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1. 发明授权

US09309565B2 Karyotyping assay 有权
标题翻译：核型分析法
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。

2. 发明申请

US20110281755A1 Karyotyping Assay 有权
标题翻译：核型分析
公开(公告)号：US20110281755A1
公开(公告)日：2011-11-17
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： C40B30/04 , C40B40/06 , 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，其中染色体通过不在其拷贝数可变区内的扩增位点进行询问。

3. 发明授权

US07601821B2 Encoding and decoding reactions for determining target molecules 失效
标题翻译：用于确定靶分子的编码和解码反应
公开(公告)号：US07601821B2
公开(公告)日：2009-10-13
申请号：US11090830
申请日：2005-03-24
申请人： Mark R. Andersen , Kenneth J. Livak , Adam Broomer , Caifu Chen
发明人： Mark R. Andersen , Kenneth J. Livak , Adam Broomer , Caifu Chen
IPC分类号： C07H21/04 , C12Q1/68
CPC分类号： C12Q1/6869 , C12Q1/6851 , C12Q2525/191 , C12Q2525/185 , C12Q2521/501 , C12Q2525/155 , C12Q2521/313 , C12Q2537/143 , C12Q2525/161
摘要： The present invention is directed to methods, reagents, and kits for detecting the presence or absence of (or quantifying) target polynucleotide sequences and proteins in at least one sample using encoding and decoding reactions. When a particular target polynucleotide is present in a sample for example, a reaction product is formed in the encoding reaction that includes addressable primer portions. At least one labeling probe and at least one address primer can be employed in the decoding amplification reaction thereby providing a detectable signal value depending upon whether a sequence is present or absent. In some embodiments, the encoding comprises a ligation reaction with linker probes, and single nucleotide polymorphisms (SNPs) are analyzed.
摘要翻译：本发明涉及用于使用编码和解码反应检测至少一个样品中靶多核苷酸序列和蛋白质的存在或不存在（或定量）的方法，试剂和试剂盒。当特定靶多核苷酸例如存在于样品中时，在包含可寻址引物部分的编码反应中形成反应产物。可以在解码扩增反应中使用至少一个标记探针和至少一个地址引物，从而根据序列是否存在提供可检测的信号值。在一些实施方案中，编码包含与接头探针的连接反应，并分析单核苷酸多态性（SNP）。

4. 发明申请

US20050260640A1 Encoding and decoding reactions for determining target molecules 失效
标题翻译：用于确定靶分子的编码和解码反应
公开(公告)号：US20050260640A1
公开(公告)日：2005-11-24
申请号：US11090830
申请日：2005-03-24
申请人： Mark Andersen , Kenneth Livak , Adam Broomer , Caifu Chen
发明人： Mark Andersen , Kenneth Livak , Adam Broomer , Caifu Chen
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6869 , C12Q1/6851 , C12Q2525/191 , C12Q2525/185 , C12Q2521/501 , C12Q2525/155 , C12Q2521/313 , C12Q2537/143 , C12Q2525/161
摘要： The present invention is directed to methods, reagents, and kits for detecting the presence or absence of (or quantifying) target polynucleotide sequences and proteins in at least one sample using encoding and decoding reactions. When a particular target polynucleotide is present in a sample for example, a reaction product is formed in the encoding reaction that includes addressable primer portions. At least one labeling probe and at least one address primer can be employed in the decoding amplification reaction thereby providing a detectable signal value depending upon whether a sequence is present or absent. In some embodiments, the encoding comprises a ligation reaction with linker probes, and single nucleotide polymorphisms (SNPs) are analyzed.
摘要翻译：本发明涉及用于使用编码和解码反应检测至少一个样品中靶多核苷酸序列和蛋白质的存在或不存在（或定量）的方法，试剂和试剂盒。当特定靶多核苷酸例如存在于样品中时，在包含可寻址引物部分的编码反应中形成反应产物。可以在解码扩增反应中使用至少一个标记探针和至少一个地址引物，从而根据序列是否存在提供可检测的信号值。在一些实施方案中，编码包含与接头探针的连接反应，并分析单核苷酸多态性（SNP）。

5. 发明授权

US09534255B2 Methods, compositions, and kits for detecting allelic variants 有权
标题翻译：用于检测等位基因变体的方法，组合物和试剂盒
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”）。

6. 发明申请

US20130127989A1 Conversion of 2-Dimensional Image Data into 3-Dimensional Image Data 有权
标题翻译：将二维图像数据转换为三维图像数据
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。

7. 发明申请

US20130011840A1 Methods, Compositions, and Kits Comprising Linker Probes for Quantifying Polynucleotides 审中-公开
标题翻译：包含用于定量多核苷酸的接头探针的方法，组合物和试剂盒
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。

8. 发明申请

US20100112573A1 Methods, Compositions, and Kits Comprising Linker Probes for Quantifying Polynucleotides 有权
标题翻译：包含用于定量多核苷酸的接头探针的方法，组合物和试剂盒
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。

9. 发明授权

US07176002B2 Universal-tagged oligonucleotide primers and methods of use 有权
标题翻译：通用标记的寡核苷酸引物和使用方法
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。

10. 发明授权

US06887664B2 Asynchronous primed PCR 有权
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.

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