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公开(公告)号：US20110029251A1
公开(公告)日：2011-02-03
申请号：US12902711
申请日：2010-10-12
申请人： Jing Huang , Keith W. Jones , Michael H. Shapero
发明人： Jing Huang , Keith W. Jones , Michael H. Shapero
CPC分类号： G06F19/18 , C12Q1/6827 , C12Q1/6837 , G06F19/20 , C12Q2545/101
摘要： Methods of identifying allele-specific changes in genomic DNA copy number are disclosed. Methods for identifying homozygous deletions and genetic amplifications are disclosed. An array of probes designed to detect presence or absence of a plurality of different sequences is also disclosed. The probes are designed to hybridize to sequences that are predicted to be present in a reduced complexity sample. The methods may be used to detect copy number changes in cancerous tissue compared to normal tissue. The methods may be used to diagnose cancer and other diseases associated with chromosomal anomalies.
摘要翻译： 公开了确定基因组DNA拷贝数中等位基因特异性变化的方法。 公开了鉴定纯合缺失和遗传扩增的方法。 还公开了一种设计用于检测多个不同序列的存在或不存在的探针阵列。 探针被设计为与预测存在于复杂度降低的样品中的序列杂交。 与正常组织相比，该方法可用于检测癌组织中的拷贝数变化。 该方法可用于诊断与染色体异常相关的癌症和其他疾病。
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公开(公告)号：US20120214704A1
公开(公告)日：2012-08-23
申请号：US13459603
申请日：2012-04-30
申请人： Jing Huang , Keith W. Jones , Michael H. Shapero
发明人： Jing Huang , Keith W. Jones , Michael H. Shapero
CPC分类号： G06F19/18 , C12Q1/6827 , C12Q1/6837 , G06F19/20 , C12Q2545/101
摘要： Methods of identifying allele-specific changes in genomic DNA copy number are disclosed. Methods for identifying homozygous deletions and genetic amplifications are disclosed. An array of probes designed to detect presence or absence of a plurality of different sequences is also disclosed. The probes are designed to hybridize to sequences that are predicted to be present in a reduced complexity sample. The methods may be used to detect copy number changes in cancerous tissue compared to normal tissue. The methods may be used to diagnose cancer and other diseases associated with chromosomal anomalies.
摘要翻译： 公开了确定基因组DNA拷贝数中等位基因特异性变化的方法。 公开了鉴定纯合缺失和遗传扩增的方法。 还公开了一种设计用于检测多个不同序列的存在或不存在的探针阵列。 探针被设计为与预测存在于复杂度降低的样品中的序列杂交。 与正常组织相比，该方法可用于检测癌组织中的拷贝数变化。 该方法可用于诊断与染色体异常相关的癌症和其他疾病。
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公开(公告)号：US07822555B2
公开(公告)日：2010-10-26
申请号：US11295225
申请日：2005-12-05
申请人： Jing Huang , Keith W. Jones , Michael H. Shapero
发明人： Jing Huang , Keith W. Jones , Michael H. Shapero
IPC分类号： G06F7/00
CPC分类号： G06F19/18 , C12Q1/6827 , C12Q1/6837 , G06F19/20 , C12Q2545/101
摘要： Methods of identifying allele-specific changes in genomic DNA copy number are disclosed. Methods for identifying homozygous deletions and genetic amplifications are disclosed. An array of probes designed to detect presence or absence of a plurality of different sequences is also disclosed. The probes are designed to hybridize to sequences that are predicted to be present in a reduced complexity sample. The methods may be used to detect copy number changes in cancerous tissue compared to normal tissue. The methods may be used to diagnose cancer and other diseases associated with chromosomal anomalies.
