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

IPC分类号： C40B20/00 ,  C12Q1/68 ,  C40B40/06 ,  C12P19/34 ,  C40B30/04

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。

公开(公告)号：US20110009294A1

公开(公告)日：2011-01-13

申请号：US12326596

申请日：2008-12-02

申请人： Keith W. Jones ,  Michael H. Shapero ,  Stephen P.A. Fodor

发明人： Keith W. Jones ,  Michael H. Shapero ,  Stephen P.A. Fodor

IPC分类号： C40B40/06

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。

公开(公告)号：US20090075345A1

公开(公告)日：2009-03-19

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

IPC分类号： C12P19/34

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。

公开(公告)号：US20120142551A1

公开(公告)日：2012-06-07

申请号：US13348394

申请日：2012-01-11

申请人： Keith W. Jones ,  Michael H. Shapero ,  Stephen P.A. Fodor

发明人： Keith W. Jones ,  Michael H. Shapero ,  Stephen P.A. Fodor

IPC分类号： C40B30/04 ,  C40B50/18 ,  C40B40/06

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。

公开(公告)号：US20090239764A1

公开(公告)日：2009-09-24

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

IPC分类号： C40B30/04 ,  C40B40/08 ,  C12Q1/68

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，其使用肌苷用于短链DNA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。

公开(公告)号：US07459273B2

公开(公告)日：2008-12-02

申请号：US10912445

申请日：2004-08-05

申请人： Keith W. Jones ,  Michael H. Shapero ,  Stephen P. A. Fodor

发明人： Keith W. Jones ,  Michael H. Shapero ,  Stephen P. A. Fodor

IPC分类号： C12Q1/68 ,  C12P19/34 ,  C07H21/00 ,  C07H21/04

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。

公开(公告)号：US20130017966A1

公开(公告)日：2013-01-17

申请号：US13365825

申请日：2012-02-03

申请人： Michael H. Shapero ,  Keith W. Jones

发明人： Michael H. Shapero ,  Keith W. Jones

IPC分类号： C40B50/06 ,  C40B40/06 ,  C40B30/04

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.

公开(公告)号：US07414108B2

公开(公告)日：2008-08-19

申请号：US10772856

申请日：2004-02-04

申请人： Reiner Laus ,  Curtis L. Ruegg ,  Michael H. Shapero ,  Demao Yang

发明人： Reiner Laus ,  Curtis L. Ruegg ,  Michael H. Shapero ,  Demao Yang

IPC分类号： C07K5/10

CPC分类号： A61K39/0011 ,  A61K38/00 ,  A61K39/00 ,  C12N9/16 ,  C12N2799/022 ,  C12N2799/026

摘要： Disclosed are a novel prostatic acid phosphatase and corresponding coding region derived from mouse. Also disclosed is a method of producing an immune response against an autologous polypeptide tumor antigen by immunizing a subject with a xenogeneic polypeptide antigen, either alone, as part of a viral antigen construct, or as part of a pulsed dendritic cell preparation.

摘要翻译： 公开了一种新型前列腺酸性磷酸酶及其衍生自小鼠的相应编码区。 还公开了通过用异种多肽抗原单独免疫受试者作为病毒抗原构建物的一部分或作为脉冲树突状细胞制剂的一部分来产生针对自体多肽肿瘤抗原的免疫应答的方法。

公开(公告)号：US06194152B1

公开(公告)日：2001-02-27

申请号：US09112096

申请日：1998-07-09

申请人： Reiner Laus ,  Michael H. Shapero ,  Larisa Tsavaler

发明人： Reiner Laus ,  Michael H. Shapero ,  Larisa Tsavaler

IPC分类号： C12Q168

CPC分类号： C07K14/705 ,  C07K2319/00

摘要： The present invention is directed to novel polynucleotides and the polypeptides encoded by them, each of which are specific to human prostate tumor cells. The present invention further provides chimeric polypeptide molecules comprising the polypeptides of the present invention fused to heterologous polypeptide sequences, and antibodies which bind to the polypeptides of the present invention. Also provided herein are methods for producing the polypeptides of the present invention, as are detection assays that detect the presence of tumor cells in tissue or bodily fluid samples and methods for identifying novel compositions which modulate the activity of prostate tumor antigens and the use of such compositions in diagnosis and treatment of disease.

摘要翻译： 本发明涉及新的多核苷酸和由它们编码的多肽，其各自对人前列腺肿瘤细胞是特异性的。 本发明进一步提供了包含与异源多肽序列融合的本发明多肽的嵌合多肽分子和结合本发明多肽的抗体。 本文还提供了用于产生本发明的多肽的方法，以及检测组织或体液样品中肿瘤细胞的存在的检测测定法以及用于鉴定调节前列腺肿瘤抗原活性的新组合物的方法及其用途 疾病诊断和治疗中的成分。

公开(公告)号：US20080293589A1

公开(公告)日：2008-11-27

申请号：US12127770

申请日：2008-05-27

申请人： Michael H. Shapero

发明人： Michael H. Shapero

IPC分类号： C40B30/04

CPC分类号： C40B30/04 ,  C12Q1/6855 ,  C40B40/06 ,  C12Q2531/125 ,  C12Q2521/501 ,  C12Q2521/301

摘要： Methods are provided for amplifying a plurality of pre-selected target sequences from a complex background of nucleic acids. The targets are selected for amplification using splint oligonucleotides that are used to modify the ends of the fragments. The fragments have known end sequences and the splints are designed to be complementary to the ends. In one aspect the splint brings the ends of the fragment together and the ends are joined to form a circle. In another aspect the splint is used to add a common priming site to the ends of the target fragments. Specific loci are amplified and can be subsequently analyzed.

摘要翻译： 提供了从核酸的复杂背景中扩增多个预先选择的靶序列的方法。 使用用于修饰片段末端的夹板寡核苷酸选择靶标进行扩增。 这些片段具有已知的末端序列，并且夹板被设计成与末端互补。 在一个方面，夹板将碎片的端部连接在一起，并且端部被接合以形成圆形。 另一方面，夹板用于在目标碎片的末端添加一个共同的引发位点。 特异性基因座被扩增并可以随后分析。