公开(公告)号：WO2012106668A3

公开(公告)日：2013-01-10

申请号：PCT/US2012023870

申请日：2012-02-03

Applicant: FLUIDIGM CORP ,  LIVAK KENNETH J

Inventor： LIVAK KENNETH J

IPC: C12Q1/68 ,  C07H21/00

CPC classification number: C12Q1/6876 ,  C12Q1/6818 ,  C12Q1/6823 ,  C12Q2525/161 ,  C12Q2525/197 ,  C12Q2565/1015

Abstract: Methods and reagents for detection and analysis of nucleic acids are provided. Certain methods involves an encoding amplification in which a target sequence is associated with probe-binding sequences and optionally with indexing sequences, (2) an optional distribution step in which the product of the encoding amplification is split into multiple aliquots, and (3) a decoding and detection step in which the presence, absence, quantity, or relative amount of the target sequence in the aliquots is determined. The detection step makes use of a multifunctional "self-digesting" molecular probe comprising a primer polynucleotide and a probe oligonucleotide, linked in a 5'-5' orientation.

Abstract translation: 提供了用于检测和分析核酸的方法和试剂。 某些方法涉及编码扩增，其中靶序列与探针结合序列和任选的索引序列相关，（2）任选的分布步骤，其中编码扩增的产物被分成多个等分试样，和（3）a 解码和检测步骤，其中确定等分试样中靶序列的存在，不存在，数量或相对量。 检测步骤使用包含以5'-5'取向连接的引物多核苷酸和探针寡核苷酸的多功能“自消化”分子探针。

公开(公告)号：WO2011082419A2

公开(公告)日：2011-07-07

申请号：PCT/US2011/020117

申请日：2011-01-04

Applicant: LIFE TECHNOLOGIES CORPORATION ,  SUN, Hongye ,  NORDMAN, Eric, S. ,  OLDHAM, Mark, F. ,  O'NEILL, John, R. ,  CONNELL, Charles ,  ULMANELLA, Umberto ,  LAU, Aldrich, N.K. ,  KOTSEROGLOU, Theofilos ,  LIVAK, Kenneth, J.

Inventor： SUN, Hongye ,  NORDMAN, Eric, S. ,  OLDHAM, Mark, F. ,  O'NEILL, John, R. ,  CONNELL, Charles ,  ULMANELLA, Umberto ,  LAU, Aldrich, N.K. ,  KOTSEROGLOU, Theofilos ,  LIVAK, Kenneth, J.

IPC: C12Q1/68 ,  G01N33/50 ,  G01N27/414

CPC classification number: C12Q1/6869 ,  B01L3/502761 ,  G01N27/3278 ,  G01N27/414 ,  G01N27/4145 ,  G01N27/4146 ,  G01N33/5438 ,  Y10S977/924 ,  Y10T436/143333 ,  C12Q2565/631

Abstract: In some embodiments, an analyte detection system is provided that includes a nanochannel, an electrode arrangement, and a plurality of nanoFET devices disposed in the nanochannel. A plurality of nucleic acid base detection components can be used that include a plurality of nanopores, a plurality of nanochannels, a plurality of hybridization probes, combinations thereof, and the like. According to other embodiments of the present teachings, different coded molecules are hybridized to a target DNA molecule and used to detect the presence of various sequences along the target molecule. A kit including mixtures of coded molecules is also provided. In some embodiments, devices including nanochannels, nanopores, and the like, are used for manipulating movement of DNA molecules, for example, in preparation for a DNA sequencing detection. Nanopore structures and methods of making the same are also provided as are methods of nucleic acid sequencing using the nanopore structures. Surface-modified nanopores are provided as are methods of making them. In some embodiments, surfaced-modified nanopores for slowing the translocation of single stranded DNA (ssDNA) through the nanopore are provided, as are nanopores configured to detect each of a plurality of different bases on an ssDNA strand.

