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    Optimization of gene expression analysis using immobilized capture probes
    1.
    发明授权
    Optimization of gene expression analysis using immobilized capture probes 有权

    公开(公告)号：US10407718B2

    公开(公告)日：2019-09-10

    申请号：US15491127

    申请日：2017-04-19

    Applicant: BioArray Solutions, Ltd.

    Inventor： Michael Seul ,  Sukanta Banerjee ,  Jiacheng Yang ,  Tatiana Vener

    IPC: C12Q1/6832 ,  C12Q1/6809 ,  C12Q1/6834 ,  C12Q1/6837

    Abstract: Disclosed are methods of multiplexed analysis of oligonucleotides in a sample, including a method of preventing a significant reduction in duplexes detectable in a hybridization assay involving (i) selecting probe lengths for sets of oligonucleotide probes, wherein probes include different subsequences such that at least one subsequence is complementary to a subsequence in a cognate target; wherein probes for longer cognate targets are longer in length than probes for shorter cognate targets, (ii) selecting, for each set of probes, a density of oligonucleotides probes attached per unit area on a solid phase carrier which is below a limit at which the significant reduction in detectable duplexes is predicated to take place, (iii) producing the probes and affixing them to different solid phase carriers at the selected density, and (iv) annealing targets to the probes, wherein signal intensities of probes and targets of different lengths are about the same.

    ANALYSIS, SECURE ACCESS TO, AND TRANSMISSION OF ARRAY IMAGES
    5.
    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：US20160267650A1

    公开(公告)日：2016-09-15

    申请号：US15010597

    申请日：2016-01-29

    Applicant: BioArray Solutions, Ltd.

    Inventor： Michael SEUL ,  Xiongwu Xia ,  Chiu CHAU ,  Scott DETERMAN

    IPC: G06T7/00 ,  G01N33/566 ,  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 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 encoding 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影响解码。 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。

    AUTOMATED ANALYSIS OF MULTIPLEXED PROBE-TARGET INTERACTION PATTERNS: PATTERN MATCHING AND ALLELE IDENTIFICATION
    6.
    发明申请
    AUTOMATED ANALYSIS OF MULTIPLEXED PROBE-TARGET INTERACTION PATTERNS: PATTERN MATCHING AND ALLELE IDENTIFICATION 审中-公开
    多重探测目标相互作用模式的自动分析：模式匹配与识别

    公开(公告)号：US20160002714A1

    公开(公告)日：2016-01-07

    申请号：US14851844

    申请日：2015-09-11

    Applicant: BioArray Solutions, Ltd.

    Inventor： Xiongwu XIA ,  Michael SEUL

    IPC: C12Q1/68 ,  G06F19/22

    CPC classification number: C12Q1/6827 ,  G16B20/00 ,  G16B30/00

    Abstract: Disclosed are methods and algorithms (and their implementation) supporting the automated analysis and interactive review and refinement (“redaction”) of the analysis within an integrated software environment, for automated allele assignments. The implementation, preferably with a software system and a program referred to as the Automated Allele Assignment (“AAA”) program, provides a multiplicity of functionalities including: data management by way of an integrated interface to a portable database to permit visualizing, importing, exporting and creating customizable summary reports; system configuration (“Set-up”) including user authorization, training set analysis and probe masking; Pattern Analysis including string matching and probe flipping; and Interactive Redaction combining real-time database computations and “cut-and-paste” editing, generating “warning” statements and supporting annotation. It also includes a thresholding function, a method of setting thresholds, a method of refining thresholds by matching an experimental binary string (“reaction pattern”) setting for that probe, probe masking of signals produced by probes which do not contribute significantly to discriminating among alleles.

    Abstract translation: 公开的方法和算法（及其实现）支持在集成软件环境中进行自动化等位基因分配的自动分析和交互式审查和细化（“编辑”）分析。 优选地使用软件系统和称为自动等位基因分配（“AAA”）程序的程序的实现提供了多种功能，包括：通过与便携式数据库的集成接口的数据管理，以允许可视化，导入， 出口和创建可定制的汇总报告; 系统配置（“设置”），包括用户授权，训练集分析和探测屏蔽; 模式分析包括字符串匹配和探针翻转; 和Interactive Redaction将实时数据库计算和“剪切和粘贴”编辑相结合，生成“警告”语句和支持注释。 它还包括阈值功能，设置阈值的方法，通过匹配用于该探针的实验二进制串（“反应模式”）设置来精确化阈值的方法，探针对由探针产生的信号进行探针掩蔽，所述探针不对显着区别于 等位基因

    Selection of Genotyped Transfusion Donors by Cross-Matching to Genotyped Recipients
    7.
    发明申请
    Selection of Genotyped Transfusion Donors by Cross-Matching to Genotyped Recipients 审中-公开
    通过与基因型受体的交叉匹配选择基因型输血供体

    公开(公告)号：US20140358446A1

    公开(公告)日：2014-12-04

    申请号：US14256579

    申请日：2014-04-18

    Applicant: BIOARRAY SOLUTIONS, LTD.

