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    PROBE DENSITY CONSIDERATIONS AND ELONGATION OF SELF-COMPLEMENTARY LOOPED PROBES WHERE PROBES ARE ATTACHED TO A SOLID PHASE
    71.
    发明申请
    PROBE DENSITY CONSIDERATIONS AND ELONGATION OF SELF-COMPLEMENTARY LOOPED PROBES WHERE PROBES ARE ATTACHED TO A SOLID PHASE 有权
    探索密集度考察和自我补充循环探测器的延伸，探头附着在固体相位

    公开(公告)号：US20150126389A1

    公开(公告)日：2015-05-07

    申请号：US14449569

    申请日：2014-08-01

    Applicant: BioArray Solutions, Ltd.

    Inventor： Michael SEUL ,  Yi ZHANG ,  Sukanta BANERJEE ,  Jiacheng YANG ,  Chiu CHAU

    IPC: C12Q1/68

    CPC classification number: C12Q1/6837 ,  C12Q1/6818 ,  C12Q1/6827 ,  C12Q2565/1015 ,  C12Q2537/143 ,  C12Q2533/101 ,  C12Q2535/125 ,  C12Q2525/301

    Abstract: In a multiplexed assay method carried out in solution, wherein the solution contains nucleic acid targets and, wherein several different types of oligonucleotide probes, each type having a different sequence in a region designated as a target binding domain, are used to detect the nucleic acid targets, said assay method including a method for increasing the effective concentration of the nucleic acid targets at the surface of a bead to which the oligonucleotide probes are bound, by one or more of the following steps:adjusting assay conditions so as to increase the effective concentration of the targets available for binding to the probes, by one or more of the following: (i) selecting a particular probe density on the surface of the bead; (ii) selecting a solution having an ionic strength greater than a threshold; (ii) selecting a target domain of a size less than a threshold; or (iii) selecting target domains within a specified proximity to a terminal end of the targets.

    Abstract translation: 在溶液中进行的多重测定方法中，其中溶液含有核酸靶，并且其中使用几个不同类型的寡核苷酸探针，每个类型在被称为靶结合结构域的区域中具有不同序列，以检测核酸 目标，所述测定方法包括通过一个或多个以下步骤增加寡核苷酸探针结合珠粒表面上的核酸靶的有效浓度的方法：调节测定条件以增加有效 通过一种或多种以下方法可用于结合探针的靶的浓度：（i）在珠的表面上选择特定的探针密度; （ii）选择具有大于阈值的离子强度的溶液; （ii）选择小于阈值的大小的目标域; 或（iii）在目标的终端的指定接近范围内选择目标域。

    ANALYSIS, SECURE ACCESS TO, AND TRANSMISSION OF ARRAY IMAGES
    74.
    发明申请
    ANALYSIS, SECURE ACCESS TO, AND TRANSMISSION OF ARRAY IMAGES 有权
    分析，安全访问和传输阵列图像

    公开(公告)号：US20140369579A1

    公开(公告)日：2014-12-18

    申请号：US14202357

    申请日：2014-03-10

    Applicant: Bioarray Solutions, Ltd.

    Inventor： Michael Seul ,  Xiongwu Xia ,  Chiu Chau ,  Scott Determan

    IPC: G06T7/00 ,  G06K9/00

    CPC classification number: G06T7/0012 ,  G01N33/566 ,  G06K9/00 ,  G06K9/00147 ,  G06K2209/07 ,  G06T7/11 ,  G06T7/155 ,  G06T7/33 ,  G06T2207/10064 ,  G06T2207/20152 ,  G06T2207/30072

    Abstract: Systems and methods are provided the autocentering, autofocusing, acquiring, decoding, aligning, analyzing and exchanging among various parties, images, where the images are of arrays of signals associated with ligand-receptor interactions, and more particularly, ligand-receptor interactions where a multitude of receptors are associated with microparticles or microbeads. The beads are encoded to indicate the identity of the receptor attached, and therefore, an assay image and a decoding image are aligned to effect the decoding. The images or data extracted from such images can be exchanged between de-centralized assay locations and a centralized location where the data are analyzed to indicate assay results. Access to data can be restricted to authorized parties in possession of certain coding information, so as to preserve confidentiality.

