公开(公告)号：WO2012109279A3

公开(公告)日：2012-10-04

申请号：PCT/US2012024194

申请日：2012-02-07

Applicant: LIFE TECHNOLOGIES CORP ,  FIKE RICHARD ,  BRANCHAUD BRUCE ,  BARRETT SHAWN

Inventor： FIKE RICHARD ,  BRANCHAUD BRUCE ,  BARRETT SHAWN

IPC: C12N5/00

CPC classification number: C12N5/0018 ,  C12N2500/34 ,  C12N2500/46

Abstract: Methods for increasing the stability of, or protecting, labile components such as ethanolamine, growth factors, vitamins, etc., in compositions such as a cell culture medium. Stability of the labile compound is increased either, by derivatization of the labile compound with chemicals, or by sequestering the labile compound. Sequestering can be done either by encapsulation within a microcapsule, or by the use of sequestering agents. Encapsulation includes the encapsulation of dendrimers complexes of susceptible compounds within the microcapsule, thereby providing the controlled release of the susceptible compound that was protected.These methods may improve and extend storage conditions of compositions comprising the labile compounds, improve shipping and handling of compositions comprising the labile compounds, such as dry media formulations, at room temperature rather than at lower temperatures thereby decreasing shipping costs. Stabilization of labile compounds in compositions such as dry format media can be viewed as a contribution to green technology.

Abstract translation: 提高组合物如细胞培养基中稳定性或保护不稳定组分如乙醇胺，生长因子，维生素等的方法。 不稳定化合物的稳定性增加，或者通过用化学物质衍生不稳定化合物，或者通过隔离不稳定化合物。 螯合可以通过封装在微胶囊内或通过使用螯合剂来完成。 封装包括将敏感化合物的树枝状聚合物复合物包封在微胶囊内，从而提供受保护的敏感化合物的受控释放。这些方法可以改善和延长包含不稳定化合物的组合物的储存条件，改善运输和处理包含 不稳定的化合物，例如干燥介质配方，在室温下而不是在较低的温度下，从而降低运输成本。 稳定化合物中的不稳定化合物如干式介质可以被看作是对绿色技术的贡献。

公开(公告)号：WO2011106634A3

公开(公告)日：2012-05-03

申请号：PCT/US2011026228

申请日：2011-02-25

Applicant: LIFE TECHNOLOGIES CORP ,  DAVIDSON JOHN F ,  HINZ WOLFGANG ,  ROTHBERG JONATHAN ,  WHITAKER RICHARD

Inventor： DAVIDSON JOHN F ,  HINZ WOLFGANG ,  ROTHBERG JONATHAN ,  WHITAKER RICHARD

IPC: C12Q1/68 ,  C12N9/12 ,  C12Q1/48

CPC classification number: C12N9/1252

Abstract: Methods, compositions, systems, apparatuses and kits comprising modified proteins, particularly modified nucleic acid-binding proteins with altered buffering properties are provided. For example, in some embodiments, methods of forming modified proteins including one or more amino acid modifications to achieve desired pKa values are described. Furthermore, the invention provides methods for using such modified proteins in ion-producing reactions, such as ion-based nucleic acid sequencing reactions.

Abstract translation: 提供了包含修饰的蛋白质，特别是具有改变的缓冲性质的修饰的核酸结合蛋白的方法，组合物，系统，装置和试剂盒。 例如，在一些实施方案中，描述了形成包含一个或多个氨基酸修饰的修饰蛋白以实现期望的pKa值的方法。 此外，本发明提供了在离子生成反应中使用这些修饰蛋白的方法，如基于离子的核酸测序反应。

公开(公告)号：WO2011163249A3

公开(公告)日：2012-04-19

申请号：PCT/US2011041275

申请日：2011-06-21

Applicant: LIFE TECHNOLOGIES CORP ,  TRINH CHRISTOPHER ,  XU TOM ,  SHI YATING ,  LE FERRIER NHAT ,  MARJORIBANKS CLAIRE

Inventor： TRINH CHRISTOPHER ,  XU TOM ,  SHI YATING ,  LE FERRIER NHAT ,  MARJORIBANKS CLAIRE

IPC: C12Q1/68 ,  C12N15/10

CPC classification number: C12Q1/686 ,  C12Q1/6848 ,  C12Y207/07007 ,  C12Q2527/125

Abstract: A composition comprising a thermostable DNA polymerase; and a PCR inhibitor blocking agent, wherein the PCR inhibitor blocking agent is present in an amount effective to enhance tolerance of an assembled PCR to a PCR inhibitor.

