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    Design and selection of genetic targets for sequence resolved organism detection and identification
    1.
    发明授权
    Design and selection of genetic targets for sequence resolved organism detection and identification 失效
    遗传目标的设计和选择，用于序列分解的生物检测和鉴定

    公开(公告)号：US07668664B2

    公开(公告)日：2010-02-23

    申请号：US11843126

    申请日：2007-08-22

    申请人： Anthony P. Malanoski ,  Zheng Wang ,  Baochuan Lin ,  David A Stenger ,  Joel M Schnur

    发明人： Anthony P. Malanoski ,  Zheng Wang ,  Baochuan Lin ,  David A Stenger ,  Joel M Schnur

    IPC分类号： G01N33/48

    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. 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. 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. Calculating the binding free energy of each fragment with a perfect complimentary sequence of the fragment. Determining which extended fragments are perfect matches to any of the probes. Assembling a base call sequence corresponding to each candidate prototype sequence.

    摘要翻译： 计算机实现的方法如下。 提供与一种或多种生物相关联的靶序列的列表。 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一组探针。 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。 生成对应于每个目标序列的一组片段。 用片段的完美互补序列计算每个片段的结合自由能。 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。

    Multiplexed polymerase chain reaction for genetic sequence analysis
    2.
    发明授权
    Multiplexed polymerase chain reaction for genetic sequence analysis 失效
    用于遗传序列分析的多重聚合酶链反应

    公开(公告)号：US07695941B2

    公开(公告)日：2010-04-13

    申请号：US11422425

    申请日：2006-06-06

    申请人： Baochuan Lin ,  Kate M. Blaney ,  Anthony P. Malanoski ,  Joel M Schnur ,  David A Stenger

    发明人： Baochuan Lin ,  Kate M. Blaney ,  Anthony P. Malanoski ,  Joel M Schnur ,  David A 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。

    COMPUTER-IMPLEMENTED BIOLOGICAL SEQUENCE IDENTIFIER SYSTEM AND METHOD
    3.
    发明申请
    COMPUTER-IMPLEMENTED BIOLOGICAL SEQUENCE IDENTIFIER SYSTEM AND METHOD 有权
    计算机实现生物学序列识别系统和方法

    公开(公告)号：US20100070195A1

    公开(公告)日：2010-03-18

    申请号：US12617025

    申请日：2009-11-12

    申请人： Anthony P. Malanoski ,  Baochuan Lin ,  Joel M. Schnur ,  David A. Stenger

    发明人： Anthony P. Malanoski ,  Baochuan Lin ,  Joel M. Schnur ,  David A. Stenger

    IPC分类号： G06F19/00

    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得分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。

    Computer-implemented biological sequence identifier system and method
    4.
    发明授权
    Computer-implemented biological sequence identifier system and method 有权
    计算机实现的生物序列识别系统及方法

    公开(公告)号：US07979446B2

    公开(公告)日：2011-07-12

    申请号：US12617025

    申请日：2009-11-12

    申请人： Anthony P. Malanoski ,  Baochuan Lin ,  Joel M Schnur ,  David A Stenger

    发明人： Anthony P. Malanoski ,  Baochuan Lin ,  Joel M Schnur ,  David A Stenger

    IPC分类号： G06F7/00 ,  G06F17/30

    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碱基呼叫转化为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。

    Computer-implemented biological sequence identifier system and method
    5.
    发明授权
    Computer-implemented biological sequence identifier system and method 失效
    计算机实现的生物序列识别系统及方法

    公开(公告)号：US07623997B2

    公开(公告)日：2009-11-24

    申请号：US11422431

    申请日：2006-06-06

    申请人： Anthony P. Malanoski ,  Baochuan Lin ,  Joel M Schnur ,  David A Stenger

    发明人： Anthony P. Malanoski ,  Baochuan Lin ,  Joel M Schnur ,  David A Stenger

    IPC分类号： G06F17/10

    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得分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碱基呼叫转化为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。

