公开(公告)号：US09534255B2

公开(公告)日：2017-01-03

申请号：US12641321

申请日：2009-12-17

申请人： Caifu Chen ,  Ruoying Tan

发明人： Caifu Chen ,  Ruoying Tan

IPC分类号： C07H21/04 ,  C12Q1/68

CPC分类号： C12Q1/6886 ,  C07H21/04 ,  C12Q1/6858 ,  C12Q2600/156 ,  C12Q2600/172 ,  C12Q2561/113 ,  C12Q2561/101 ,  C12Q2537/161

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”).

摘要翻译： 在一些实施方案中，本发明一般涉及用于区分不同等位基因之间的序列变异的组合物，方法和试剂盒。 更具体地说，在一些实施方案中，本发明提供了用于定量稀少（例如，突变体）等位基因变体如SNP或核苷酸（NT）插入或缺失的组合物，方法和试剂盒，其包含丰富的（例如，野生型 ）等位基因变体，具有高特异性和选择性。 特别地，在一些实施方案中，本发明涉及用于突变检测的高选择性方法，称为竞争性等位基因特异性TaqMan PCR（“cast-PCR”）。

公开(公告)号：US09309565B2

公开(公告)日：2016-04-12

申请号：US13107786

申请日：2011-05-13

申请人： Adam Broomer ,  Kelly Li ,  Andreas R. Tobler ,  Caifu Chen ,  David N. Keys, Jr.

发明人： Adam Broomer ,  Kelly Li ,  Andreas R. Tobler ,  Caifu Chen ,  David N. Keys, Jr.

IPC分类号： C12Q1/68

CPC分类号： C12Q1/6844 ,  C12Q2537/16

摘要： This disclosure relates to methods and kits for karyotyping in which chromosomes are interrogated by amplifying loci that are not within copy number variable regions thereof.

摘要翻译： 本公开涉及用于核型分析的方法和试剂盒，其中染色体通过扩增不在其拷贝数可变区内的位点进行询问。

公开(公告)号：US20130127989A1

公开(公告)日：2013-05-23

申请号：US13302445

申请日：2011-11-22

申请人： Caifu Chen ,  Junhua Zhou

发明人： Caifu Chen ,  Junhua Zhou

IPC分类号： H04N13/00 ,  G06T15/00

CPC分类号： G06T7/579 ,  G06T7/11 ,  H04N13/261

摘要： Two dimensional data is converted into three dimensional picture data in a method that can provide a real time high quality display during conversion. Pixels of a frame of picture data are segmented to create pixel segments by applying a k-means algorithm. The k-means algorithm groups pixels based on closeness of a combined value that includes luma, chroma, and motion information. By balancing this information the algorithm collects pixels into groups that are assigned relative depths to turn the two-dimensional information into three-dimensional information for display. Another method includes determining a depth map for the different pixel segments by determining an amount of motion of one of the pixel segments between two frames of a video and scaling the three-dimensional depth of one of the pixel segments based on the amount of motion between the two frames.

摘要翻译： 二维数据可以在转换期间提供实时高质量显示的方法中被转换为三维图像数据。 分割图像数据帧的像素以通过应用k均值算法来创建像素段。 k-means算法基于包含亮度，色度和运动信息的组合值的接近度对像素进行分组。 通过平衡该信息，算法将像素收集到被分配相对深度的组中，以将二维信息转换为三维信息以供显示。 另一种方法包括：通过确定视频的两个帧之间的像素段之一的运动量并且基于所述像素段之一之间的运动量来缩放像素段之一的三维深度来确定不同像素段的深度图 两帧。

公开(公告)号：US20130011840A1

公开(公告)日：2013-01-10

申请号：US13612485

申请日：2012-09-12

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

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：US20100112573A1

公开(公告)日：2010-05-06

申请号：US12543466

申请日：2009-08-18

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

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：US07176002B2

公开(公告)日：2007-02-13

申请号：US10151061

申请日：2002-05-16

申请人： Kai Qin Lao ,  Caifu Chen ,  Ryan T. Koehler ,  Charles Scafe ,  Gary Schroth

发明人： Kai Qin Lao ,  Caifu Chen ,  Ryan T. Koehler ,  Charles Scafe ,  Gary Schroth

IPC分类号： C12P19/34 ,  C07H21/04

CPC分类号： C07H21/00 ,  C12Q1/686 ,  C12Q2525/179 ,  C12Q2525/15

摘要： The present invention relates to universal-tagged oligonucleotide primers, and to methods of using the primers for amplifying the genome.

摘要翻译： 本发明涉及通用标记的寡核苷酸引物，以及使用引物扩增基因组的方法。

公开(公告)号：US06887664B2

公开(公告)日：2005-05-03

申请号：US09875211

申请日：2001-06-05

申请人： Caifu Chen ,  Michael Egholm ,  Lawrence A. Haff

发明人： Caifu Chen ,  Michael Egholm ,  Lawrence A. Haff

IPC分类号： G01N33/53 ,  C12N15/09 ,  C12Q1/68 ,  G01N33/566 ,  C07H21/00 ,  C07H21/02 ,  C12P19/34

CPC分类号： C12Q1/686 ,  C12Q2561/101 ,  C12Q2527/113 ,  C12Q2527/107

摘要： An asynchronous thermal cycling protocol for nucleic acid amplification uses two primers with thermal melting temperatures different by about 10 to 30° C. After the higher melting primer has annealed and polymerase mediated extension, the uncopied, single-stranded target sequence may be hybridized and detected by a probe. DNA probes may be cleaved by the exonuclease activity of a polymerase. The probe may be a non-cleaving analog such as PNA. When a probe is labelled with a reporter dye and a quencher selected to undergo energy transfer, e.g. FRET, fluorescence from the reporter dye may be effectively quenched when the probe is unbound. Upon hybridization of the probe to complementary target or upon cleavage while bound to target, the reporter dye is no longer quenched, resulting in a detectable amount of fluorescence. The second, lower-melting primer may be annealed and extended to generate a double-stranded nucleic acid. Amplification may be monitored in real time, including each cycle, or at the end point. The asynchronous PCR thermal cycling protocol can generate a preponderance of the PCR amplicon in single-stranded form by repetition at the end of the protocol of annealing and extension of the higher melting primer.

公开(公告)号：US20140024543A1

公开(公告)日：2014-01-23

申请号：US13555399

申请日：2012-07-23

申请人： Caifu CHEN

发明人： Caifu CHEN

IPC分类号： C40B30/04 ,  C07H21/04 ,  C40B40/06 ,  G01N21/64

CPC分类号： C12Q1/04 ,  C12Q1/26 ,  C12Q1/58 ,  C12Q1/66 ,  C12Q1/689

摘要： The invention provides nucleic acids, collections of nucleic acids, assay kits, and methods for the sensitive and specific detection of microorganisms in a foodstuff. The nucleic acid consists of a nucleotide sequence selected from the group consisting of SEQ ID NOs: 1-45.

摘要翻译： 本发明提供核酸，核酸的集合，测定试剂盒以及用于敏感和特异性检测食品中的微生物的方法。 核酸由选自SEQ ID NO：1-45的核苷酸序列组成。

公开(公告)号：US20090087858A1

公开(公告)日：2009-04-02

申请号：US12330460

申请日：2008-12-08

申请人： Andrew K. Finn ,  Caifu Chen

发明人： Andrew K. Finn ,  Caifu Chen

IPC分类号： C12Q1/68

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：US20070259356A1

公开(公告)日：2007-11-08

申请号：US11609767

申请日：2006-12-12

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

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

IPC分类号： C12Q1/68 ,  C12P19/34

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.