公开(公告)号：WO2008024827A2

公开(公告)日：2008-02-28

申请号：PCT/US2007/076499

申请日：2007-08-22

Applicant: THE GOVERNMENT OF THE UNITED STATES OF AMERICA, AS REPRESENTED BY THE SECRETARY OF THE NAVY ,  MALANOSKI, Anthony, P. ,  WANG, Zheng ,  LIN, Baochuan ,  STENGER, David, A. ,  SCHNUR, Joel, M.

Inventor： MALANOSKI, Anthony, P. ,  WANG, Zheng ,  LIN, Baochuan ,  STENGER, David, A. ,  SCHNUR, Joel, M.

IPC: C12Q1/68 ,  C12M1/34

CPC classification number: G06F19/22 ,  C12Q1/6834 ,  C12Q1/701 ,  C12Q2600/112 ,  C12Q2600/158 ,  G06F19/20

Abstract: 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.

Abstract translation: 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。

公开(公告)号：WO2007142692A2

公开(公告)日：2007-12-13

申请号：PCT/US2006/060867

申请日：2006-11-14

Applicant: THE GOVERNMENT OF THE USA, AS REPRESENTED BY THE SECRETARY OF THE NAVY ,  LIGLER, Frances, S. ,  STENGER, David, A. ,  ERICKSON, Jeff ,  ARCHER, Marie

Inventor： LIGLER, Frances, S. ,  STENGER, David, A. ,  ERICKSON, Jeff ,  ARCHER, Marie

IPC: C12Q1/68 ,  C12P19/34

CPC classification number: B01L3/5027 ,  B01L7/52 ,  B01L2200/028 ,  B01L2200/04 ,  B01L2200/0631 ,  B01L2200/10 ,  B01L2200/16 ,  B01L2300/0636 ,  B01L2300/0681 ,  B01L2300/0816 ,  B01L2300/1827 ,  B01L2400/0421 ,  B01L2400/0439 ,  B01L2400/0487 ,  C12Q2565/629 ,  G01N2035/00158

Abstract: 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.

Abstract translation: 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。

公开(公告)号：WO2007011412A2

公开(公告)日：2007-01-25

申请号：PCT/US2005/040196

申请日：2005-11-07

Applicant: THE GOVERNMENT OF THE UNITED STATES OF AMERICA, AS REPRESENTED BY THE SECRETARY OF THE NAVY ,  AGAN, Brian, K. ,  HANSON, Eric, H. ,  JENKINS, Michael, J ,  LIN, Baochuan ,  OLSEN, Chris, C. ,  ROWLEY, Robb, K. ,  STENGER, David, A. ,  THACH, Dzung, C. ,  TIBBETTS, Clark, J. ,  WALTER, Elizabeth, A. ,  LIU, Jinny, Lin

Inventor： AGAN, Brian, K. ,  HANSON, Eric, H. ,  JENKINS, Michael, J ,  LIN, Baochuan ,  OLSEN, Chris, C. ,  ROWLEY, Robb, K. ,  STENGER, David, A. ,  THACH, Dzung, C. ,  TIBBETTS, Clark, J. ,  WALTER, Elizabeth, A. ,  LIU, Jinny, Lin

IPC: C12Q1/68

CPC classification number: C12Q1/6883 ,  C12Q1/6806 ,  C12Q2600/158

Abstract: 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.

Abstract translation: 本发明提供了一组来自外周血白细胞的特定基因表达标记，其指示宿主对暴露，应答和恢复传染性病原体感染的应答。 本发明进一步提供了鉴定特定组基因表达标记物的方法，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作的方法，以及诊断感染性病原体感染的方法和鉴定 涉及病原体。

公开(公告)号：WO2006088493A3

公开(公告)日：2006-08-24

申请号：PCT/US2005/024054

申请日：2005-07-05

Applicant: THE GOVERNMENT OF THE UNITED STATES OF AMERICA, AS REPRESENTED BY THE SECRETARY OF THE NAVY ,  AGAN, Brian ,  HANSON, Eric, H. ,  KRUZELOCK, Russell, P. ,  LIN, Boachuan ,  ROWLEY, Robb ,  SETO, Don ,  STENGER, David ,  THORNTON, Jennifer ,  TIBBETTS, Clark ,  THACH, Dzung ,  VORA, Gary ,  WALTER, Elizabeth ,  WANG, Zheng

Inventor： AGAN, Brian ,  HANSON, Eric, H. ,  KRUZELOCK, Russell, P. ,  LIN, Boachuan ,  ROWLEY, Robb ,  SETO, Don ,  STENGER, David ,  THORNTON, Jennifer ,  TIBBETTS, Clark ,  THACH, Dzung ,  VORA, Gary ,  WALTER, Elizabeth ,  WANG, Zheng

IPC: C12Q1/68

Abstract: 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. The present invention also provides 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.

公开(公告)号：WO2006088493A2

公开(公告)日：2006-08-24

申请号：PCT/US2005024054

申请日：2005-07-05

Applicant: US GOV SEC NAVY ,  AGAN BRIAN ,  HANSON ERIC H ,  KRUZELOCK RUSSELL P ,  LIN BOACHUAN ,  ROWLEY ROBB ,  SETO DON ,  STENGER DAVID ,  THOMTON JENNIFER ,  TIBBETTS CLARK ,  THACH DZUNG ,  VORA GARY ,  WALTER ELIZABETH ,  WANG ZHENG

Inventor： AGAN BRIAN ,  HANSON ERIC H ,  KRUZELOCK RUSSELL P ,  LIN BOACHUAN ,  ROWLEY ROBB ,  SETO DON ,  STENGER DAVID ,  THOMTON JENNIFER ,  TIBBETTS CLARK ,  THACH DZUNG ,  VORA GARY ,  WALTER ELIZABETH ,  WANG ZHENG

IPC: C12Q1/70 ,  C12M1/34 ,  C12Q1/68

CPC classification number: G06F19/22 ,  C12Q1/6874 ,  C12Q1/6888 ,  C12Q1/689 ,  C12Q1/6893 ,  C12Q1/701

Abstract: 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. The present invention also provides 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.

Abstract translation: 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。 本发明还提供了一种计算机实现的生物序列标识符（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：WO2006138182A3

公开(公告)日：2009-04-23

申请号：PCT/US2006022622

申请日：2006-06-09

Applicant: US GOV SEC NAVY ,  MALANOSKI ANTHONY P ,  LIN BAOCHUAN ,  SCHNUR JOEL M ,  STENGER DAVID A

Inventor： MALANOSKI ANTHONY P ,  LIN BAOCHUAN ,  SCHNUR JOEL M ,  STENGER DAVID A

IPC: C12Q1/68 ,  C12P19/34 ,  G06F17/11

CPC classification number: G06F19/22 ,  G06F19/18 ,  G06F19/20 ,  Y10S707/99936

Abstract: 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.

Abstract translation: 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。