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    Method and system for determining a zero point for array-based comparative genomic hybridization data
    1.
    发明申请
    Method and system for determining a zero point for array-based comparative genomic hybridization data 审中-公开
    用于确定基于阵列的比较基因组杂交数据的零点的方法和系统

    公开(公告)号：US20070174008A1

    公开(公告)日：2007-07-26

    申请号：US11338515

    申请日：2006-01-24

    申请人： Zohar Yakhini ,  Doron Lipson ,  Amir Ben-Dor

    发明人： Zohar Yakhini ,  Doron Lipson ,  Amir Ben-Dor

    IPC分类号： G06F19/00

    CPC分类号： G16B25/00 ,  G16B45/00

    摘要： Various embodiments of the present invention determine a zero point, or centralization constant ζ, for an array-based comparative genomic hybridization (“aCGH”) data set by identifying a zero-point value, or centralization constant ζ, that, when used in an aberration-calling analysis of the aCGH data, results in the fewest number of array-probe-complementary genomic sequences identified as having abnormal copy numbers with respect to a control genome, or, in other words, results in the greatest number of array-probe-complementary genomic sequences identified as having normal copy numbers. In one embodiment, interval-based analysis of an aCGH data set may be carried out using a range of putative zero-point values, and the zero-point value for which the maximum number of genomic sequences are determined to have normal copy numbers may then be selected.

    摘要翻译： 本发明的各种实施方案通过鉴定零点值或中心常数zeta来确定基于阵列的比较基因组杂交（“aCGH”）数据集的零点或中心常数zeta，当在 aCGH数据的像差调查分析导致被认为具有相对于对照基因组具有异常拷贝数的阵列 - 探针互补基因组序列数量最少，换句话说，导致阵列探针数量最多 鉴定为具有正常拷贝数的互补基因组序列。 在一个实施例中，可以使用推定的零点值的范围来执行aCGH数据集的基于时间的分析，并且可以将确定具有正常拷贝数的最大数目的基因组序列的零点值 被选中。

    Analyzing and visualizing enrichment in DNA sequence alterations
    2.
    发明申请
    Analyzing and visualizing enrichment in DNA sequence alterations 审中-公开
    分析和可视化DNA序列变异中的富集

    公开(公告)号：US20060173635A1

    公开(公告)日：2006-08-03

    申请号：US11049565

    申请日：2005-02-01

    申请人： Zohar Yakhini ,  Amir Ben-Dor ,  Anya Tsalenko ,  Doron Lipson

    发明人： Zohar Yakhini ,  Amir Ben-Dor ,  Anya Tsalenko ,  Doron Lipson

    IPC分类号： G06F19/00

    CPC分类号： G16B25/00 ,  G16B20/00

    摘要： Methods, tools, systems and computer readable media for analyzing CGH data, together with data from an independent source. Independent data is compared with the CGH data, wherein the CGH data is characterized by sets of defined regions differentiated by at least one property. Enrichment is assessed for at least one subset of the data from an independent source with regard to at least one of the sets of defined regions in the CGH data. Methods, tools, systems and computer readable media for visualizing CGH data as it is impacted by data from an independent source are also provided. A relationship between at least one defined set of the CGH data and at least one set of sequence elements defined in the data from an independent source may be visualized.

    摘要翻译： 用于分析CGH数据的方法，工具，系统和计算机可读介质，以及来自独立源的数据。 将独立数据与CGH数据进行比较，其中CGH数据由通过至少一个属性区分的限定区域的集合来表征。 相对于CGH数据中的至少一个限定区域的集合，来自独立源的至少一个数据子集的浓度被评估。 还提供了用于可视化CGH数据的方法，工具，系统和计算机可读介质，因为它受来自独立源的数据的影响。 至少一个定义的CGH数据集与来自独立源的数据中定义的至少一组序列元素之间的关系可以被可视化。

    Methods and systems for joint analysis of array CGH data and gene expression data
    3.
    发明申请
    Methods and systems for joint analysis of array CGH data and gene expression data 审中-公开
    数组CGH数据和基因表达数据联合分析的方法和系统

    公开(公告)号：US20050170378A1

    公开(公告)日：2005-08-04

    申请号：US10964207

    申请日：2004-10-12

    申请人： Zohar Yakhini ,  Doron Lipson ,  Amir Ben-Dor

    发明人： Zohar Yakhini ,  Doron Lipson ,  Amir Ben-Dor

    IPC分类号： C12Q1/68 ,  G01N33/48 ,  G01N33/50 ,  G06F19/00

    CPC分类号： G16B25/00 ,  G16B40/00

    摘要： Methods, systems and computer readable media for identifying a high-scoring, significantly altered genomic-continuous submatrix, wherein each genomic-continuous submatrix contains a subset of a set of genes measured across a set of samples to generate a DNA copy number data matrix and a gene expression data matrix. The subset of the genes is a genomic-continuous set of genes, and each genomic-continuous submatrix contains a subset of the set of samples measured to generate the DNA copy number data matrix and the gene expression data matrix.