摘要翻译： 公开了确定基因组DNA拷贝数中等位基因特异性变化的方法。 公开了鉴定纯合缺失和遗传扩增的方法。 还公开了一种设计用于检测多个不同序列的存在或不存在的探针阵列。 探针被设计为与预测存在于复杂度降低的样品中的序列杂交。 与正常组织相比，该方法可用于检测癌组织中的拷贝数变化。 该方法可用于诊断与染色体异常相关的癌症和其他疾病。
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公开(公告)号：US07424368B2
公开(公告)日：2008-09-09
申请号：US10712616
申请日：2003-11-12
申请人： Jing Huang , Keith W Jones , Michael H. Shapero
发明人： Jing Huang , Keith W Jones , Michael H. Shapero
CPC分类号： G06F19/20 , C12Q1/6827 , C12Q1/6837 , G06F19/18 , C12Q2545/101
摘要： Methods of estimating genomic DNA copy number are disclosed. Amplified genomic DNA is hybridized to an array of allele specific SNP probes to generate a hybridization pattern. A value, S, is calculated for individual SNPs in the experimental sample, where S is the log of the arithmetic average of the intensities of the perfect match probes for the SNP. S is calculated for the SNP in reference samples that are matched to the experimental sample in genotype. The mean and standard deviation for the S values of the reference samples are calculated and a log intensity difference is calculated by subtracting the mean values for the reference and experimental samples. The copy number of the SNP region is estimated using the difference between the mean for the SNP in the reference samples and the S value for the SNP in the experimental sample in a log-log linear model.
摘要翻译： 公开了估计基因组DNA拷贝数的方法。 扩增的基因组DNA与等位基因特异性SNP探针的阵列杂交以产生杂交模式。 对于实验样品中的单个SNP计算值S，其中S是SNP完美匹配探针的强度的算术平均值的对数。 对于与基因型实验样品匹配的参考样品中的SNP计算S。 计算参考样品的S值的平均值和标准偏差，并通过减去参考和实验样品的平均值计算对数强度差。 使用对数线性模型中的参考样本中的SNP的平均值与实验样品中的SNP的S值之间的差来估计SNP区域的拷贝数。
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公开(公告)号：US10108777B2
公开(公告)日：2018-10-23
申请号：US13459603
申请日：2012-04-30
申请人： Jing Huang , Keith W. Jones , Michael H. Shapero
发明人： Jing Huang , Keith W. Jones , Michael H. Shapero
IPC分类号： G06F19/00 , G06F19/18 , C12Q1/6827 , C12Q1/6837 , G06F19/20
摘要： Methods of identifying allele-specific changes in genomic DNA copy number are disclosed. Methods for identifying homozygous deletions and genetic amplifications are disclosed. An array of probes designed to detect presence or absence of a plurality of different sequences is also disclosed. The probes are designed to hybridize to sequences that are predicted to be present in a reduced complexity sample. The methods may be used to detect copy number changes in cancerous tissue compared to normal tissue. The methods may be used to diagnose cancer and other diseases associated with chromosomal anomalies.
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公开(公告)号：US08190373B2
公开(公告)日：2012-05-29
申请号：US12902711
申请日：2010-10-12
申请人： Jing Huang , Keith W. Jones , Michael H. Shapero
发明人： Jing Huang , Keith W. Jones , Michael H. Shapero
IPC分类号： G06F7/00
CPC分类号： G06F19/18 , C12Q1/6827 , C12Q1/6837 , G06F19/20 , C12Q2545/101
摘要： Methods of identifying allele-specific changes in genomic DNA copy number are disclosed. Methods for identifying homozygous deletions and genetic amplifications are disclosed. An array of probes designed to detect presence or absence of a plurality of different sequences is also disclosed. The probes are designed to hybridize to sequences that are predicted to be present in a reduced complexity sample. The methods may be used to detect copy number changes in cancerous tissue compared to normal tissue. The methods may be used to diagnose cancer and other diseases associated with chromosomal anomalies.
摘要翻译： 公开了确定基因组DNA拷贝数中等位基因特异性变化的方法。 公开了鉴定纯合缺失和遗传扩增的方法。 还公开了一种设计用于检测多个不同序列的存在或不存在的探针阵列。 探针被设计为与预测存在于复杂度降低的样品中的序列杂交。 与正常组织相比，该方法可用于检测癌组织中的拷贝数变化。 该方法可用于诊断与染色体异常相关的癌症和其他疾病。
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公开(公告)号：US20110251798A1
公开(公告)日：2011-10-13
申请号：US13167264
申请日：2011-06-23
申请人： Jing Huang , Keith W. Jones
发明人： Jing Huang , Keith W. Jones
CPC分类号： G06F19/18 , C12Q2600/156
摘要： Methods for genotyping polymorphisms using allele specific probes are disclosed. A training set is used to generate a model for each polymorphism to be interrogated. The training set is used to obtain an estimate of the asymmetry between an intensity measurement for a first allele and an intensity measurement for a second allele of the same polymorphism. The intensity measurement obtained for a test sample is adjusted using the estimate of asymmetry prior to using the intensity measurements to make a genotyping call. In preferred embodiments the adjustment is applied to polymorphisms that have a likelihood of being heterozygous that is above a specified threshold.
