还提供了将丙烯酸酯封端的寡核苷酸与糖丙酯单体和二丙烯酸酯交联剂共聚的方法。

7. 发明申请

US20070092901A1 AUTOMATED SAMPLE-TO-MICROARRAY SYSTEM 有权
标题翻译：自动样本到微型系统
公开(公告)号：US20070092901A1
公开(公告)日：2007-04-26
申请号：US11559513
申请日：2006-11-14
申请人： Frances Ligler , David Stenger , Jeff Erickson , Marie Archer
发明人： Frances Ligler , David Stenger , Jeff Erickson , Marie Archer
IPC分类号： C12Q1/68 , C12M1/34
CPC分类号： B01L3/5027 , B01L7/52 , B01L2200/10 , B01L2300/0636 , B01L2300/087 , B01L2300/1827 , B01L2400/0481 , B01L2400/0487 , G01N2035/00158
摘要： An apparatus having within or as part of a housing; a sample port; a microarray port; a lysis module; a purification module for containing a solid phase for binding of oligonucleotides; a thermocycling module for containing a polymerase chain reaction; a fragmentation module; and a microarray module for holding a microarray and a liquid in contact with the microarray. The apparatus is configured to be coupled to a device for: pumping a liquid through, in order, the lysis, purification, thermocycling, fragmentation, and microarray modules; sonicating any contents of the lysis module; thermocycling the thermocycling module to perform the polymerase chain reaction; heating the fragmentation module to fragment any oligonucleotides contained therein; circulating a fluid over the surface of the microarray; and performing one or more washing or staining steps on the microarray.
摘要翻译：具有在壳体内或作为壳体的一部分的装置; 样品端口一个微阵列港口裂解模块; 用于含有寡核苷酸结合的固相的纯化模块; 用于含有聚合酶链式反应的热循环模块; 碎片模块; 以及用于保持微阵列和与微阵列接触的液体的微阵列模块。该装置被配置为耦合到装置，用于：按顺序泵送液体裂解，纯化，热循环，碎裂和微阵列模块; 超声处理裂解模块的任何内容物; 热循环模块进行聚合酶链反应; 加热片段化模块以使其中所含的任何寡核苷酸片段化; 使流体在微阵列的表面上循环; 并在微阵列上进行一个或多个洗涤或染色步骤。

8. 发明申请

US20060246499A1 Sugar-containing hydrogel for immobilization 有权
标题翻译：含糖水凝胶用于固定
公开(公告)号：US20060246499A1
公开(公告)日：2006-11-02
申请号：US11444819
申请日：2006-05-19
申请人： Mark Spector , David Stenger , Charles Patterson , Brett Martin , Paul Charles
发明人： Mark Spector , David Stenger , Charles Patterson , Brett Martin , Paul Charles
IPC分类号： C12Q1/68 , C08G63/91 , C12M1/34
CPC分类号： G01N33/548 , G01N33/54353
摘要： We describe the novel use of a sugar-containing hydrogels as very highly porous, aqueous support material for the immobilization of oligonucleotides, peptides, proteins, antigens, antibodies, polysaccharides, and other biomolecules for sensor applications. The unusually large sizes of the interconnected pores allow large target molecules to pass rapidly into and through the gel and bind to immobilized biomolecules. An additional advantage of the sugar-containing hydrogels are their extremely low non-specific absorption of labeled target molecules, providing low background levels. State-of-the-art hydrogel materials do not have this type of homogeneous interconnected macroporosity, thus large target molecules cannot readily diffuse through them. In addition, they nearly always experience non-specific (background) absorption of labeled target molecules, limiting their usefulness in sensor applications. This invention provides a method for preparing a sugar polyacrylate hydrogel with functional chemical groups which covalently bond oligonucleotides and peptides. A method for copolymerizing acrylate-terminated oligonucleotides with sugar acrylate monomers and diacrylate cross-linking agents is also provided.
摘要翻译：我们描述了含糖水凝胶作为用于固定寡核苷酸，肽，蛋白质，抗原，抗体，多糖和其他用于传感器应用的生物分子的非常高度多孔的水性载体材料的新用途。互连孔的异常大尺寸允许大的目标分子快速通过并穿过凝胶并结合固定的生物分子。含糖水凝胶的另外的优点是它们非常低的标记靶分子的非特异性吸收，提供低的背景水平。最先进的水凝胶材料不具有这种类型的均匀相互连接的大孔隙度，因此大的靶分子不能容易地通过它们扩散。此外，它们几乎总是经历非特异性（背景）吸收标记的靶分子，限制了它们在传感器应用中的用途。本发明提供了制备具有共价键合寡核苷酸和肽的功能化学基团的糖聚丙烯酸酯水凝胶的方法。还提供了将丙烯酸酯封端的寡核苷酸与糖丙酯单体和二丙烯酸酯交联剂共聚的方法。

9. 发明申请

US20070065832A1 Computer-implemented biological sequence identifier system and method 有权
标题翻译：计算机实现的生物序列识别系统及方法
公开(公告)号：US20070065832A1
公开(公告)日：2007-03-22
申请号：US11177647
申请日：2005-07-02
申请人： David Stenger , Jennifer Thornton
发明人： David Stenger , Jennifer Thornton
IPC分类号： C12Q1/68 , G06F19/00
CPC分类号： G06F19/22 , C12Q1/6874 , C12Q1/6888 , C12Q1/689 , C12Q1/6893 , C12Q1/701
摘要： A computer-implemented biological sequence identifier (CIBSI) system and method for selecting a subsequence from biological sequence data according to at least one selection parameter. The at least one selection parameter corresponds to a likelihood of returning a meaningful result from a similarity search.
摘要翻译：一种计算机实现的生物序列识别器（CIBSI）系统和方法，用于根据至少一个选择参数从生物序列数据中选择子序列。所述至少一个选择参数对应于从相似性搜索返回有意义的结果的可能性。

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