    摘要翻译： 用于识别高得分，显着改变的基因组连续子矩阵的方法，系统和计算机可读介质，其中每个基因组连续子矩阵包含跨越一组样本测量的一组基因的子集，以产生DNA拷贝数数据矩阵， 基因表达数据矩阵。 基因的子集是基因组连续的基因组，每个基因组连续子矩阵包含测量的一组样本的子集以产生DNA拷贝数数据矩阵和基因表达数据矩阵。

    Method and system for computational detection of common aberrations from multi-sample comparative genomic hybridization data sets
    4.
    发明申请
    Method and system for computational detection of common aberrations from multi-sample comparative genomic hybridization data sets 审中-公开
    用于多样本比较基因组杂交数据集的常见像差的计算检测方法和系统

    公开(公告)号：US20070203653A1

    公开(公告)日：2007-08-30

    申请号：US11363699

    申请日：2006-02-28

    申请人： Amir Ben-Dor ,  Anya Tsalenko ,  Doron Lipson ,  Zohar Yakhini

    发明人： Amir Ben-Dor ,  Anya Tsalenko ,  Doron Lipson ,  Zohar Yakhini

    IPC分类号： G06F19/00

    CPC分类号： G16B25/00 ,  G16B30/00 ,  G16B40/00

    摘要： Various embodiments of the present invention are directed to methods and systems for automatic, statistically meaningful detection of aberrations common to multiple samples within a sample set. Many various aberration-calling techniques are used to identify aberrant intervals within each of the samples of the sample set. A set of candidate intervals is constructed to include the aberrant intervals identified by the aberration-calling technique, as well as two-way intersections of the identified aberrant intervals. A score indicating the statistical relevance of each candidate interval with respect to each sample is next assigned to each candidate interval. Then, a total significance score is assigned to each candidate interval based on the individual scores for the candidate interval with respect to each sample. The most statistically significant candidate intervals may be selected based on the total significance scores assigned to the candidate intervals.

    摘要翻译： 本发明的各种实施例涉及用于对样本集合内的多个样本共同的像差进行自动统计学上有意义的检测的方法和系统。 使用许多各种像差调用技术来识别样本集合的每个样本内的异常间隔。 一组候选间隔被构造成包括由像差调用技术识别的异常间隔以及所识别的异常间隔的双向交叉。 指示每个候选间隔相对于每个样本的统计学相关性的分数接下来分配给每个候选间隔。 然后，基于针对每个样本的候选间隔的各个评分，将总重要性得分分配给每个候选间隔。 可以基于分配给候选间隔的总重要性得分来选择最具统计意义的候选间隔。

    Comprehensive, quality-based interval scores for analysis of comparative genomic hybridization data
    5.
    发明申请
    Comprehensive, quality-based interval scores for analysis of comparative genomic hybridization data 审中-公开
    综合，基于质量的间隔评分用于分析比较基因组杂交数据

    公开(公告)号：US20060173634A1

    公开(公告)日：2006-08-03

    申请号：US11049183

    申请日：2005-02-02

    申请人： Amir Ben-Dor ,  Doron Lipson ,  Zohar Yakhini

    发明人： Amir Ben-Dor ,  Doron Lipson ,  Zohar Yakhini

    IPC分类号： G06F19/00

    CPC分类号： G16B40/00 ,  G16B25/00 ,  G16B45/00

    摘要： Embodiments of the present invention are directed to increasing the reliability, precision, and resolution of identification, by analysis of comparative genomic hybridization (“CGH”) data and array-based comparative genomic hybridization (“aCGH”) data, of intervals along one or more chromosomes in which the copy number of the DNA subsequence within the interval in a sample genome is difference from the copy number of the DNA subsequence within a standard, or normal, genome. In various embodiments of the present invention, statistical data-quality measures are incorporated into comprehensive, quality-based interval-scores. In one described embodiment of the present invention, standard deviations for log ratios of signal intensities obtained by instrumental analysis of a microarray are used, along with the log ratios of signal intensities, to compute, for each interval, a weighted interval mean and interval variance, which are mathematically combined to produce a comprehensive, quality-based interval score that can be used to more reliably, precisely, and with greater resolution identify intervals along one or more chromosomes.