    Abstract translation: 系统和方法提供了各方之间的自动对中，自动聚焦，获取，解码，对齐，分析和交换，其中图像是与配体 - 受体相互作用相关联的信号阵列，更具体地，配体 - 受体相互作用，其中 许多受体与微粒或微珠相关。 编码珠子以指示所连接的受体的身份，因此，分析图像和解码图像被对准以实现解码。 从这样的图像提取的图像或数据可以在非集中测定位置和数据被分析以指示测定结果的集中位置之间交换。 访问数据可以限于拥有某些编码信息的授权方，以保护机密性。

    CORRECTING AN ASSAY IMAGE OF AN ARRAY OF SIGNALS GENERATED FROM A MULTIPLEXED HYBRIDIZATION-MEDIATED ASSAY
    78.
    发明申请
    CORRECTING AN ASSAY IMAGE OF AN ARRAY OF SIGNALS GENERATED FROM A MULTIPLEXED HYBRIDIZATION-MEDIATED ASSAY 审中-公开
    校正由多重混合介质测定产生的信号阵列的测定图像

    公开(公告)号：US20110262911A1

    公开(公告)日：2011-10-27

    申请号：US12796232

    申请日：2010-06-08

    Applicant: Ghazala Hashmi ,  Michael Seul

    Inventor： Ghazala Hashmi ,  Michael Seul

    IPC: C12Q1/68

    CPC classification number: C12Q1/6883 ,  C12Q1/6809 ,  C12Q1/6827 ,  C12Q1/6837 ,  C12Q2600/156 ,  C12Q2600/16 ,  Y10S436/80 ,  Y10S436/805 ,  Y10T436/143333 ,  C12Q2565/543 ,  C12Q2563/107 ,  C12Q2565/501

    Abstract: Described are methods of assay design and assay image correction, useful for multiplexed genetic screening for mutations and polymorphisms, including CF-related mutants and polymorphs, using an array of probe pairs (in one aspect, where one member is complementary to a particular mutant or polymorphic allele and the other member is complementary to a corresponding wild type allele), with probes bound to encoded particles (e.g., beads) wherein the encoding allows identification of the attached probe. The methods relate to avoiding cross-hybridization by selection of probes and amplicons, as well as separation of reactions of certain probes and amplicons where a homology threshold is exceeded. Methods of correcting a fluorescent image using a background map, where the particles also contain an optical encoding system, are also disclosed.

    Abstract translation: 描述了测定设计和测定图像校正的方法，其可用于使用探针对阵列（在一个方面中，其中一个成员与特定突变体互补的突变和多态性）的多重遗传筛选（包括CF相关突变体和多态性） 多态等位基因和另一个成员与相应的野生型等位基因互补），其中探针与编码的颗粒结合（例如，珠粒），其中编码允许鉴定附着的探针。 该方法涉及通过选择探针和扩增子来避免交叉杂交，以及分离某些探针和扩增子的反应，其中超过同源性阈值。 还公开了使用背景图校正荧光图像的方法，其中颗粒还包含光编码系统。

    Concurrent optimization in selection of primer and capture probe sets for nucleic acid analysis
    79.
    发明授权
    Concurrent optimization in selection of primer and capture probe sets for nucleic acid analysis 有权
    选择引物和捕获探针组进行核酸分析的并发优化

