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    System and computer software products for comparative gene expression analysis
    4.
    发明授权
    System and computer software products for comparative gene expression analysis 有权
    用于比较基因表达分析的系统和计算机软件产品

    公开(公告)号：US07197400B2

    公开(公告)日：2007-03-27

    申请号：US09735574

    申请日：2000-12-12

    申请人： Wei-min Liu ,  Xiaojun Di

    发明人： Wei-min Liu ,  Xiaojun Di

    IPC分类号： G01N33/48

    CPC分类号： G06F19/20

    摘要： Methods and computer software products are provided for analyzing gene expression data. In one embodiment, methods, systems and computer software are provided for comparative gene expression analysis using intensity dependent normalization factors.

    摘要翻译： 提供方法和计算机软件产品，用于分析基因表达数据。 在一个实施例中，提供方法，系统和计算机软件用于使用强度依赖的归一化因子的比较基因表达分析。

    Methods for genotyping polymorphisms in humans
    6.
    发明申请
    Methods for genotyping polymorphisms in humans 失效
    人类基因分型多态性的方法

    公开(公告)号：US20060024715A1

    公开(公告)日：2006-02-02

    申请号：US11175859

    申请日：2005-07-05

    申请人： Guoying Liu ,  Simon Cawley ,  Hajime Matsuzaki ,  Earl Hubbell ,  Geoffrey Yang ,  Teresa Webster ,  Rui Mei ,  Xiaojun Di ,  Richard Chiles

    发明人： Guoying Liu ,  Simon Cawley ,  Hajime Matsuzaki ,  Earl Hubbell ,  Geoffrey Yang ,  Teresa Webster ,  Rui Mei ,  Xiaojun Di ,  Richard Chiles

    IPC分类号： C12Q1/68 ,  C12M1/34

    CPC分类号： C12Q1/6883 ,  C12Q2600/156

    摘要： Methods, kits and arrays of nucleic acid probes for genotyping large numbers of human SNPs in parallel are provided. A set of more than 100,000 human SNPs, known to be biallelic in at least two populations is provided. Allele specific perfect match probes and genotyping probe sets are provided for each allele of each biallelic SNP in a set of human SNPs that is useful for genetic analysis within and across populations. Probe sets that include perfect match and mismatch probes are provided. The probe sets are suitable for inclusion in an array. The invention provides the SNP and surrounding sequence and provides the sequences in such a way as to make them available for a variety of analyses including genotyping. As such, the invention relates to diverse fields impacted by the nature of genetics, including biology, medicine, and medical diagnostics.

    摘要翻译： 提供了用于并行分析大量人类SNP的核酸探针的方法，试剂盒和阵列。 提供了一组超过100,000个人类SNP，已知在至少两个人群中是双向的。 为一组人类SNP中的每个双重性SNP的每个等位基因提供等位基因特异性完全匹配探针和基因分型探针组，其可用于群体内和跨群体的遗传分析。 提供包括完美匹配和不匹配探针的探针组。 探头组适合包含在阵列中。 本发明提供了SNP和周围序列，并提供了这样的序列，使得它们可用于各种分析，包括基因分型。 因此，本发明涉及受遗传学性质影响的不同领域，包括生物学，医学和医学诊断。

    System, method, and computer software product for generating genotype calls
    7.
    发明申请
    System, method, and computer software product for generating genotype calls 审中-公开
    用于生成基因型呼叫的系统，方法和计算机软件产品

    公开(公告)号：US20050123971A1

    公开(公告)日：2005-06-09

    申请号：US10986963

    申请日：2004-11-12

    申请人： Xiaojun Di ,  Teresa Webster ,  Daniel Bartell ,  Richard Chiles

    发明人： Xiaojun Di ,  Teresa Webster ,  Daniel Bartell ,  Richard Chiles

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

    CPC分类号： C12Q1/6827 ,  G16B20/00 ,  G16B25/00 ,  G16B40/00 ,  C12Q2565/501

    摘要： A method for calling the genotype of a sample is described comprising the acts of receiving emission data for one or more target sequences each hybridized to a plurality of probe sets, where each of the probe sets comprises a plurality of probe features; calculating a set of values for each of the probe sets associated with each target sequence; selecting one of the set of values for each of the probe sets associated with each target sequence, wherein the value is selected if it is greater than a reference value; determining a significance value from the selected values of all the probe sets associated with each target sequence; and producing a genotype call for each target sequence based upon the significance value.