    SOLID PHASE FOR CAPTURE OF NUCLEIC ACIDS
    9.
    发明申请
    SOLID PHASE FOR CAPTURE OF NUCLEIC ACIDS 有权
    固体捕获核酸的相

    公开(公告)号：US20080293594A1

    公开(公告)日：2008-11-27

    申请号：US11751096

    申请日：2007-05-21

    申请人： Marie J. Archer ,  Baochuan Lin ,  David A. Stenger

    发明人： Marie J. Archer ,  Baochuan Lin ,  David A. Stenger

    IPC分类号： C40B40/08 ,  C40B50/18

    CPC分类号： C12N15/1006 ,  C07B2200/11 ,  C12N15/1013 ,  C12Q1/68 ,  C40B30/04 ,  C40B40/08 ,  C40B50/18

    摘要： A method of: providing a solid surface having a dendrimer molecule bound thereto and a single-stranded probe nucleic acid immobilized to the dendrimer; contacting the solid surface with a sample suspected or known to contain a double-stranded complimentary target nucleic acid; denaturing the target nucleic acids at thermal conditions and in a salt concentration sufficient to denature the target nucleic acids to produce denatured nucleic acids; and cooling the sample to allow hybridization of the denatured nucleic acids to the probe nucleic acids. An article having: one or more paramagnetic microbeads; a dendrimer molecule bound to the beads; and a probe nucleic acid immobilized to the dendrimer.

    摘要翻译： 一种方法：提供具有结合到其上的树枝状大分子分子的固体表面和固定在树状聚合物上的单链探针核酸; 使所述固体表面与疑似或已知含有双链互补靶核酸的样品接触; 在热条件下和在足以使目标核酸变性以产生变性核酸的盐浓度下使目标核酸变性; 并冷却样品以允许变性核酸与探针核酸杂交。 一种具有：一个或多个顺磁性微珠的物品; 与珠结合的树枝状大分子; 和固定在树状聚合物上的探针核酸。

    Solid phase for capture of nucleic acids
    10.
    发明授权
    Solid phase for capture of nucleic acids 有权
    固相捕获核酸

    公开(公告)号：US09096849B2

    公开(公告)日：2015-08-04

    申请号：US11751096

    申请日：2007-05-21

    申请人： Marie J. Archer ,  Baochuan Lin ,  David A Stenger

    发明人： Marie J. Archer ,  Baochuan Lin ,  David A Stenger

    IPC分类号： C12Q1/68 ,  C12N15/10 ,  C40B30/04 ,  C40B40/08 ,  C40B50/18

    CPC分类号： C12N15/1006 ,  C07B2200/11 ,  C12N15/1013 ,  C12Q1/68 ,  C40B30/04 ,  C40B40/08 ,  C40B50/18

    摘要： A method of: providing a solid surface having a dendrimer molecule bound thereto and a single-stranded probe nucleic acid immobilized to the dendrimer; contacting the solid surface with a sample suspected or known to contain a double-stranded complimentary target nucleic acid; denaturing the target nucleic acids at thermal conditions and in a salt concentration sufficient to denature the target nucleic acids to produce denatured nucleic acids; and cooling the sample to allow hybridization of the denatured nucleic acids to the probe nucleic acids. An article having: one or more paramagnetic microbeads; a dendrimer molecule bound to the beads; and a probe nucleic acid immobilized to the dendrimer.

    摘要翻译： 一种方法：提供具有结合到其上的树枝状大分子分子的固体表面和固定在树状聚合物上的单链探针核酸; 使所述固体表面与疑似或已知含有双链互补靶核酸的样品接触; 在热条件下和在足以使目标核酸变性以产生变性核酸的盐浓度下使目标核酸变性; 并冷却样品以允许变性核酸与探针核酸杂交。 一种具有：一个或多个顺磁性微珠的物品; 与珠结合的树枝状大分子; 和固定在树状聚合物上的探针核酸。