    Inventor： Yi Zhang ,  Michael Seul

    IPC: G06F19/00

    CPC classification number: G06F19/3456 ,  G06F19/3481 ,  G16B20/00 ,  G16B25/00 ,  G16B30/00 ,  G16B40/00 ,  G16H10/60 ,  G16H50/70

    Abstract: Disclosed are methods for establishing the compatibility between two blood types on the basis of cross-matching (under a designated rule of stringency) the minor blood group genotypes of recipient and prospective donors. To determine compatibility, the blood group genotypes are mapped to corresponding phenotypes according to the expression states associated with a set of underlying haplotypes, and compatibility is established by establishing the compatibility of blood types constructed as a combination of constituent phenotypes. The bit strings are matched, preferably using an algorithm expression. Where ambiguity in mapping genotypes to haplotypes exists, it can be reduced based on frequency of occurrence of the haplotypes in the sample population, or resolved by gametic phasing. Such reduction or resolution of ambiguity is particularly desirable where mismatches in the antigens expressed by the constituent haplotypes have greater clinical significance.

    Abstract translation: 公开的是基于接受者和潜在供体的次要血型基因型的交叉匹配（在指定的严格规则）的基础上建立两种血型之间的相容性的方法。 为了确定相容性，根据与一组潜在单倍型相关联的表达状态，将血型基因型映射到相应的表型，并且通过建立构成为构成表型的组合的血型相容性建立相容性。 比特串匹配，最好使用算法表达式。 如果存在将基因型映射到单倍型的歧义，则可以根据样本群体中单倍型的发生频率来减少，或者通过配子定相来解决。 在组成单元型表达的抗原中的错配具有更大的临床意义的情况下，这种模糊的减少或解决是特别理想的。

    Microparticles with enhanced covalent binding capacity and their uses
    8.
    发明授权
    Microparticles with enhanced covalent binding capacity and their uses 有权
    具有增强的共价结合能力的微粒及其用途

    公开(公告)号：US08691754B2

    公开(公告)日：2014-04-08

    申请号：US12795198

    申请日：2010-06-07

    Applicant: Xinwen Wang ,  Sukanta Banerjee

    Inventor： Xinwen Wang ,  Sukanta Banerjee

    IPC: C07K14/00

    CPC classification number: C12Q1/6834 ,  C07H21/04 ,  G01N33/54353 ,  C12Q2563/119

    Abstract: A polyelectrolyte having multiple exposed functional groups, each such group being capable of covalently bonding to a molecule, is immobilized on a surface for the purpose of bonding to a biomolecule. The biomolecule can be, for example, a nucleic acid, e.g., an amine functionalized oligonucleotide. The polyelectrolyte can include, e.g., BSA (Bovine Serum Albumin) which is bound to a functionalized surface using a covalent immobilization strategy, e.g., reaction with the surface of a tosyl-activated microparticle. Following such reaction, exposed reactive functional groups on the protein, such as amine, carboxyl, thiol, hydroxyl groups can further be utilized to covalently couple the oligonucleotide of interest using suitable chemistry.

    Abstract translation: 具有多个暴露的官能团的聚电解质，每个这样的基团能够共价键合到分子，固定在表面上用于与生物分子结合的目的。 生物分子可以是例如核酸，例如胺官能化的寡核苷酸。 聚电解质可以包括例如BSA（牛血清白蛋白），其使用共价固定策略结合到官能化表面，例如与甲苯磺酰基活化的微粒的表面反应。 在这样的反应之后，蛋白质上暴露的反应性官能团如胺，羧基，硫醇，羟基可进一步用于使用合适的化学物质共价连接感兴趣的寡核苷酸。

    Message abundance and allele copy number determination using IVT with single-stranded primer-promoter-selector constructs
    9.
    发明授权
    Message abundance and allele copy number determination using IVT with single-stranded primer-promoter-selector constructs 有权
    使用IVT与单链引物启动子选择构建体的消息丰度和等位基因拷贝数确定

    公开(公告)号：US08206953B2

    公开(公告)日：2012-06-26

    申请号：US11525064

    申请日：2006-09-21

    Applicant: Nataliya Korzheva ,  Michael Seul

    Inventor： Nataliya Korzheva ,  Michael Seul

    IPC: C12P19/34

    CPC classification number: C12Q1/6837 ,  C12N15/1096 ,  C12Q1/6858 ,  C12Q1/6865 ,  C12Q1/6876 ,  C12Q2521/107 ,  C12Q2525/143 ,  C12Q2563/179 ,  C12Q2565/137 ,  C12Q2545/114 ,  C12Q2531/113

    Abstract: Disclosed is a single stranded primer-promoter-selector construct comprising (in 3′ to 5′ orientation) a primer subsequence annealing to the target, a T7 or other promoter subsequence (the template strand), and a selector subsequence. The primer can be extended by template mediated elongation, including reverse transcription, or ligation to another oligonucleotide. The promoter sequence is oriented to direct the in-vitro transcription (IVT) opposite to that of primer extension, where the selector subsequence serves as a template for IVT. The selector is associated with the target subsequence of interest and it, and the amplified product are unique subsequences, dissimilar to other sequence present in the sample. The construct's is useful for determination of the presence and relative abundance of designated subsequences in the sample, multiplex gene expression analysis, multiplex allele counting, determination of polymorphic/mutation site, and loss of heterozygosity.

    Abstract translation: 公开了一种单链引物 - 启动子选择构建体，其包含（靶向3'至5'取向）引物亚序列退火，T7或其它启动子亚序列（模板链）和选择子序列。 引物可通过模板介导的延伸扩增，包括逆转录或连接至另一寡核苷酸。 启动子序列被定向以引导与引物延伸相反的体外转录（IVT），其中选择子序列用作IVT的模板。 选择器与感兴趣的目标子序列相关联，并且扩增产物是与样本中存在的其他序列不同的唯一子序列。 该构建体可用于确定样品中指定的子序列的存在和相对丰度，多重基因表达分析，多重等位基因计数，多态/突变位点的确定和杂合性的丧失。

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