Abstract translation: 在一些实施例中，提供了分析物检测系统，其包括纳米通道，电极布置以及设置在纳米通道中的多个纳米器件器件。 可以使用多个核酸碱基检测组分，其包括多个纳米孔，多个纳米通道，多个杂交探针及其组合等。 根据本教导的其他实施方案，将不同的编码分子与靶DNA分子杂交并用于检测沿着靶分子的各种序列的存在。 还提供了包含编码分子混合物的试剂盒。 在一些实施方案中，包括纳米通道，纳米孔等的装置用于操纵DNA分子的移动，例如用于DNA测序检测的准备。 还提供了制备其的纳米孔结构及其制备方法，使用纳米孔结构的核酸测序方法也是如此。 提供表面改性的纳米孔是制备它们的方法。 在一些实施方案中，提供了用于减缓通过纳米孔的单链DNA（ssDNA）易位的表面改性的纳米孔，以及配置成检测ssDNA链上的多个不同碱基中的每一个的纳米孔。

公开(公告)号：WO2009100449A1

公开(公告)日：2009-08-13

申请号：PCT/US2009/033586

申请日：2009-02-09

Applicant: FLUIDIGM CORPORATION ,  LIVAK, Kenneth J. ,  UNGER, Marc

Inventor： LIVAK, Kenneth J. ,  UNGER, Marc

IPC: C12M1/34

CPC classification number: C12Q1/686 ,  C12Q1/6834 ,  C12Q2565/629

Abstract: High throughput methods are used that combine the features of using a matrix-type microfluidic device, labeled nucleic acid probes, and homogenous assays to detect and/or quantify nucleic acid analytes. The high throughput methods are capable of detecting nucleic acid analyes with high PCR and probe specificity, producing a low fluorescence background and therefore, a high signal to noise ratio. Additionally, the high throughput methods are capable of detecting low copy number nucleic acid analyte per cell.

Abstract translation: 使用高通量方法，其结合使用基质型微流体装置，标记的核酸探针和均质测定的特征来检测和/或定量核酸分析物。 高通量方法能够以高PCR和探针特异性检测核酸分析，产生低荧光背景，因此具有高的信噪比。 此外，高通量方法能够检测每个细胞的低拷贝数核酸分析物。

公开(公告)号：WO2005113818A2

公开(公告)日：2005-12-01

申请号：PCT/US2005016395

申请日：2005-05-11

Applicant: APPLERA CORP ,  LIVAK KENNETH J ,  STEVENS JUNKO ,  LAZARUK KATHERINE D ,  ZIEGLE JANET S ,  WONG LILY Y

Inventor： LIVAK KENNETH J ,  STEVENS JUNKO ,  LAZARUK KATHERINE D ,  ZIEGLE JANET S ,  WONG LILY Y

IPC: C12Q1/68

CPC classification number: G06F19/18 ,  C12Q1/6827 ,  C12Q1/6851 ,  C12Q2600/156 ,  C12Q2563/107 ,  C12Q2545/101 ,  C12Q2565/101 ,  C12Q2563/173 ,  C12Q2565/1015

Abstract: Methods of detecting a candidate genetic anomaly such as a candidate duplication in a genome are disclosed. The methods comprise quantifying fluorogenic assays for alleles of a genetic locus from a plurality of individual genomes, identifying ranges of fluorescent intensities indicative of individual genomes homozygous for a first allele, homozygous for a second allele, or heterozygous for both alleles, and identifying individual genomes in which the fluorescence intensities are outside the range of intensities indicative of homozygosity or heterozygosity for the genetic locus.

Abstract translation: 公开了检测候选遗传异常（例如基因组中候选重复）的方法。 所述方法包括定量来自多个单个基因组的遗传基因座的等位基因的荧光测定，鉴定指示第一等位基因纯合的单个基因组的荧光强度的范围，对于第二等位基因纯合，或对于两个等位基因是杂合的，以及鉴定个体基因组 其中荧光强度在表示遗传基因座的纯合性或杂合性的强度范围之外。

公开(公告)号：WO2004111072A2

公开(公告)日：2004-12-23

申请号：PCT/US2004/018800

申请日：2004-06-10

Applicant: APPLERA CORPORATION ,  LIVAK, Kenneth, J. ,  MULLAH, K., Bashar

Inventor： LIVAK, Kenneth, J. ,  MULLAH, K., Bashar

IPC: C07H21/00

CPC classification number: C12Q1/6811 ,  C07H21/00 ,  C07H21/04 ,  C12Q2525/197 ,  C12Q2525/117

Abstract: The invention relates to insulating combinatorial nucleobase oligomers that comprise universal base analogs, where the oligomers are formed by the ligation of two or more oligomer "blocks" via a covalent linkage. Universal bases may serve to insulate specifically binding nucleobases from the effects of the covalent linker region joining two oligomer blocks together, so that the universal bases at least partially negate the T m penalty caused by the covalent linkage, effective to reduce the required minimal length of the oligomer blocks and the combinatorial oligomer. The resulting insulating nucleobase combinatorial oligomers find use in any hybridization-based application, including use as probes and primers. The combinatorial oligomers of the present invention provide advantages over existing combinatorial oligomer systems currently known in the art.

