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公开(公告)号：US08114978B2
公开(公告)日：2012-02-14
申请号：US12326596
申请日：2008-12-02
CPC分类号： C12Q1/6827 , C12Q1/6809 , C12Q1/6837 , C12Q1/6855 , C12Q2600/156
摘要： Methods for genotyping polymorphisms using a locus specific primer that is complementary to a region near a selected polymorphism are described. Methods for synthesizing pools of locus specific primers that incorporate some degenerate positions are also disclosed. A plurality of different sequence capture probes are synthesized simultaneously using degenerate oligonucleotide synthesis. The sequence of the locus specific regions of the capture probes are related in that they have some bases that are identical in each sequence in the plurality of sequences and positions that vary from one locus specific region to another. The sequences are selected based on proximity to a polymorphism of interest and because they conform to a similar sequence pattern.
摘要翻译： 描述使用与选定多态性附近的区域互补的位点特异性引物进行基因分型多态性的方法。 还公开了合并含有一些退化位置的基因座特异性引物库的方法。 使用简并寡核苷酸合成同时合成多个不同的序列捕获探针。 捕获探针的基因座特异性区域的序列是相关的，因为它们具有在从一个基因座特异性区域到另一个基因座特异性区域变化的多个序列和位置中的每个序列中具有相同的一些碱基。 基于与感兴趣的多态性的接近度并且因为它们符合类似的序列模式来选择序列。
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公开(公告)号：US07459273B2
公开(公告)日：2008-12-02
申请号：US10912445
申请日：2004-08-05
CPC分类号： C12Q1/6809 , C12Q1/6837 , C12Q2600/156
摘要： Methods for genotyping polymorphisms using a locus specific primer that is complementary to a region near a selected polymorphism are described. Methods for synthesizing pools of locus specific primers that incorporate some degenerate positions are also disclosed. A plurality of different sequence capture probes are synthesized simultaneously using degenerate oligonucleotide synthesis. The sequence of the locus specific regions of the capture probes are related in that they have some bases that are identical in each sequence in the plurality of sequences and positions that vary from one locus specific region to another. The sequences are selected based on proximity to a polymorphism of interest and because they conform to a similar sequence pattern.
摘要翻译： 描述使用与选定多态性附近的区域互补的位点特异性引物进行基因分型多态性的方法。 还公开了合并含有一些退化位置的基因座特异性引物库的方法。 使用简并寡核苷酸合成同时合成多个不同的序列捕获探针。 捕获探针的基因座特异性区域的序列是相关的，因为它们具有在从一个基因座特异性区域到另一个基因座特异性区域变化的多个序列和位置中的每个序列中具有相同的一些碱基。 基于与感兴趣的多态性的接近度并且因为它们符合类似的序列模式来选择序列。
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公开(公告)号：US08808995B2
公开(公告)日：2014-08-19
申请号：US13348394
申请日：2012-01-11
CPC分类号： C12Q1/6827 , C12Q1/6809 , C12Q1/6837 , C12Q1/6855 , C12Q2600/156
摘要： Methods for genotyping polymorphisms using a locus specific primer that is complementary to a region near a selected polymorphism are described. Methods for synthesizing pools of locus specific primers that incorporate some degenerate positions are also disclosed. A plurality of different sequence capture probes are synthesized simultaneously using degenerate oligonucleotide synthesis. The sequence of the locus specific regions of the capture probes are related in that they have some bases that are identical in each sequence in the plurality of sequences and positions that vary from one locus specific region to another. The sequences are selected based on proximity to a polymorphism of interest and because they conform to a similar sequence pattern.
摘要翻译： 描述使用与选定多态性附近的区域互补的位点特异性引物进行基因分型多态性的方法。 还公开了合并含有一些退化位置的基因座特异性引物库的方法。 使用简并寡核苷酸合成同时合成多个不同的序列捕获探针。 捕获探针的基因座特异性区域的序列是相关的，因为它们具有在从一个基因座特异性区域到另一个基因座特异性区域变化的多个序列和位置中的每个序列中具有相同的一些碱基。 基于与感兴趣的多态性的接近度并且因为它们符合类似的序列模式来选择序列。
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公开(公告)号：US08133667B2
公开(公告)日：2012-03-13
申请号：US12272370
申请日：2008-11-17
申请人： Michael H. Shapero , Keith W. Jones
发明人： Michael H. Shapero , Keith W. Jones
CPC分类号： C12Q1/683
摘要： The present invention provides methods for reducing the complexity of a nucleic acid sample to interrogate a collection of target sequences. Complexity reduction can be accomplished by fragmenting the nucleic acid sample with a restriction enzyme that has at least one variable position in the recognition sequence. In some aspects adaptors that ligate to some but not all possible overhangs generated by digestion are ligated to the fragments. This selective adaptor ligation allows for selective amplification of a subset of the fragments using primers complementary to the adaptor sequence. In another aspect primers that are complementary to a subset of the fragments after adaptor ligation are used for amplification. Amplified fragments may be analyzed to genotype polymorphisms by hybridization to an array of probes that are complementary to target sequences that will be amplified.
