公开(公告)号：WO2012106481A1

公开(公告)日：2012-08-09

申请号：PCT/US2012/023556

申请日：2012-02-01

Applicant: LIFE TECHNOLOGIES COPORATION ,  MAJUMDAR, Nivedita ,  LEONG, Harrison ,  WU, Ruoyun

Inventor： MAJUMDAR, Nivedita ,  LEONG, Harrison ,  WU, Ruoyun

IPC: G06F19/26

CPC classification number: G06F19/26 ,  G06F3/0482 ,  G06F3/04847 ,  G06F19/24 ,  G06T11/206 ,  G06T2200/24

Abstract: The present teachings relate to embodiments of systems and methods for the analysis of melt curve data for a plurality of samples. According to various embodiments, a melting temperature (Tm) may be determined across a range of different types of protein melt curve data, having variability over a plurality of analytical attributes in order to accommodate the complexity of protein melt curve data. The combination of a plurality of samples, coupled with the complexity of the data gives rise for a need to process the data in a manner that readily facilitates end-user to analysis of the data. Various embodiments of an interactive graphical user interface (GUI) according to the present teachings provide for rapid and sequential changes that may be made by an end user to displayed protein melt curve data to allow such analysis.

Abstract translation: 本教导涉及用于分析多个样品的熔体曲线数据的系统和方法的实施例。 根据各种实施方案，可以在不同类型的蛋白质熔融曲线数据的范围内确定熔解温度（Tm），其具有多个分析属性的变异性，以适应蛋白质熔融曲线数据的复杂性。 多个样本的组合以及数据的复杂性导致需要以容易促进最终用户分析数据的方式处理数据。 根据本发明的交互式图形用户界面（GUI）的各种实施例提供了可以由终端用户进行快速和顺序改变以显示蛋白质熔解曲线数据以允许这种分析。

公开(公告)号：WO2012006565A3

公开(公告)日：2012-04-19

申请号：PCT/US2011043419

申请日：2011-07-08

Applicant: LIFE TECHNOLOGIES CORP ,  LEONG HARRISON ,  WU RUOYUN ,  LEE THIAM CHYE

Inventor： LEONG HARRISON ,  WU RUOYUN ,  LEE THIAM CHYE

IPC: G06F19/10 ,  G06F3/048 ,  G06F3/14

CPC classification number: B01L7/52 ,  B01L3/5085 ,  B01L3/50851 ,  B01L99/00 ,  B01L2300/023 ,  B01L2300/024 ,  B01L2300/025 ,  B01L2300/027 ,  B01L2300/046 ,  B01L2300/0654 ,  B01L2300/0822 ,  B01L2300/0829 ,  G01N2035/00891

Abstract: Systems and methods for assigning attributes to a plurality of samples are provided. An exemplary system includes an instrument configured to perform an experiment on a plurality of samples in a multi- sample support device and to produce a plurality of measured values. The system further includes a computer system in communication with the instrument. The computer system is configured to receive the plurality of measured values from the instrument, store the plurality of measured values in a memory configured as a grid of cells representing the grid of the multi- sample support device, display the grid of cells in a graphical user interface, receive a selected cell from the graphical user interface, receive two or more attribute values for the selected cell from the graphical user interface, and store the two or more assigned attribute values along with a measured value of the selected cell in the memory configured as a grid of cells.

Abstract translation: 提供了将属性分配给多个样本的系统和方法。 示例性系统包括被配置为对多样本支持装置中的多个样本执行实验并产生多个测量值的仪器。 该系统还包括与仪器通信的计算机系统。 计算机系统被配置为从仪器接收多个测量值，将多个测量值存储在被配置为表示多样本支持设备的网格的单元格网格的存储器中，将单元格网格显示在图形中 用户界面，从图形用户界面接收所选择的单元，从图形用户界面接收所选单元格的两个或多个属性值，并将所分配的两个或更多个属性值连同选定单元格的测量值一起存储在存储器中 配置为单元格网格。

公开(公告)号：WO2010104893A2

公开(公告)日：2010-09-16

申请号：PCT/US2010/026726

申请日：2010-03-09

Applicant: LIFE TECHNOLOGIES CORPORATION ,  LEONG, Harrison M. ,  BARBACIORU, Catalin ,  JANAWAY, Gordon A.

Inventor： LEONG, Harrison M. ,  BARBACIORU, Catalin ,  JANAWAY, Gordon A.

IPC: C12Q1/68 ,  G06F19/00

CPC classification number: G06F19/22 ,  C12Q1/6827 ,  G06F19/18 ,  G06F19/24 ,  G06N7/005

Abstract: Methods for the determination of a copy number of a target genomic sequence; either a target gene or genomic sequence of interest, in a biological sample are described. Various methods utilize a model drawn from a probability density function (PDF) for the assignment of a copy number of a target genomic sequence in a biological sample. Additionally, the methods provide for the determination of a confidence value for a copy number assigned to a sample based on attributes of the sample data. Accordingly, the various methods for the determination of a copy number provide the end user with significant information for the evaluation of a copy number of a target genomic sequence; either a gene or genomic sequence of interest.

