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    Methods for detecting genome-wide sequence variations associated with a phenotype
    1.
    发明申请
    Methods for detecting genome-wide sequence variations associated with a phenotype 审中-公开
    用于检测与表型相关的全基因组序列变异的方法

    公开(公告)号：US20070015200A1

    公开(公告)日：2007-01-18

    申请号：US11520964

    申请日：2006-09-14

    申请人： Pascal Mayer ,  Ilia Leviev ,  Magne Osteras ,  Laurent Farinelli

    发明人： Pascal Mayer ,  Ilia Leviev ,  Magne Osteras ,  Laurent Farinelli

    IPC分类号： C12Q1/68 ,  G06F19/00

    CPC分类号： C12Q1/6809 ,  C12Q1/6876 ,  C12Q2521/301

    摘要： The invention provides methods for determining genome-wide sequence variations associated with a phenotype of a species in a hypothesis-free manner. In the methods of the invention, a set of restriction fragments for each of a sub-population of individuals having the phenotype are generated by digesting nucleic acids from the individual using one or more different restriction enzymes. A set of restriction sequence tags for the individual is then determined from the set of restriction fragments. The restriction sequence tags for the sub-population of organisms are compared and grouped into one or more groups, each of which comprising restriction sequence tags that comprise homologous sequences. The obtained one or more groups of restriction sequence tags identify the sequence variations associated with the phenotype. The methods of the invention can be used for, e.g., analysis of large numbers of sequence variants in many patient samples to identify subtle genetic risk factors.

    摘要翻译： 本发明提供了以无假设方式确定与物种表型相关的全基因组序列变异的方法。 在本发明的方法中，通过使用一种或多种不同的限制酶消化来自个体的核酸，产生一组具有表型的个体亚群的限制性片段。 然后从该组限制性片段确定针对个体的一组限制性序列标签。 将生物体亚群的限制性序列标签进行比较并分组成一个或多个组，每组包含包含同源序列的限制性序列标签。 获得的一组或多组限制性序列标签鉴定与表型相关的序列变异。 本发明的方法可用于例如许多患者样品中大量序列变体的分析以鉴定微妙的遗传风险因子。

    System and apparatus for sequential processing of analytes
    2.
    发明授权
    System and apparatus for sequential processing of analytes 有权
    用于顺序处理分析物的系统和设备

    公开(公告)号：US06969488B2

    公开(公告)日：2005-11-29

    申请号：US09908131

    申请日：2001-07-17

    申请人： John Bridgham ,  Kevin Corcoran ,  George Golda ,  Sydney Brenner ,  Michael C. Pallas

    发明人： John Bridgham ,  Kevin Corcoran ,  George Golda ,  Sydney Brenner ,  Michael C. Pallas

    IPC分类号： B01L3/00 ,  G01N15/14 ,  G01N21/25 ,  G01N33/48

    CPC分类号： G01N21/253 ,  B01J2219/00274 ,  B01L3/5027 ,  B01L3/502715 ,  B01L3/502761 ,  B01L2200/0647 ,  B01L2200/10 ,  B01L2300/0877 ,  B01L2400/0403 ,  B01L2400/0475 ,  B01L2400/0622 ,  B01L2400/0644 ,  G01N2015/144 ,  G01N2015/1452 ,  G01N2035/00158 ,  Y10S435/81 ,  Y10T436/13 ,  Y10T436/143333

    摘要： An apparatus and system are provided for simultaneously analyzing a plurality of analytes anchored to microparticles. Microparticles each having a uniform population of a single kind of analyte attached are disposed as a substantially immobilized planar array inside of a flow chamber where steps of an analytical process are carried out by delivering a sequence of processing reagents to the microparticles by a fluidic system under microprocessor control. In response to such process steps, an optical signal is generated at the surface of each microparticle which is characteristic of the interaction between the analyte carried by the microparticle and the delivered processing reagent. The plurality of analytes are simultaneously analyzed by collecting and recording images of the optical signals generated by all the microparticles in the planar array. A key feature of the invention is the correlation of the sequence of optical signals generated by each microparticle in the planar array during the analytical process.