Abstract translation: 包含热稳定DNA聚合酶的组合物; 和PCR抑制剂封闭剂，其中所述PCR抑制剂封闭剂以有效增加组装的PCR对PCR抑制剂的耐受性的量存在。

公开(公告)号：WO2011143194A3

公开(公告)日：2012-04-19

申请号：PCT/US2011035894

申请日：2011-05-10

Applicant: LIFE TECHNOLOGIES CORP ,  SONG MAENGSEOK ,  KARGER ACHIM ,  KINNEY PATRICK

Inventor： SONG MAENGSEOK ,  KARGER ACHIM ,  KINNEY PATRICK

IPC: C12Q1/68 ,  C12M1/00 ,  C12N15/10 ,  G01N33/48

CPC classification number: B01L3/502761 ,  B01F5/0652 ,  B01F2003/0823 ,  B01L7/52 ,  B01L2200/0673 ,  B01L2400/0439 ,  C12Q1/6806

Abstract: Systems and methods for processing a biological sample are provided herein. For example, the system can be configured to deaggregate/declump a sample before, during, and/or after sample preparation and/or sample analysis. For example, the system can include a deaggregation device/system in communication with, for example, a nucleic acid amplification process (e.g., an ePCR system). Various embodiments of the deaggregation device are provided herein. For example, in some embodiments, the deaggregation device can include a valve, a valve manifold, a conduit, a channel, or some combinations thereof.

Abstract translation: 本文提供了用于处理生物样品的系统和方法。 例如，可以将系统配置为在样品制备和/或样品分析之前，期间和/或之后对样品进行解聚/递归。 例如，该系统可以包括与例如核酸扩增过程（例如，ePCR系统）通信的解聚集装置/系统。 本文提供了解聚集装置的各种实施例。 例如，在一些实施例中，解聚装置可以包括阀，阀歧管，导管，通道或其一些组合。

公开(公告)号：WO2011143611A3

公开(公告)日：2012-04-05

申请号：PCT/US2011036516

申请日：2011-05-13

Applicant: LIFE TECHNOLOGIES CORP ,  BROOMER ADAM ,  LI KELLY ,  TOBLER ANDREAS ,  CHEN CAIFU ,  KEYS JR DAVID

Inventor： BROOMER ADAM ,  LI KELLY ,  TOBLER ANDREAS ,  CHEN CAIFU ,  KEYS JR DAVID

IPC: C12Q1/68 ,  C12N15/11

CPC classification number: C12Q1/6844 ,  C12Q2537/16

Abstract: 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.

Abstract translation: 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：WO2011137356A3

公开(公告)日：2012-03-01

申请号：PCT/US2011034592

申请日：2011-04-29

Applicant: LIFE TECHNOLOGIES CORP ,  VATTA PAOLO ,  SAKARYA ONUR ,  BREU HEINZ ,  POPESCU LIVIU ,  SIDDIQUI ASIM ,  HYLAND FIONA

Inventor： VATTA PAOLO ,  SAKARYA ONUR ,  BREU HEINZ ,  POPESCU LIVIU ,  SIDDIQUI ASIM ,  HYLAND FIONA

IPC: G06F19/22 ,  C12Q1/68 ,  G06F19/28

CPC classification number: G06F19/22

Abstract: Systems and methods are used to identify an exon junction from a single read of a transcript. A transcript sample is interrogated and a read sequence is produced using a nucleic acid sequencer. A first exon sequence and a second exon sequence are obtained using the processor. The first exon sequence is mapped to a prefix of the read sequence using the processor. The second exon sequence is mapped to a suffix of the read sequence using the processor. A sum of a number of sequence elements of the first exon sequence that overlap the prefix of the read sequence, of a number of sequence elements of the second exon sequence that overlap the suffix of the read sequence, and of a constant is calculated using the processor. If the sum equals a length of the read sequence, a junction is identified in the read using the processor.

Abstract translation: 系统和方法用于从单次阅读誊本中鉴定外显子结。 询问转录物样品，并使用核酸测序仪产生读序列。 使用处理器获得第一外显子序列和第二外显子序列。 使用处理器将第一个外显子序列映射到读取序列的前缀。 第二个外显子序列使用处理器映射到读序列的后缀。 与第一外显子序列的重叠序列的序列的多个序列元素的总和，与读取序列的后缀重叠的第二外显子序列的多个序列元件的数量以及常数的序列元素的总和，使用 处理器。 如果总和等于读取序列的长度，则使用处理器在读取中识别结。

公开(公告)号：WO2011082419A3

公开(公告)日：2012-02-09

申请号：PCT/US2011020117

申请日：2011-01-04

Applicant: LIFE TECHNOLOGIES CORP ,  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 ,  G01N27/414 ,  G01N33/50

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，电极装置和设置在纳米通道中的多个纳米器件。 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也是制备它们的方法。 在一些实施方案中，提供用于减缓单链DNA（ssDNA）穿过纳米孔的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：WO2011137368A2

