公开(公告)号：US20100285478A1

公开(公告)日：2010-11-11

申请号：US12748329

申请日：2010-03-26

申请人： Caifu Chen ,  Ruoying Tan

发明人： Caifu Chen ,  Ruoying Tan

IPC分类号： C12Q1/68

CPC分类号： C12Q1/6858 ,  C12Q1/686 ,  C12Q1/6883 ,  C12Q2600/156 ,  C12Q2561/113 ,  C12Q2561/101 ,  C12Q2537/161 ,  C12Q2525/186 ,  C12Q2565/107 ,  C12Q2535/125

摘要： In some embodiments, the present inventions relates generally to compositions, methods and kits for use in discriminating sequence variation between different alleles. More specifically, in some embodiments, the present invention provides for compositions, methods and kits for quantitating rare (e.g., mutant) allelic variants, such as SNPs, or nucleotide (NT) insertions or deletions, in samples comprising abundant (e.g., wild type) allelic variants with high specificity and selectivity. In particular, in some embodiments, the invention relates to a highly selective method for mutation detection referred to as competitive allele-specific TaqMan PCR (“cast-PCR”).

公开(公告)号：US20100015631A1

公开(公告)日：2010-01-21

申请号：US12559476

申请日：2009-09-14

申请人： Caifu CHEN ,  Kevin Hennessy ,  Kai Qin Lao ,  Teodoro Paner ,  Vinod Mirchandani

发明人： Caifu CHEN ,  Kevin Hennessy ,  Kai Qin Lao ,  Teodoro Paner ,  Vinod Mirchandani

IPC分类号： C12Q1/68 ,  C07H21/04

CPC分类号： C12Q1/6876 ,  C12Q1/6816 ,  C12Q2533/107 ,  C12Q2525/301

摘要： The present teachings relate to methods, compositions, and kits for detecting one or more target polynucleotide sequences in a sample, and methods compositions and kits for forming concatameric ligation products. In some embodiments of the present teachings, oligonucleotides are hybridized to complementary target polynucleotides and are ligated together to form a concatameric ligation product. In some embodiments of the present teachings, the concatameric ligation product can be amplified, and the identity and quantity of the target polynucleotides determined based on sequence introduced in the ligation reaction. Some embodiments of the present teachings provide methods for removing unligated probes from the reaction mixture. Some embodiments of the present teachings provide for highly multiplexed detection, identification, and quantification of a plurality of target polynucleotides using a variety of analytical procedures.

摘要翻译： 本教导涉及用于检测样品中的一种或多种靶多核苷酸序列的方法，组合物和试剂盒，以及用于形成连续连接产物的方法组合物和试剂盒。 在本教导的一些实施方案中，寡核苷酸与互补靶多核苷酸杂交并连接在一起以形成连接产物。 在本教导的一些实施方案中，可以扩增连续连接产物，并且基于在连接反应中引入的序列确定靶多核苷酸的身份和数量。 本教导的一些实施方案提供从反应混合物中除去未螯合的探针的方法。 本教导的一些实施方案使用各种分析程序提供多重检测，鉴定和定量多个靶多核苷酸。

公开(公告)号：US07642055B2

公开(公告)日：2010-01-05

申请号：US11232475

申请日：2005-09-21

申请人： Andrew K. Finn ,  Caifu Chen

发明人： Andrew K. Finn ,  Caifu Chen

IPC分类号： C12P19/34 ,  C07H21/04

CPC分类号： C12Q1/6818 ,  C12Q1/6851 ,  C12Q2565/1025 ,  C12Q2537/143 ,  C12Q2525/161 ,  C12Q2525/301

摘要： The present invention is directed to methods, reagents, kits, and compositions for detecting target polynucleotide sequences, especially small target polynucleotides such as miRNAs, between two samples. A pair of linker probes can be employed in two different reactions to query a particular species of target polynucleotide. A pair of detector probes, a single forward primer specific for the target polynucleotide, and a reverse primer can be employed in an amplification reaction to query the difference in expression level of the target polynucleotide between the two samples. In some embodiments a plurality of small miRNAs are queried with a plurality of linker probes. The plurality of queried miRNAs can then be decoded in a plurality of amplification reactions.

