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    Sieving of Nucleic Acid Samples
    92.
    发明申请
    Sieving of Nucleic Acid Samples 有权
    筛分核酸样品

    公开(公告)号：US20130029855A1

    公开(公告)日：2013-01-31

    申请号：US13190163

    申请日：2011-07-25

    Applicant: Michael Seul

    Inventor： Michael Seul

    IPC: C40B20/04

    CPC classification number: C40B20/04 ,  B01J2219/00576 ,  B01J2219/00592 ,  B01J2219/00722 ,  B01J2219/00725 ,  C12Q1/6858 ,  C40B50/10 ,  C40B50/16 ,  C12Q2535/125 ,  C12Q2537/143 ,  C12Q2563/149 ,  C12Q2563/179

    Abstract: A method of selecting nucleic acid samples from a plurality of nucleic acid samples based on desired alleles including the steps of performing a first reaction in a plurality of pools of the alleles to be identified to produce reaction products including a source tag identifying said each pool; pooling the pools to provide pooled pools; for each of the desired alleles to be identified, performing a second reaction using said reaction products to produce allele-specific second reaction products comprising a marker tag and a derived source tag; identifying said allele-specific second reaction products to select nucleic acid sample. In some embodiments, the first reaction may not be performed. A source tag sharing number “d” may be determined for each of the alleles. Alleles may be binned together.

    Abstract translation: 基于所需等位基因从多个核酸样品中选择核酸样品的方法，包括以下步骤：在待鉴定的等位基因的多个池中进行第一反应，以产生包括识别所述每个池的源标签的反应产物; 集中池塘提供池池; 对于待鉴定的每个所需等位基因，使用所述反应产物进行第二反应以产生包含标记标签和衍生源标签的等位基因特异性第二反应产物; 鉴定所述等位基因特异性第二反应产物以选择核酸样品。 在一些实施方案中，可能不执行第一反应。 可以为每个等位基因确定共享号码d的源标签。 等位基因可以合并在一起。

    Method for Determining an Attribute Profile of Biological Samples
    93.
    发明申请
    Method for Determining an Attribute Profile of Biological Samples 有权
    确定生物样品属性剖面的方法

    公开(公告)号：US20130029854A1

    公开(公告)日：2013-01-31

    申请号：US13190154

    申请日：2011-07-25

    Applicant: Michael Seul

    Inventor： Michael Seul

    IPC: C40B20/04

    CPC classification number: C40B20/04 ,  G01N33/50 ,  G01N33/582 ,  G01N33/80 ,  G01N2458/10 ,  G06F19/10

    Abstract: A method of identifying attributes in a plurality of biological samples including the steps of determining a source tag sharing number “d” for each of the attributes; providing a plurality of pools for the source tag sharing number “d” wherein each pool comprising a pooled subset of biological samples; for each pool of the plurality of pools, producing at least one pooled pool comprising attribute-specific reaction products comprising a marker tag that uniquely identifies an attribute and a source tag identifying said pool; and identifying said attribute-specific reaction products to identify the attributes. If “d” is equal to or larger than a maximum pool size, the reaction products may not comprise a source tag identifying each pool. Attributes may be binned together.

    Abstract translation: 一种识别多个生物样本中的属性的方法，包括以下步骤：为每个属性确定源标签共享号码d; 为源标签共享号码d提供多个池，其中每个池包括生物样本的汇集子集; 对于所述多个池中的每个池，产生至少一个池化池，其包括属性特异性反应产物，其包括唯一地识别属性的标记标签和标识所述池的源标签; 并识别所述属性特异性反应产物以识别属性。 如果d等于或大于最大池大小，反应产物可能不包含标识每个池的源标签。 属性可以合并在一起。

    CORRECTING AN ASSAY IMAGE OF AN ARRAY OF SIGNALS GENERATED FROM A MULTIPLEXED HYBRIDIZATION-MEDIATED ASSAY
    95.
    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
    96.
    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
    97.
    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。

    Analyzing Blood Type with Identification of Patient by Genotyping
    99.
    发明申请
    Analyzing Blood Type with Identification of Patient by Genotyping 有权
    通过基因分型分析患者的血型

    公开(公告)号：US20090264318A1

    公开(公告)日：2009-10-22

    申请号：US12113402

    申请日：2008-05-01

    Applicant: Ghazala Hashmi ,  Michael Seul ,  Joachim Messing

    Inventor： Ghazala Hashmi ,  Michael Seul ,  Joachim Messing

    IPC: C40B40/08

    CPC classification number: C12Q1/6827 ,  B82Y5/00 ,  B82Y10/00 ,  B82Y20/00 ,  C12Q1/6837 ,  C12Q2565/102 ,  C12Q2563/149 ,  C12Q2537/143

    Abstract: This invention provides compositions and methods for genetic testing of an organism and for correlating the results of the genetic testing with a unique marker that unambiguously identifies the organism. The markers may be internal markers, such as for example single nucleotide polymorphisms (SNPs), short tandem repeats (STRs), or other sites within a genomic locus. Alternatively, the markers may be external, such that they are separately added to the genetic sample before testing.

    Abstract translation: 本发明提供了用于生物体的遗传测试的组合物和方法，并且用于将遗传测试的结果与明确识别生物体的唯一标记相关联。 标记可以是内部标记，例如单核苷酸多态性（SNP），短串联重复序列（STR）或基因组基因座内的其他位点。 或者，标记可以是外部的，使得它们在测试之前分开地添加到遗传样品中。

    Differentiating homozygous, heterozygous and wild-type alleles using a multiplexed hybridization-mediated assay
    100.
    发明授权
    Differentiating homozygous, heterozygous and wild-type alleles using a multiplexed hybridization-mediated assay 有权
    使用多重杂交介导的测定法分化纯合，杂合和野生型等位基因

    公开(公告)号：US07501266B2

    公开(公告)日：2009-03-10

    申请号：US11439697

    申请日：2006-05-23

    Applicant: Ghazala Hashmi ,  Michael Seul

    Inventor： Ghazala Hashmi ,  Michael Seul

    IPC: C12Q1/68 ,  C12P19/34 ,  C12N9/00 ,  G01N33/53 ,  C07H21/04

    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。

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