摘要翻译： 本发明提供降低核酸样品复杂性以询问靶序列集合的方法。 可以通过在识别序列中具有至少一个可变位置的限制酶片段化核酸样品来实现复杂性降低。 在一些方面，连接到通过消化产生的一些但不是所有可能的突出端的衔接子被连接到片段。 该选择性衔接子连接允许使用与衔接子序列互补的引物选择性扩增片段的一个子集。 另一方面，在衔接子连接后与片段的子集互补的引物用于扩增。 可以通过与将被扩增的靶序列互补的探针阵列杂交来分析扩增片段以基因型多态性。
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公开(公告)号：US07452671B2
公开(公告)日：2008-11-18
申请号：US11381125
申请日：2006-05-01
申请人： Michael H. Shapero , Keith W. Jones
发明人： Michael H. Shapero , Keith W. Jones
CPC分类号： C12Q1/683
摘要： The present invention provides methods for reducing the complexity of a nucleic acid sample to interrogate a collection of target sequences. Complexity reduction can be accomplished by fragmenting the nucleic acid sample with a restriction enzyme that has at least one variable position in the recognition sequence. In some aspects adaptors that ligate to some but not all possible overhangs generated by digestion are ligated to the fragments. Selective adaptor ligation allows for selective amplification of a subset of the fragments using primers complementary to the adaptor sequence. In another aspect primers that are complementary to a subset of the fragments after adaptor ligation are used for amplification. Reduced complexity samples generated by the disclosed methods may be interrogated for the genotypes of SNPs in the sample.
摘要翻译： 本发明提供降低核酸样品复杂性以询问靶序列集合的方法。 可以通过在识别序列中具有至少一个可变位置的限制酶片段化核酸样品来实现复杂性降低。 在一些方面，连接到通过消化产生的一些但不是所有可能的突出端的衔接子被连接到片段。 选择性衔接子连接允许使用与衔接子序列互补的引物选择性扩增片段的一个子集。 另一方面，在衔接子连接后与片段的子集互补的引物用于扩增。 可以询问由所公开的方法产生的降低的复杂度样品用于样品中SNP的基因型。
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公开(公告)号：US09074244B2
公开(公告)日：2015-07-07
申请号：US12402486
申请日：2009-03-11
申请人： Andrew Sparks , Michael H. Shapero , Glenn K. Fu , Keith W. Jones
发明人： Andrew Sparks , Michael H. Shapero , Glenn K. Fu , Keith W. Jones
CPC分类号： C12Q1/6883 , C12Q1/6827 , C12Q2600/16 , G06F19/20 , C12Q2565/513 , C12Q2539/101 , C12Q2525/155
摘要： Methods for detecting genomic rearrangements are provided. In one embodiment, methods are provided for the use of paired end tags from restriction fragments to detect genomic rearrangements. Sequences from the ends of the fragments are brought together to form ditags and the ditags are detected. Combinations of ditags are detected by an on-chip sequencing strategy that is described herein, using inosine for de novo sequencing of short segments of DNA. In another aspect, translocations are identified by using target specific capture and analysis of the captured products on a tiling array.
摘要翻译： 提供了检测基因组重排的方法。 在一个实施方案中，提供了使用来自限制性片段的配对末端标签来检测基因组重排的方法。 将片段末端的序列汇集在一起以形成二重态，并检测二重态。 通过本文所述的片上测序策略检测ditag的组合，其使用肌苷进行DNA短链段的重新测序。 在另一方面，通过使用平铺阵列上捕获的产物的目标特异性捕获和分析来鉴定易位。
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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：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：US20120010087A1
公开(公告)日：2012-01-12
申请号：US13176437
申请日：2011-07-05
申请人： Michael H. Shapero , Keith W. Jones
发明人： Michael H. Shapero , Keith W. Jones
CPC分类号： C12Q1/6858 , C12Q1/6809 , C12Q1/6837 , C12Q1/6855 , C12Q1/686 , C12Q1/6876 , C12Q2600/156 , C12Q2565/514 , C12Q2563/149 , C12Q2521/301 , C12Q2525/155 , C12Q2563/131 , C12Q2565/537 , C12Q2537/143 , C12Q2531/113 , C12Q2565/501 , C12Q2521/307
摘要： Novel methods and kits are disclosed for reducing the complexity of a nucleic acid sample to interrogate a collection of target sequences, for example, to discriminating between alleles at polymorphic positions in a genome. Complexity reduction can be accomplished by extension of a capture probes followed by amplification of the extended capture probe using common primers. The capture probes may be locus specific and allele-specific. The amplified sample may be hybridized to an array designed to interrogate the desired fragments for the presence or absence of a polymorphism. In some aspects the methods employ allele-specific extension of oligonucleotides that are complementary to one of the alleles at the 3′ end of the oligonucleotide. The allele-specific oligonucleotides are resistant to proof reading activity from a polymerase and may be extended in an allele-specific manner by a DNA polymerase with a functional 3′ to 5′ exonuclease activity.
摘要翻译： 公开了新的方法和试剂盒，用于降低核酸样品的复杂性以询问靶序列的集合，例如区分基因组中多态性位置处的等位基因。 通过扩增捕获探针，然后使用普通引物扩增扩增的捕获探针可以实现复杂性降低。 捕获探针可以是特异性基因座和等位基因特异性的。 扩增的样品可以与设计成询问所需片段的阵列的多态性的存在或不存在相互杂交。 在一些方面，所述方法采用与寡核苷酸3'末端的等位基因之一互补的寡核苷酸的等位基因特异性延伸。 等位基因特异性寡核苷酸对来自聚合酶的校对阅读活性具有抗性，并且可以通过具有功能3'至5'核酸外切酶活性的DNA聚合酶以等位基因特异性方式延伸。
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