Abstract translation: 本发明涉及包含通用碱基类似物的绝缘组合核碱基寡聚体，其中通过共价键连接两个或多个低聚物“嵌段”形成低聚物。 通用碱基可以用于将特异性结合的核碱基与连接两个低聚物嵌段的共价连接体区域的作用绝缘，使得通用碱基至少部分地消除由共价键引起的Tm损失，有效地减少所需的最小长度 低聚物嵌段和组合低聚物。 所得到的绝缘核碱基组合寡聚体可用于任何基于杂交的应用，包括用作探针和引物。 本发明的组合寡聚体提供优于现有技术中已知的组合式低聚物体系的优点。

公开(公告)号：WO2012154876A1

公开(公告)日：2012-11-15

申请号：PCT/US2012/037155

申请日：2012-05-09

Applicant: FLUIDIGM CORPORATION ,  LIVAK, Kenneth J. ,  MYERS, Stacey ,  WANG, Xiaohui ,  WANG, Jun

Inventor： LIVAK, Kenneth J. ,  MYERS, Stacey ,  WANG, Xiaohui ,  WANG, Jun

IPC: C12Q1/68

CPC classification number: C12Q1/6818 ,  C12Q2525/151

Abstract: The invention provides a method for detecting a target nucleotide sequence by tagging the nucleotide sequence with a nucleotide tag, providing a probe oligonucleotide with a melting temperature Tm1, comprising a regulatory sequence and a nucleotide tag recognition sequence; incorporating the probe oligonucleotide into the tagged polynucleotide in a polynucleotide amplification reaction, providing a regulatory oligonucleotide with a melting temperature Tm2, comprising a sequence segment that is at least partially complementary to the regulatory sequence, amplifying the tagged target nucleic acid sequence in a PCR amplification reaction using the probe oligonucleotide as a primer, and detecting the amplification product; wherein Tm1 and Tm2 are higher than the annealing temperature associated with the polynucleotide amplification reaction.

Abstract translation: 本发明提供了通过用核苷酸标签标记核苷酸序列来检测靶核苷酸序列的方法，提供了具有调节序列和核苷酸标签识别序列的融解温度Tm1的探针寡核苷酸; 在多核苷酸扩增反应中将探针寡核苷酸掺入标记的多核苷酸中，提供具有解链温度Tm2的调节性寡核苷酸，其包含与调节序列至少部分互补的序列片段，在PCR扩增中扩增标记的靶核酸序列 使用探针寡核苷酸作为引物的反应，检测扩增产物; 其中Tm1和Tm2高于与多核苷酸扩增反应相关的退火温度。

公开(公告)号：WO2011142836A9

公开(公告)日：2012-01-05

申请号：PCT/US2011000887

申请日：2011-05-16

Applicant: FLUIDIGM CORP ,  JONES ROBERT C ,  LIVAK KENNETH J ,  MAY ANDREW ,  MIR ALAIN ,  PIEPRZYK MARTIN ,  QIN JIAN ,  RAMAKRISHNAN RAMESH ,  SPURGEON SANDRA ,  WANG JUN ,  ZIMMERMANN BERNHARD G

Inventor： JONES ROBERT C ,  LIVAK KENNETH J ,  MAY ANDREW ,  MIR ALAIN ,  PIEPRZYK MARTIN ,  QIN JIAN ,  RAMAKRISHNAN RAMESH ,  SPURGEON SANDRA ,  WANG JUN ,  ZIMMERMANN BERNHARD G

IPC: C12Q1/68 ,  G01N33/52 ,  G06F19/18

CPC classification number: C12Q1/6851 ,  C12Q1/6855 ,  C12Q1/6858 ,  G01N33/542 ,  G01N33/582 ,  G01N33/6893 ,  G01N2800/368 ,  C12Q2521/301 ,  C12Q2521/501 ,  C12Q2525/155 ,  C12Q2535/131 ,  C12Q2537/143 ,  C12Q2537/16 ,  C12Q2563/173

Abstract: The present invention provides amplification-based methods for detection of genotype, mutations, and/or aneuploidy. These methods have broad applicability, but are particularly well-suited to detecting and quantifying target nucleic acids in free fetal DNA present in a maternal bodily fluid sample.