摘要翻译： 公开了使用等位基因特异性探针进行基因分型多态性的方法。 训练集用于生成要查询的每个多态性的模型。 训练集用于获得第一等位基因的强度测量与相同多态性的第二等位基因的强度测量之间的不对称性的估计。 在使用强度测量进行基因分型调用之前，使用不对称估计来调整测试样品获得的强度测量值。 在优选实施方案中，调整适用于具有高于特定阈值的杂合可能性的多态性。
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公开(公告)号：US20100144542A1
公开(公告)日：2010-06-10
申请号：US12638939
申请日：2009-12-15
申请人： Jing Huang , Keith W. Jones
发明人： Jing Huang , Keith W. Jones
CPC分类号： G06F19/18 , C12Q2600/156
摘要： Methods for genotyping polymorphisms using allele specific probes are disclosed. A training set is used to generate a model for each polymorphism to be interrogated. The training set is used to obtain an estimate of the asymmetry between an intensity measurement for a first allele and an intensity measurement for a second allele of the same polymorphism. The intensity measurement obtained for a test sample is adjusted using the estimate of asymmetry prior to using the intensity measurements to make a genotyping call. In preferred embodiments the adjustment is applied to polymorphisms that have a likelihood of being heterozygous that is above a specified threshold.
摘要翻译： 公开了使用等位基因特异性探针进行基因分型多态性的方法。 训练集用于生成要查询的每个多态性的模型。 训练集用于获得第一等位基因的强度测量与相同多态性的第二等位基因的强度测量之间的不对称性的估计。 在使用强度测量进行基因分型呼叫之前，使用不对称性的估计来调整测试样品获得的强度测量。 在优选实施方案中，调整适用于具有高于特定阈值的杂合可能性的多态性。
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公开(公告)号：US07634363B2
公开(公告)日：2009-12-15
申请号：US11608233
申请日：2006-12-07
申请人： Jing Huang , Keith W. Jones
发明人： Jing Huang , Keith W. Jones
CPC分类号： G06F19/18 , C12Q2600/156
摘要： Methods for genotyping polymorphisms using allele specific probes are disclosed. A training set is used to generate a model for each polymorphism to be interrogated. The training set is used to obtain an estimate of the asymmetry between an intensity measurement for a first allele and an intensity measurement for a second allele of the same polymorphism. The intensity measurement obtained for a test sample is adjusted using the estimate of asymmetry prior to using the intensity measurements to make a genotyping call. In preferred embodiments the adjustment is applied to polymorphisms that have a likelihood of being heterozygous that is above a specified threshold.
摘要翻译： 公开了使用等位基因特异性探针进行基因分型多态性的方法。 训练集用于生成要查询的每个多态性的模型。 训练集用于获得第一等位基因的强度测量与相同多态性的第二等位基因的强度测量之间的不对称性的估计。 在使用强度测量进行基因分型调用之前，使用不对称估计来调整测试样品获得的强度测量值。 在优选实施方案中，调整适用于具有高于特定阈值的杂合可能性的多态性。
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公开(公告)号：US07991564B2
公开(公告)日：2011-08-02
申请号：US12638939
申请日：2009-12-15
申请人： Jing Huang , Keith W. Jones
发明人： Jing Huang , Keith W. Jones
CPC分类号： G06F19/18 , C12Q2600/156
摘要： Methods for genotyping polymorphisms using allele specific probes are disclosed. A training set is used to generate a model for each polymorphism to be interrogated. The training set is used to obtain an estimate of the asymmetry between an intensity measurement for a first allele and an intensity measurement for a second allele of the same polymorphism. The intensity measurement obtained for a test sample is adjusted using the estimate of asymmetry prior to using the intensity measurements to make a genotyping call. In preferred embodiments the adjustment is applied to polymorphisms that have a likelihood of being heterozygous that is above a specified threshold.
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