    摘要翻译： 提供了一种用于同时分析锚定到微粒的多个分析物的装置和系统。 每个具有单一类型分析物的均匀群体的微粒被布置为在流动室内部基本上固定的平面阵列，其中分析过程的步骤通过将一系列处理试剂通过流体系统递送到微粒进行， 微处理器控制。 响应于这样的处理步骤，在每个微粒的表面产生光信号，其特征在于微粒携带的分析物与递送的处理试剂之间的相互作用。 通过收集和记录由平面阵列中的所有微粒产生的光学信号的图像来同时分析多个分析物。 本发明的一个关键特征是在分析过程中由平面阵列中的每个微粒产生的光信号序列的相关性。

    Method for determining relative abundance of nucleic acid sequences
    4.
    发明授权
    Method for determining relative abundance of nucleic acid sequences 失效
    确定核酸序列相对丰度的方法

    公开(公告)号：US06897023B2

    公开(公告)日：2005-05-24

    申请号：US09967238

    申请日：2001-09-27

    申请人： Rongdian Fu ,  Sydney Brenner ,  Glenn Albrecht

    发明人： Rongdian Fu ,  Sydney Brenner ,  Glenn Albrecht

    IPC分类号： C07H21/00 ,  C07H21/02 ,  C07H21/04 ,  C12N15/10 ,  C12P19/34 ,  C12Q1/68

    CPC分类号： C12Q1/6809 ,  C12Q2545/114 ,  C12Q2563/179 ,  C12Q2565/626

    摘要： Disclosed are methods for identifying nucleic acid sequences which are of different abundances in different nucleic acid source populations, e.g. differentially expressed genes or genomic variations among individuals or populations of individuals. In one embodiment, probes derived from the source nucleic acid populations are derivatized with a terminal sample ID (SID) sequence characteristic of that population. Upon competitive hybridization of the probes to a reference or index nucleic acid library containing all the sequences in the populations being compared, the SID tags remain single stranded, and those from the different sources are then annealed to one another. Unhybridized (remainder) SID sequences are then quantified. By labeling such remainder SID sequences with a fluorescent dye, FACS sorting of beads containing the hybridized probes can be carried out. The signal ratio upon which such sorting is based is enhanced compared to competitive hybridization using labeled probes without SID sequences.

    摘要翻译： 公开了用于鉴定在不同核酸源群体中具有不同丰度的核酸序列的方法，例如， 差异表达基因或个体个体或个体群体的基因组变异。 在一个实施方案中，衍生自源核酸群体的探针用该群体特征的终端样品ID（SID）序列衍生化。 当探针与包含正在比较的群体中的所有序列的参考或指数核酸文库竞争性杂交时，SID标签保持单链，然后来自不同来源的那些序列彼此退火。 然后对未杂交（其余）SID序列进行定量。 通过用荧光染料标记这些剩余的SID序列，可以进行含有杂交探针的珠的FACS分选。 与使用没有SID序列的标记探针的竞争性杂交相比，这种分选所基于的信号比率增加。

    Method and compositions for ordering restriction fragments
    5.
    发明授权
    Method and compositions for ordering restriction fragments 有权
    用于排序限制性片段的方法和组合物

    公开(公告)号：US07598035B2

    公开(公告)日：2009-10-06

    申请号：US10962337

    申请日：2004-10-08

    申请人： Stephen C. Macevicz

    发明人： Stephen C. Macevicz

    IPC分类号： C12Q1/68 ,  C12P19/34 ,  C07H21/02 ,  C07H21/04 ,  C07H21/00

    CPC分类号： C12Q1/6874 ,  C12N15/10 ,  C12N15/64 ,  C12N15/66 ,  C12Q1/6809 ,  C12Q1/683 ,  C12Q1/6841 ,  C12Q1/6869 ,  C12Q1/6872 ,  G06F19/22 ,  C12Q2521/501 ,  C12Q2521/301

    摘要： The invention provides a method for constructing a high resolution physical map of a polynucleotide. In accordance with the invention, nucleotide sequences are determined at the ends of restriction fragments produced by a plurality of digestions with a plurality of combinations of restriction endonucleases so that a pair of nucleotide sequences is obtained for each restriction fragment. A physical map of the polynucleotide is constructed by ordering the pairs of sequences by matching the identical sequences among the pairs.