Abstract translation: 本发明提供了用于检测基因型，突变和/或非整倍性的基于扩增的方法。 这些方法具有广泛的适用性，但特别适合于检测和定量存在于母体液样品中的游离胎儿DNA中的靶核酸。

公开(公告)号：WO2007128004A3

公开(公告)日：2007-11-08

申请号：PCT/US2007/068046

申请日：2007-05-02

Applicant: APPLERA CORPORATION ,  RUFF, David W. ,  SHANNON, Mark E. ,  LIVAK, Kenneth, J. ,  GUEGLER, Karl J. ,  HENNESSY, Kevin M.

Inventor： RUFF, David W. ,  SHANNON, Mark E. ,  LIVAK, Kenneth, J. ,  GUEGLER, Karl J. ,  HENNESSY, Kevin M.

IPC: C12P19/00 ,  C12P19/34 ,  C12Q1/68 ,  C12Q1/70 ,  G01N33/53 ,  G01N33/543

Abstract: The present teachings provide methods, compositions, and kits for detecting the presence of protein aggregates. In some embodiments, the protein aggregate is treated with a labeled precursor, and the labeled precursor is incorporated into the protein aggregate to form a labeled protein aggregate. The labeled protein aggregate is then measured, thus detecting the presence of the protein aggregate. In some embodiments, the labeled protein aggregate is detected by interaction of labeled precursors, for example by a proximity ligation assay.

公开(公告)号：WO2005098040A8

公开(公告)日：2005-12-01

申请号：PCT/US2005010184

申请日：2005-03-24

Applicant: APPLERA CORP ,  ANDERSEN MARK R ,  LIVAK KENNETH J ,  BROOMER ADAM ,  CHEN CAIFU

Inventor： ANDERSEN MARK R ,  LIVAK KENNETH J ,  BROOMER ADAM ,  CHEN CAIFU

IPC: C12Q1/68

CPC classification number: C12Q1/6869 ,  C12Q1/6851 ,  C12Q2525/191 ,  C12Q2525/185 ,  C12Q2521/501 ,  C12Q2525/155 ,  C12Q2521/313 ,  C12Q2537/143 ,  C12Q2525/161

Abstract: 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.

Abstract translation: 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）。

公开(公告)号：WO2003064694A1

公开(公告)日：2003-08-07

申请号：PCT/US2002/034599

申请日：2002-10-30

Applicant: APPLERA CORPORATION ,  KOEHLER, Ryan, T. ,  LIVAK, Kenneth, J. ,  STEVENS, Junko ,  DE LA VEGA, Francisco, M. ,  RHODES, Michael ,  BELLON, Laurent, R.

Inventor： KOEHLER, Ryan, T. ,  LIVAK, Kenneth, J. ,  STEVENS, Junko ,  DE LA VEGA, Francisco, M. ,  RHODES, Michael ,  BELLON, Laurent, R.

IPC: C12Q1/68

CPC classification number: C12Q1/686

Abstract: A method for distributing a product to a consumer includes utilizing a computer network to interact with the consumer to obtain information that includes at least one target nucleic acid sequence; providing a forward primer sequence, a reverse primer sequence and a probe sequence having specified characteristics, wherein the forward primer sequence and the reverse primer sequence together define an amplicon sequence, the amplicon lies within the target nucleic acid sequence, and the probe sequence is complementary to a portion of the amplicon sequence; manufacturing at least one assay that includes a forward primer in accordance with the forward primer sequence, a reverse primer in accordance with the reverse primer sequence, and a probe in accordance with the probe sequence; validating one or more of the forward primer, the reverse primer, and the probe; and delivering the manufactured assay to the consumer.

Abstract translation: 将产品分发给消费者的方法包括利用计算机网络与消费者进行交互以获得包括至少一个靶核酸序列的信息; 提供具有特定特征的正向引物序列，反向引物序列和探针序列，其中正向引物序列和反向引物序列共同限定扩增子序列，扩增子位于靶核酸序列内，探针序列互补 到扩增子序列的一部分; 制备至少一种包括根据正向引物序列的正向引物，根据反向引物序列的反向引物和根据探针序列的探针的测定法; 验证一个或多个正向引物，反向引物和探针; 并将所制造的测定物递送给消费者。