    摘要翻译： 本发明的实施例旨在通过分析比较基因组杂交（“CGH”）数据和基于阵列的比较基因组杂交（“aCGH”）数据来提高识别的可靠性，精确度和分辨率， 更多的染色体，其中样品基因组间隔内的DNA亚序列的拷贝数与标准或正常基因组内的DNA亚序列的拷贝数不同。 在本发明的各种实施例中，将统计数据质量度量纳入综合的基于质量的间隔分数。 在本发明的一个描述的实施例中，使用通过微阵列的仪器分析获得的信号强度的对数比的标准偏差以及信号强度的对数比，以计算每个间隔的加权间隔平均值和间隔方差 ，其被数学地组合以产生综合的基于质量的间隔分数，其可以更可靠地，精确地并且以更大的分辨率识别沿着一个或多个染色体的间隔。

    GENOME ANALYSIS USING A NICKING ENDONUCLEASE
    8.
    发明申请
    GENOME ANALYSIS USING A NICKING ENDONUCLEASE 审中-公开
    使用内分泌酶的基因组分析

    公开(公告)号：US20100330556A1

    公开(公告)日：2010-12-30

    申请号：US12495199

    申请日：2009-06-30

    申请人： Brian Jon Peter ,  Amir Ben-Dor ,  Zohar Yakhini ,  Holly Hogrefe

    发明人： Brian Jon Peter ,  Amir Ben-Dor ,  Zohar Yakhini ,  Holly Hogrefe

    IPC分类号： C12Q1/68

    CPC分类号： C12Q1/6809 ,  C12Q1/683 ,  C12Q1/6858 ,  C12Q2535/101 ,  C12Q2523/303 ,  C12Q2521/307

    摘要： A method of genome analysis is provided. In certain embodiments, the method of comprises: a) contacting a genomic sample comprising a double-stranded DNA with a site-specific nicking endonuclease to provide a nicked double-stranded DNA comprising a plurality of nick sites, in which the nicking endonuclease nicks a site adjacent to a variable nucleotide; b) contacting the nicked double-stranded DNA with a polymerase in the presence of a nucleotide composition comprising a first labeled nucleotide comprising a first label, thereby producing a labeled double-stranded DNA that is not labeled at every nick site; c) stretching out the labeled double-stranded DNA to provide a stretched, labeled double-stranded DNA; and d) imaging the stretched, labeled double-stranded DNA to identify a labeling pattern on the stretched labeled double-stranded DNA.

    摘要翻译： 提供了一种基因组分析方法。 在某些实施方案中，所述方法包括：a）将包含双链DNA的基因组样品与位点特异性切口内切核酸酶接触以提供包含多个切口位点的切口双链DNA，其中所述切口内切核酸酶切除 邻近可变核苷酸的位点; b）在含有包含第一标记的第一标记核苷酸的核苷酸组合物存在的情况下使所述切口双链DNA与聚合酶接触，从而产生未在每个切口位点标记的标记的双链DNA; c）拉伸标记的双链DNA以提供拉伸的标记的双链DNA; 和d）对拉伸的标记的双链DNA进行成像，以鉴定拉伸标记的双链DNA上的标记图谱。

    Atherosclerosis genes and related reagents and methods of use thereof
    10.
    发明申请
    Atherosclerosis genes and related reagents and methods of use thereof 审中-公开
    动脉粥样硬化基因及相关试剂及其使用方法

    公开(公告)号：US20070253901A1

    公开(公告)日：2007-11-01

    申请号：US11412437

    申请日：2006-04-27

    申请人： David Deng ,  Anya Tsalenko ,  Amir Ben-Dor ,  Zohar Yakhini ,  Thomas Quertermous ,  Euan Ashley ,  Eugene Yang ,  Raymond Tabibiazar ,  Philip Tsao

    发明人： David Deng ,  Anya Tsalenko ,  Amir Ben-Dor ,  Zohar Yakhini ,  Thomas Quertermous ,  Euan Ashley ,  Eugene Yang ,  Raymond Tabibiazar ,  Philip Tsao

    IPC分类号： A61K51/00 ,  A61K49/10 ,  C07K16/46 ,  C07K14/54

    CPC分类号： G01N33/6893 ,  G01N2800/323

    摘要： The invention provides genes (DEA genes) that are differentially expressed in atherosclerotic lesions and polypeptides encoded by these genes. The invention provides compositions comprising a targeting agent conjugated to a functional moiety, wherein the targeting agent selectively binds to a polypeptide encoded by one a DEA gene. The functional moiety can be an imaging agent, therapeutic agent, etc. The invention further provides methods for providing diagnostic or prognostic information related to atherosclerosis involving detecting expression or activity of an expression product of one or more of the DEA genes. The invention further provides therapeutic methods comprising administering to a subject a composition comprising a targeting agent conjugated to a functional moiety that binds selectively binds to a polypeptide encoded by a DEA gene.

    摘要翻译： 本发明提供在动脉粥样硬化病变和由这些基因编码的多肽中差异表达的基因（DEA基因）。 本发明提供了包含与功能部分缀合的靶向剂的组合物，其中所述靶向剂选择性地结合由DEA基因之一编码的多肽。 功能部分可以是显像剂，治疗剂等。本发明还提供了提供涉及检测一种或多种DEA基因的表达产物的表达或活性的动脉粥样硬化相关的诊断或预后信息的方法。 本发明进一步提供治疗方法，包括向受试者施用包含与功能性部分缀合的靶向试剂的组合物，其结合选择性结合由DEA基因编码的多肽。