公开(公告)日：2011-11-03

申请号：PCT/US2011034611

申请日：2011-04-29

Applicant: LIFE TECHNOLOGIES CORP ,  ZHANG ZHENG ,  GUO DANWEI ,  LOU YUANDAN ,  BRINZA DUMITRU

Inventor： ZHANG ZHENG ,  GUO DANWEI ,  LOU YUANDAN ,  BRINZA DUMITRU

IPC: G06F19/22 ,  C12Q1/68 ,  G06F19/28

CPC classification number: G06F19/22

Abstract: Nucleic acid sequence mapping/assembly methods are disclosed. The methods initially map only a contiguous portion of each read to a reference sequence and then extends the mapping of the read at both ends of the mapped contiguous portion until the entire read is mapped (aligned). In various embodiments, a mapping score can be calculated for the read alignment using a scoring function, score (i, j) = M+mx, where M can be the number of matches in the extended alignment, x can be the number of mismatches in the alignment, and m can be a negative penalty for each mismatch. The mapping score can be utilized to rank or choose the best alignment for each read.

Abstract translation: 公开了核酸序列作图/装配方法。 这些方法首先将每个读取的连续部分映射到参考序列，然后扩展映射的连续部分的两端的读取映射，直到整个读取被映射（对齐）。 在各种实施例中，可以使用评分函数score（i，j）= M + mx来计算读取对齐的映射分数，其中M可以是扩展对齐中的匹配数，x可以是不匹配的数量 在对齐中，m可以是每个不匹配的负面惩罚。 映射分数可用于对每次读取进行排序或选择最佳对齐。

公开(公告)号：WO2011130184A2

公开(公告)日：2011-10-20

申请号：PCT/US2011031988

申请日：2011-04-11

Applicant: LIFE TECHNOLOGIES CORP ,  GEORGE WALLACE R

Inventor： GEORGE WALLACE R

IPC: G06F19/12 ,  C12Q1/68 ,  G01N33/50 ,  G06F17/50 ,  G06F19/28

CPC classification number: G06F19/12 ,  C12Q1/6851 ,  G06F19/24 ,  C12Q2537/165

Abstract: A method for determining a cycle threshold for a PCR amplification curve is provided. The method includes receiving a data set for a plurality of biological samples for a PCR amplification reaction. The data set includes a plurality of amplification curves, each amplification curve associated with a biological sample of the plurality of biological samples. The method further includes performing a nonlinear optimization comprising a fit of each amplification curve to a complementary modeled amplification curve to determine a best-fit set of parameters for a modeled efficiency curve and associated amplification curve. The modeled amplification curve is based on a modeled efficiency curve. The method includes determining a cycle threshold value for each biological sample based on a complementary relationship of the modeled efficiency curve to the modeled amplification curve. In an embodiment, the nonlinear optimization is a constrained nonlinear optimization.

Abstract translation: 提供了用于确定PCR扩增曲线的循环阈值的方法。 该方法包括接收多个用于PCR扩增反应的生物样品的数据集。 数据集包括多个扩增曲线，每个扩增曲线与多个生物样品的生物样品相关联。 该方法还包括执行非线性优化，其包括将每个扩增曲线拟合到互补建模的扩增曲线，以确定用于建模效率曲线和相关联的扩增曲线的最佳拟合参数集合。 模拟的扩增曲线基于模型效率曲线。 该方法包括基于模拟效率曲线与建模的扩增曲线的互补关系来确定每个生物样品的周期阈值。 在一个实施例中，非线性优化是受限非线性优化。

公开(公告)号：WO2011046972A3

公开(公告)日：2011-09-22

申请号：PCT/US2010052387

申请日：2010-10-12

Applicant: LIFE TECHNOLOGIES CORP ,  SCHROEDER BENJAMIN ,  WENZ MICHAEL

Inventor： SCHROEDER BENJAMIN ,  WENZ MICHAEL

IPC: C12Q1/68 ,  C12N15/10

CPC classification number: C12Q1/6848 ,  C12Q2527/127

Abstract: The present disclosure generally provides compositions, methods and kits for reducing unwanted primer interactions (e.g., primer dimer structure formation). More specifically, the disclosure provides for compositions, methods and kits for reducing non-specific side products and/or interactions resulting from primer dimer formation prior to or during amplification of target nucleic acids.

Abstract translation: 本公开一般提供用于减少不需要的引物相互作用（例如，引物二聚体结构形成）的组合物，方法和试剂盒。 更具体地说，本公开内容提供了用于在扩增靶核酸之前或期间减少由引物二聚体形成导致的非特异性副产物和/或相互作用的组合物，方法和试剂盒。