    摘要翻译： 描述了用于调用样本的基因型的方法，其包括接收与多个探针组杂交的一个或多个靶序列的发射数据的动作，其中每个探针组包括多个探针特征; 计算与每个目标序列相关联的每个探针组的值集合; 为与每个目标序列相关联的每个探针组选择所述一组值中的一个，其中如果所述值大于参考值则选择该值; 从与每个目标序列相关联的所有探针组的选定值中确定显着值; 并根据显着性值对每个靶序列产生基因型调用。

    System and method for improved genotype calls using microarrays
    8.
    发明申请
    System and method for improved genotype calls using microarrays 审中-公开
    使用微阵列改进基因型调用的系统和方法

    公开(公告)号：US20050287575A1

    公开(公告)日：2005-12-29

    申请号：US11157768

    申请日：2005-06-21

    申请人： Xiaojun Di ,  Simon Cawley

    发明人： Xiaojun Di ,  Simon Cawley

    IPC分类号： C12Q1/68 ,  G06F19/00

    CPC分类号： G16B20/00 ,  G16B25/00 ,  G16B30/00

    摘要： An embodiment of a method for calling the genotype of a biological sequence is described that comprises receiving sets of intensity data each comprising an intensity value for each probe feature associated with a probe set disposed on a probe array; independently applying filters to the intensity values of a probe set associated with a forward strand and of a probe set associated with a reverse strand, where the probe sets interrogate the same sequence position; independently applying models to the filtered intensity values for the forward strand and the reverse strand, where the models produce a genotype call for each strand; combining the genotype call for the forward strand and the genotype call for the reverse strand to generate a final genotype call; and testing the reliability of the final genotype call.

    摘要翻译： 描述了用于调用生物序列的基因型的方法的实施例，其包括接收强度数据组，每组强度数据包括与设置在探针阵列上的探针组相关联的每个探针特征的强度值; 独立地将滤波器应用于与正向链相关联的探针组和与反向链相关联的探针组的强度值，其中探针组询问相同的序列位置; 独立地将模型应用于前向链和反向链的过滤强度值，其中模型产生每条链的基因型呼叫; 组合正向链的基因型呼叫和反向链的基因型呼叫以产生最终的基因型呼叫; 并测试最终基因型呼叫的可靠性。

    Methods for genotyping polymorphisms in humans
    10.
    发明授权
    Methods for genotyping polymorphisms in humans 失效
    人类基因分型多态性的方法

    公开(公告)号：US07361468B2

    公开(公告)日：2008-04-22

    申请号：US11175859

    申请日：2005-07-05

    申请人： Guoying Liu ,  Simon Cawley ,  Hajime Matsuzaki ,  Earl A. Hubbell ,  Geoffrey Yang ,  Teresa A. Webster ,  Rui Mei ,  Xiaojun Di ,  Richard Chiles

    发明人： Guoying Liu ,  Simon Cawley ,  Hajime Matsuzaki ,  Earl A. Hubbell ,  Geoffrey Yang ,  Teresa A. Webster ,  Rui Mei ,  Xiaojun Di ,  Richard Chiles

    IPC分类号： C12Q1/68 ,  C07H21/04 ,  C12M3/00 ,  C12M1/34

    CPC分类号： C12Q1/6883 ,  C12Q2600/156

    摘要： Methods, kits and arrays of nucleic acid probes for genotyping large numbers of human SNPs in parallel are provided. A set of more than 100,000 human SNPs, known to be biallelic in at least two populations is provided. Allele specific perfect match probes and genotyping probe sets are provided for each allele of each biallelic SNP in a set of human SNPs that is useful for genetic analysis within and across populations. Probe sets that include perfect match and mismatch probes are provided. The probe sets are suitable for inclusion in an array. The invention provides the SNP and surrounding sequence and provides the sequences in such a way as to make them available for a variety of analyses including genotyping. As such, the invention relates to diverse fields impacted by the nature of genetics, including biology, medicine, and medical diagnostics.

    摘要翻译： 提供了用于并行分析大量人类SNP的核酸探针的方法，试剂盒和阵列。 提供了一组超过100,000个人类SNP，已知在至少两个人群中是双向的。 为一组人类SNP中的每个双重性SNP的每个等位基因提供等位基因特异性完全匹配探针和基因分型探针组，其可用于群体内和跨群体的遗传分析。 提供包括完美匹配和不匹配探针的探针组。 探头组适合包含在阵列中。 本发明提供了SNP和周围序列，并提供了这样的序列，使得它们可用于各种分析，包括基因分型。 因此，本发明涉及受遗传学性质影响的不同领域，包括生物学，医学和医学诊断。