    公开(公告)号：US07970553B2

    公开(公告)日：2011-06-28

    申请号：US12502725

    申请日：2009-07-14

    Applicant: Michael Seul ,  Tatiana Vener ,  Xiongwu Xia

    Inventor： Michael Seul ,  Tatiana Vener ,  Xiongwu Xia

    IPC: G01N33/48

    CPC classification number: C12Q1/6876 ,  C12Q2600/16 ,  G06F19/20 ,  G06F19/22

    Abstract: Disclosed is a method of iteratively optimizing two (or more) interrelated sets of probes for the multi-step analysis of sets of designated sequences, each such sequence requiring, for conversion, at least one conversion probe (“primer”), and each converted sequence requiring, for detection, at least one capture probe. The iterative method disclosed herein for the concurrent optimization of primer and probe selection invokes fast logical string matching functions to perform a complete cross-correlation of probe sequences and target sequences. The score function assigns to each probe-target alignment a “degree of matching” score on the basis of position-weighted Hamming distance functions introduced herein. Pairs of probes in the final selection may differ in several positions, while other pairs of probes may differ in only a single position. Not all such positions are of equal importance, and a score function is introduced, reflecting the position of the mismatch within the probe sequence.

    Abstract translation: 公开了一种迭代优化两个（或多个）相互关联的探针组的方法，用于多步分析指定序列集合，每个这样的序列需要转化至少一个转化探针（“引物”），并且每个转化 用于检测至少一个捕获探针的序列。 本文公开的用于并行优化引物和探针选择的迭代方法调用快速逻辑串匹配函数来执行探针序列和靶序列的完全互相关。 得分函数根据本文介绍的位置加权汉明距离函数将每个探针 - 目标对准分配给“匹配度”得分。 最终选择中的一对探针在几个位置可能有所不同，而其他探针对只能在一个位置上不同。 并不是所有这样的位置都是同等重要的，并且引入了分数函数，反映了探针序列内不匹配的位置。

    Method of probe design for nucleic acid analysis by multiplexed hybridization
    80.
    发明授权
    Method of probe design for nucleic acid analysis by multiplexed hybridization 有权
    通过多重杂交进行核酸分析的探针设计方法

    公开(公告)号：US07858301B2

    公开(公告)日：2010-12-28

    申请号：US10841931

    申请日：2004-05-07

    Applicant: Vera Cherepinsky ,  Bhubaneswar Mishra ,  Ghazala Hashmi ,  Michael Seul

    Inventor： Vera Cherepinsky ,  Bhubaneswar Mishra ,  Ghazala Hashmi ,  Michael Seul

    IPC: C12Q1/68 ,  C07H21/02 ,  C07H21/04

    CPC classification number: G06F19/20 ,  G06F19/22

    Abstract: Disclosed is an analysis method useful in multiplexed hybridization-mediated analysis of polymorphisms, i.e., wherein a labeled nucleic acid of interest (“target”) interacts with two or more pairs of immobilized degenerate capture probes. In one embodiment, one member of each pair has a sequence that is complementary to the normal (“wild-type”) sequence in a designated location of the target, while the other member of each pair has a sequence that is complementary to an anticipated variant (“mutant” or “polymorph”) sequence in that location of the target. These methods permit selection of two or more probe pairs such that, for each pair of probes interacting with a given target strand, interaction of the target with a preferred member of the probe pair is optimized. Also interpreting results obtained by multiplexed hybridization of the target to two or more pairs of probes under conditions permitting competitive hybridization is disclosed.

    Abstract translation: 公开了一种分析方法，用于多重杂交介导的多态性分析，即其中所标记的目标核酸（“靶”）与两对或更多对固定的简并捕获探针相互作用。 在一个实施方案中，每对中的一个成员具有与目标的指定位置中的正常（“野生型”）序列互补的序列，而每对的另一个成员具有与预期的互补序列 变体（“突变”或“多态”）序列。 这些方法允许选择两个或更多个探针对，使得对于与给定靶链相互作用的每对探针，优化靶与探针对的优选成员的相互作用。 还公开了通过在允许竞争性杂交的条件下将靶多重杂交到两对或更多对探针获得的结果。

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