    摘要翻译： 本发明提供了构建多核苷酸的高分辨率物理图的方法。 根据本发明，通过多个限制性内切核酸酶组合的多次消化产生的限制性片段的末端确定核苷酸序列，从而获得每个限制性片段的一对核苷酸序列。 通过使对中的相同序列匹配来排序序列对来构建多核苷酸的物理图谱。

    Polymorphic DNA fragments and uses thereof
    6.
    发明申请
    Polymorphic DNA fragments and uses thereof 审中-公开
    多态性DNA片段及其用途

    公开(公告)号：US20060199198A1

    公开(公告)日：2006-09-07

    申请号：US11331661

    申请日：2006-01-13

    申请人： Sydney Brenner

    发明人： Sydney Brenner

    IPC分类号： C40B40/08

    CPC分类号： C12Q1/683 ,  C12Q1/6809 ,  C12Q1/6837

    摘要： The invention provides methods and materials for generating a reference library of restriction fragments from pooled nucleic acids that contain a sequence polymorphism. Preferably, such a library is formed by digesting genomic DNA from a pool of individuals with a first and a second restriction endonuclease to form a population of restriction fragments; isolating restriction fragments of the population digested by both the first and second restriction endonucleases and forming a first single stranded fragment population therefrom; separately isolating restriction fragments from the population digested by the first restriction endonuclease but not the second restriction endonuclease and forming a second single stranded fragment population therefrom; hybridizing the first and second single stranded fragment populations to form a population of duplexes; and isolating the population of duplexes to form a reference library of restriction fragments that contain sequence polymorphism. An important aspect of the invention is the use of the reference population of restriction fragments to compare the frequencies of polymorphic sequences between different population pools. Such comparisons may be accomplished by competively hybridizing DNA from the respective pools which has been enriched for the presence of a restriction site polymorphism with DNA from the reference population. Preferably, such competitive hybridization reactions are carried out the reference library attached to one or more solid phase supports. Most preferably, members of the reference library are attached to individual microparticles so that each microparticle has a unique fragment attached. After competitive hybridization, the microparticles may be analyzed and sorted for identifying those microparticles carrying sequences for which the pools being compared exhibit different polymorphic frequencies.

    摘要翻译： 本发明提供用于从含有序列多态性的合并的核酸产生限制性片段的参考文库的方法和材料。 优选地，通过用具有第一和第二限制性内切核酸酶的来自个体池的基因组DNA消化形成这样的文库，以形成一组限制性片段; 分离由第一和第二限制性内切核酸酶消化的群体的限制性片段，并从其形成第一单链片段群体; 分别从由第一限制性内切核酸酶消化但不是第二限制性内切核酸酶消化的群体中分离限制性片段，并从其形成第二单链片段群体; 杂交第一和第二单链片段群体以形成双链体群体; 并分离双链体群体以形成含有序列多态性的限制性片段的参考文库。 本发明的一个重要方面是使用限制性片段的参照群来比较不同种群间的多态性序列的频率。 这种比较可以通过竞争性地杂交来自相应的库的DNA来完成，这些DNA已被富集以限制性位点多态性与来自参照群体的DNA的存在。 优选地，这种竞争性杂交反应是在连接到一个或多个固相载体上的参考文库进行的。 最优选地，参考文库的成员附着到单个微粒，使得每个微粒具有附着的独特片段。 竞争性杂交后，可以对微粒进行分析和分选，以鉴定携带具有不同多态性频率的比较池的携带序列的那些微粒。

    Methods of nucleic acid amplification and sequencing
    8.
    发明申请
    Methods of nucleic acid amplification and sequencing 有权
    核酸扩增和测序方法

    公开(公告)号：US20080160580A1

    公开(公告)日：2008-07-03

    申请号：US11506146

    申请日：2006-08-17

    申请人： Celine Adessi ,  Eric Kawashima ,  Pascal Mayer ,  Jean-Jacques Mermod ,  Gerardo Turcatti

    发明人： Celine Adessi ,  Eric Kawashima ,  Pascal Mayer ,  Jean-Jacques Mermod ,  Gerardo Turcatti

