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    System and method for improved genotype calls using microarrays
    1.
    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
    2.
    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。

    Methods for genotyping polymorphisms in humans
    4.
    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 GENOTYPE DETERMINATION USING PROBE ARRAY DATA
    10.
    发明申请
    SYSTEM, METHOD, AND COMPUTER SOFTWARE PRODUCT FOR GENOTYPE DETERMINATION USING PROBE ARRAY DATA 有权
    系统，方法和计算机软件产品使用探针阵列数据进行基因组测定

    公开(公告)号：US20080287308A1

    公开(公告)日：2008-11-20

    申请号：US12123463

    申请日：2008-05-19

    申请人： Earl A. Hubbell ,  Simon Cawley

    发明人： Earl A. Hubbell ,  Simon Cawley

    IPC分类号： C40B30/02

    CPC分类号： G06F19/18 ,  G06F19/20 ,  G06F19/24

    摘要： An embodiment of a method of analyzing data from processed images of biological probe arrays is described that comprises receiving a plurality of files comprising a plurality of intensity values associated with a probe on a biological probe array; normalizing the intensity values in each of the data files; determining an initial assignment for a plurality of genotypes using one or more of the intensity values from each file for each assignment; estimating a distribution of cluster centers using the plurality of initial assignments; combining the normalized intensity values with the cluster centers to determine a posterior estimate for each cluster center; and assigning a plurality of genotype calls using a distance of the one or more intensity values from the posterior estimate.

    摘要翻译： 描述了从生物探针阵列的处理图像分析数据的方法的实施例，其包括：接收包括与生物探针阵列上的探针相关联的多个强度值的多个文件; 对每个数据文件中的强度值进行归一化; 使用来自每个文件的每个分配的一个或多个强度值来确定多个基因型的初始分配; 使用所述多个初始分配估计聚类中心的分布; 将归一化强度值与聚类中心组合以确定每个聚类中心的后验估计; 以及使用来自所述后验估计的所述一个或多个强度值的距离来分配多个基因型呼叫。