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。

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。

公开(公告)号：US09430610B2

公开(公告)日：2016-08-30

申请号：US12100519

申请日：2008-04-10

申请人： Brian K Agan ,  Eric H Hanson ,  Russell P Kruzelock ,  Baochuan Lin ,  Robb K Rowley ,  Donald Seto ,  David A Stenger ,  Jennifer Johnson ,  Clark J Tibbetts ,  Dzung C Thach ,  Gary J Vora ,  Elizabeth A Walter ,  Zheng Wang

发明人： Brian K Agan ,  Eric H Hanson ,  Russell P Kruzelock ,  Baochuan Lin ,  Robb K Rowley ,  Donald Seto ,  David A Stenger ,  Jennifer Johnson ,  Clark J Tibbetts ,  Dzung C Thach ,  Gary J Vora ,  Elizabeth A Walter ,  Zheng Wang

IPC分类号： C12Q1/68 ,  G06F19/22 ,  C12Q1/70

CPC分类号： G06F19/22 ,  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.

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。

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。

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。

公开(公告)号：US08032310B2

公开(公告)日：2011-10-04

申请号：US11177647

申请日：2005-07-02

申请人： David A Stenger ,  Jennifer Thornton

发明人： David A Stenger ,  Jennifer Thornton

IPC分类号： G01N33/48

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。

公开(公告)号：US08965710B2

公开(公告)日：2015-02-24

申请号：US11559513

申请日：2006-11-14

申请人： Frances S Ligler ,  David A Stenger ,  Jeff Erickson ,  Marie Archer

发明人： Frances S Ligler ,  David A Stenger ,  Jeff Erickson ,  Marie Archer

IPC分类号： G06F19/20 ,  C12Q1/68 ,  C12M1/34 ,  B01L3/00 ,  B01L7/00 ,  G01N35/00

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。