    IPC分类号： C12P19/34

    CPC分类号： C12N15/1068 ,  C12Q1/6837 ,  C12Q1/686 ,  C12Q1/6869 ,  C12Q1/6874 ,  C12Q2565/543

    摘要： Methods for amplification and sequencing of at least one nucleic acid comprising the following steps: (1) forming at least one nucleic acid template comprising the nucleic acid(s) to be amplified or sequenced, wherein said nucleic acid(s) contains at the 5′ end an oligonucleotide sequence Y and at the 3′ end an oligonucleotide sequence Z and, in addition, the nucleic acid(s) carry at the 5′ end a means for attaching the nucleic acid(s) to a solid support; (2) mixing said nucleic acid template(s) with one or more colony primers X, which can hybridize to the oligonucleotide sequence Z and carries at the 5′ end a means for attaching the colony primers to a solid support, in the presence of a solid support so that the 5′ ends of both the nucleic acid template and the colony primers bind to the solid support; (3) performing one or more nucleic acid amplification reactions on the bound template(s), so that nucleic acid colonies are generated and optionally, performing at least one step of sequence determination of one or more of the nucleic acid colonies generated. Solid supports, kits and apparatus for use in these methods.

    摘要翻译： 用于扩增和测序至少一种核酸的方法，包括以下步骤：（1）形成至少一个核酸模板，其包含待扩增或测序的核酸，其中所述核酸包含在5 '结束寡核苷酸序列Y，在3'端有寡核苷酸序列Z，另外核酸在5'端带有用于将核酸连接到固体支持物上的方法; （2）将所述核酸模板与一个或多个菌落引物X混合，其可与寡核苷酸序列Z杂交，并在5'末端携带用于将菌落引物连接至固体支持物的手段，在存在 固体支持物，使得核酸模板和集落引物的5'末端与固体支持物结合; （3）对结合的模板进行一个或多个核酸扩增反应，从而产生核酸集落，并且任选地，进行生成的一个或多个核酸集落的至少一个序列测定步骤。 用于这些方法的固体支撑物，试剂盒和仪器。

    System and apparatus for sequential processing of analytes
    9.
    发明授权
    System and apparatus for sequential processing of analytes 有权
    用于顺序处理分析物的系统和设备

    公开(公告)号：US07282370B2

    公开(公告)日：2007-10-16

    申请号：US11207443

    申请日：2005-08-18

    申请人： John Bridgham ,  Kevin Corcoran ,  George Golda ,  Michael C. Pallas ,  Sydney Brenner

    发明人： John Bridgham ,  Kevin Corcoran ,  George Golda ,  Michael C. Pallas ,  Sydney Brenner

    IPC分类号： G01N21/76 ,  G01N21/00 ,  G01N37/00

    CPC分类号： G01N21/253 ,  B01J2219/00274 ,  B01L3/5027 ,  B01L3/502715 ,  B01L3/502761 ,  B01L2200/0647 ,  B01L2200/10 ,  B01L2300/0877 ,  B01L2400/0403 ,  B01L2400/0475 ,  B01L2400/0622 ,  B01L2400/0644 ,  G01N2015/144 ,  G01N2015/1452 ,  G01N2035/00158 ,  Y10S435/81 ,  Y10T436/13 ,  Y10T436/143333

    摘要： An apparatus and system are provided for simultaneously analyzing a plurality of analytes anchored to microparticles. Microparticles each having a uniform population of a single kind of analyte attached are disposed as a substantially immobilized planar array inside of a flow chamber where steps of an analytical process are carried out by delivering a sequence of processing reagents to the microparticles by a fluidic system under microprocessor control. In response to such process steps, an optical signal is generated at the surface of each microparticle which is characteristic of the interaction between the analyte carried by the microparticle and the delivered processing reagent. The plurality of analytes are simultaneously analyzed by collecting and recording images of the optical signals generated by all the microparticles in the planar array. A key feature of the invention is the correlation of the sequence of optical signals generated by each microparticle in the planar array during the analytical process.

    摘要翻译： 提供了一种用于同时分析锚定到微粒的多个分析物的装置和系统。 每个具有单一类型分析物的均匀群体的微粒被布置为在流动室内部基本上固定的平面阵列，其中分析过程的步骤通过将一系列处理试剂通过流体系统递送到微粒进行， 微处理器控制。 响应于这样的处理步骤，在每个微粒的表面产生光信号，其特征在于微粒携带的分析物与递送的处理试剂之间的相互作用。 通过收集和记录由平面阵列中的所有微粒产生的光学信号的图像来同时分析多个分析物。 本发明的一个关键特征是在分析过程中由平面阵列中的每个微粒产生的光信号序列的相关性。