摘要翻译： 本发明涉及用于在两个样品之间检测靶多核苷酸序列，特别是小目标多核苷酸如miRNA的方法，试剂，试剂盒和组合物。 可以在两个不同的反应中使用一对接头探针来查询特定种类的靶多核苷酸。 可以在扩增反应中使用一对检测器探针，针对靶多核苷酸特异性的单一正向引物和反向引物来查询两个样品之间的靶多核苷酸表达水平的差异。 在一些实施方案中，使用多个接头探针查询多个小miRNA。 然后可以在多个扩增反应中解码多个查询的miRNA。

公开(公告)号：US07601495B2

公开(公告)日：2009-10-13

申请号：US11142720

申请日：2005-05-31

申请人： Caifu Chen ,  Dana Ridzon ,  Zhaohui Zhou ,  Kai Q. Lao ,  Neil A. Straus

发明人： Caifu Chen ,  Dana Ridzon ,  Zhaohui Zhou ,  Kai Q. Lao ,  Neil A. Straus

IPC分类号： C12Q1/68 ,  C12P19/34

CPC分类号： C12Q1/6876 ,  C07H21/04 ,  C12N9/00 ,  C12P19/34 ,  C12Q1/686 ,  C12Q2525/301 ,  C12Q2600/16 ,  C12Q2600/178

摘要： The present invention is directed to methods, reagents, kits, and compositions for identifying and quantifying target polynucleotide sequences. A linker probe comprising a 3′ target specific portion, a loop, and a stem is hybridized to a target polynucleotide and extended to form a reaction product that includes a reverse primer portion and the stem nucleotides. A detector probe, a specific forward primer, and a reverse primer can be employed in an amplification reaction wherein the detector probe can detect the amplified target polynucleotide based on the stem nucleotides introduced by the linker probe. In some embodiments a plurality of short miRNAs are queried with a plurality of linker probes, wherein the linker probes all comprise a universal reverse primer portion a different 3′ target specific portion and different stems. The plurality of queried miRNAs can then be decoded in a plurality of amplification reactions.

摘要翻译： 本发明涉及用于鉴定和定量靶多核苷酸序列的方法，试剂，试剂盒和组合物。 包含3'靶特异性部分，环和茎的接头探针与目标多核苷酸杂交并延伸以形成包含反向引物部分和茎核苷酸的反应产物。 可以在扩增反应中使用检测器探针，特异性正向引物和反向引物，其中检测器探针可以基于由接头探针引入的干核苷酸检测扩增的靶多核苷酸。 在一些实施方案中，使用多个接头探针查询多个短miRNA，其中所述连接物探针都包含不同3'靶特异性部分和不同茎的通用反向引物部分。 然后可以在多个扩增反应中解码多个查询的miRNA。

公开(公告)号：US07575863B2

公开(公告)日：2009-08-18

申请号：US10947460

申请日：2004-09-21

申请人： Caifu Chen ,  Dana Ridzon ,  Zhaohui Zhou ,  Kai Qin Lao ,  Neil A. Straus

发明人： Caifu Chen ,  Dana Ridzon ,  Zhaohui Zhou ,  Kai Qin Lao ,  Neil A. Straus

IPC分类号： C12Q1/68 ,  C12P19/34

CPC分类号： C12Q1/6876 ,  C07H21/04 ,  C12N9/00 ,  C12P19/34 ,  C12Q1/686 ,  C12Q2525/301 ,  C12Q2600/16 ,  C12Q2600/178

摘要： The present invention is directed to methods, reagents, kits, and compositions for identifying and quantifying target polynucleotide sequences. A linker probe comprising a 3′ target specific portion, a loop, and a stem is hybridized to a target polynucleotide and extended to form a reaction product that includes a reverse primer portion and the stem nucleotides. A detector probe, a specific forward primer, and a reverse primer can be employed in an amplification reaction wherein the detector probe can detect the amplified target polynucleotide based on the stem nucleotides introduced by the linker probe. In some embodiments a plurality of short miRNAs are queried with a plurality of linker probes, wherein the linker probes all comprise a universal reverse primer portion a different 3′ target specific portion and different stems. The plurality of queried miRNAs can then be decoded in a plurality of amplification reactions.

公开(公告)号：US20070111226A1

公开(公告)日：2007-05-17

申请号：US11467125

申请日：2006-08-24

申请人： Ruoying Tan ,  Caifu Chen ,  Karl Guegler

发明人： Ruoying Tan ,  Caifu Chen ,  Karl Guegler

IPC分类号： C12Q1/68 ,  C12P19/34

CPC分类号： C12Q1/6855 ,  C12Q1/6851 ,  C12Q2525/301 ,  C12Q2525/207 ,  C12Q2521/501 ,  C12Q2537/143

摘要： The present teachings provide methods, compositions, and kits for quantifying target polynucleotides. In some embodiments, a reverse stem-loop ligation probe is ligated to the 3′ end of a target polynucleotide, using a ligase that can ligate the 3′ end of RNA to the 5′ end of DNA using a DNA template, such as T4 DNA ligase. Following digestion to form an elongated target polynucleotide with a liberated end, a reverse transcription reaction can be performed, followed by a PCR. In some embodiments, the methods of the present teachings can discriminate between polymorphic polynucleoitides that vary by as little as one nucleotide.

摘要翻译： 本教导提供了用于定量靶多核苷酸的方法，组合物和试剂盒。 在一些实施方案中，使用连接酶将反向茎环结合探针连接到靶多核苷酸的3'末端，该连接酶可以使用DNA模板如T4连接DNA的3'末端至DNA的5'末端 DNA连接酶。 在消化形成具有释放末端的细长靶多核苷酸之后，可以进行逆转录反应，随后进行PCR。 在一些实施方案中，本教导的方法可以区分多达一个核苷酸变化的多核苷酸多核苷酸。

公开(公告)号：US20050266418A1

公开(公告)日：2005-12-01

申请号：US10947460

申请日：2004-09-21

申请人： Caifu Chen ,  Dana Ridzon

发明人： Caifu Chen ,  Dana Ridzon

IPC分类号： C12P19/34 ,  C12Q1/68

CPC分类号： C12Q1/6876 ,  C07H21/04 ,  C12N9/00 ,  C12P19/34 ,  C12Q1/686 ,  C12Q2525/301 ,  C12Q2600/16 ,  C12Q2600/178

摘要： The present invention is directed to methods, reagents, kits, and compositions for identifying and quantifying target polynucleotide sequences. A linker probe comprising a 3′ target specific portion, a loop, and a stem is hybridized to a target polynucleotide and extended to form a reaction product that includes a reverse primer portion and the stem nucleotides. A detector probe, a specific forward primer, and a reverse primer can be employed in an amplification reaction wherein the detector probe can detect the amplified target polynucleotide based on the stem nucleotides introduced by the linker probe. In some embodiments a plurality of short miRNAs are queried with a plurality of linker probes, wherein the linker probes all comprise a universal reverse primer portion a different 3′ target specific portion and different stems. The plurality of queried miRNAs can then be decoded in a plurality of amplification reactions.

摘要翻译： 本发明涉及用于鉴定和定量靶多核苷酸序列的方法，试剂，试剂盒和组合物。 包含3'靶特异性部分，环和茎的接头探针与目标多核苷酸杂交并延伸以形成包含反向引物部分和茎核苷酸的反应产物。 可以在扩增反应中使用检测器探针，特异性正向引物和反向引物，其中检测器探针可以基于由接头探针引入的干核苷酸检测扩增的靶多核苷酸。 在一些实施方案中，使用多个接头探针查询多个短miRNA，其中所述连接物探针都包含不同3'靶特异性部分和不同茎的通用反向引物部分。 然后可以在多个扩增反应中解码多个查询的miRNA。