Abstract translation: 用于确定靶基因组序列拷贝数的方法; 描述了生物样品中的靶基因或目的基因组序列。 各种方法利用从概率密度函数（PDF）中提取的模型来分配生物样品中靶基因组序列的拷贝数。 另外，这些方法提供了基于样本数据的属性确定分配给样本的副本编号的置信度值。 因此，用于确定拷贝数的各种方法为终端用户提供了用于评价目标基因组序列拷贝数的重要信息; 是感兴趣的基因或基因组序列。

公开(公告)号：WO2008070328A2

公开(公告)日：2008-06-12

申请号：PCT/US2007/082458

申请日：2007-10-24

Applicant: Applera Corporation ,  LEONG, Harrison

Inventor： LEONG, Harrison

IPC: C12Q1/68 ,  G01N33/48 ,  G06F19/00

CPC classification number: G06K9/00523

Abstract: Systems and methods according to embodiments of the present teachings incorporate a set of possible signal transforms that can be used to examine the baseline region of an amplification profile for noise. In embodiments, a difference time series analysis can be performed to determine deviations of detected fluorescent or other signal intensity in the early cycles of a PCR or other reaction over a median difference time series magnitude. In embodiments, difference time series analysis or other detection techniques can be performed over different hop sizes producing a multi-resolution analysis. In embodiments, the amplification profile can be transmitted to a set of noise detectors whose individual results or decisions are polled or weighted to determine the presence of noise in the baseline or other region. In embodiments, a second derivative analysis on the baseline region can be performed.

Abstract translation: 根据本教导实施例的系统和方法包括可用于检查用于噪声的放大曲线的基线区域的一组可能的信号变换。 在实施例中，可以执行差分时间序列分析以确定在PCR或其他反应的早期循环中的检测到的荧光或其他信号强度在中值差异时间序列幅度上的偏差。 在实施例中，差分时间序列分析或其他检测技术可以在产生多分辨率分析的不同跳数上执行。 在实施例中，放大曲线可以被发送到一组噪声检测器，其单独的结果或决策被轮询或加权以确定基线或其他区域中的噪声的存在。 在实施例中，可以执行对基线区域的二进制分析。

公开(公告)号：WO2012068276A2

公开(公告)日：2012-05-24

申请号：PCT/US2011/061034

申请日：2011-11-16

Applicant: LIFE TECHNOLOGIES CORPORATION ,  LEONG, Harrison ,  MAJUMDAR, Nivedita ,  SWARTZMAN, Elana

Inventor： LEONG, Harrison ,  MAJUMDAR, Nivedita ,  SWARTZMAN, Elana

IPC: G06F19/00

CPC classification number: G06F19/18 ,  G06F19/24

Abstract: A proximity binding assay (PBA) is performed on at least one test sample, at least one reference sample, a background sample, and one or more calibration samples using a thermal cycler instrument. Ct values are determined for at least one set of test sample data and at least one set of reference sample data. Background corrected Ct values are calculated using a corresponding value in a background sample data set. A linear range is determined for the background corrected Ct values as a function of sample quantity. A linear regression line is calculated for each linear range. One or more parameter values of an exponential model (EM) fold change formula are estimated from the one or more sets of calibration sample data. A target protein quantity and associated confidence interval are calculated using the linear regression lines and the EM fold change formula.

Abstract translation: 使用热循环仪在至少一个测试样品，至少一个参考样品，背景样品和一个或多个校准样品上进行接近结合测定（PBA）。 对于至少一组测试样本数据和至少一组参考样本数据确定Ct值。 使用背景样本数据集中的对应值计算背景校正的Ct值。 确定背景校正的Ct值作为样品量的函数的线性范围。 对于每个线性范围计算线性回归线。 从一组或多组校准样本数据估计指数模型（EM）倍数变化公式的一个或多个参数值。 使用线性回归线和EM倍数变化公式计算靶蛋白质量和相关置信区间。

公开(公告)号：WO2010104893A3

公开(公告)日：2011-01-13

申请号：PCT/US2010026726

申请日：2010-03-09

Applicant: LIFE TECHNOLOGIES CORP ,  LEONG HARRISON M ,  BARBACIORU CATALIN ,  JANAWAY GORDON A

Inventor： LEONG HARRISON M ,  BARBACIORU CATALIN ,  JANAWAY GORDON A

IPC: C12Q1/68 ,  G06F19/00

CPC classification number: G06F19/22 ,  C12Q1/6827 ,  G06F19/18 ,  G06F19/24 ,  G06N7/005

Abstract: Methods for the determination of a copy number of a target genomic sequence; either a target gene or genomic sequence of interest, in a biological sample are described. Various methods utilize a model drawn from a probability density function (PDF) for the assignment of a copy number of a target genomic sequence in a biological sample. Additionally, the methods provide for the determination of a confidence value for a copy number assigned to a sample based on attributes of the sample data. Accordingly, the various methods for the determination of a copy number provide the end user with significant information for the evaluation of a copy number of a target genomic sequence; either a gene or genomic sequence of interest.

Abstract translation: 用于确定靶基因组序列拷贝数的方法; 描述了生物样品中的靶基因或目的基因组序列。 各种方法利用从概率密度函数（PDF）中提取的模型来分配生物样品中靶基因组序列的拷贝数。 另外，这些方法提供了基于样本数据的属性确定分配给样本的副本编号的置信度值。 因此，用于确定拷贝数的各种方法为终端用户提供了用于评价目标基因组序列拷贝数的重要信息; 是感兴趣的基因或基因组序列。

公开(公告)号：WO2008070328A3

公开(公告)日：2008-11-13

申请号：PCT/US2007082458

申请日：2007-10-24

Applicant: APPLERA CORP ,  LEONG HARRISON

Inventor： LEONG HARRISON

IPC: C12P19/34 ,  G06F19/00

CPC classification number: G06K9/00523

Abstract: Systems and methods according to embodiments of the present teachings incorporate a set of possible signal transforms that can be used to examine the baseline region of an amplification profile for noise. In embodiments, a difference time series analysis can be performed to determine deviations of detected fluorescent or other signal intensity in the early cycles of a PCR or other reaction over a median difference time series magnitude. In embodiments, difference time series analysis or other detection techniques can be performed over different hop sizes producing a multi-resolution analysis. In embodiments, the amplification profile can be transmitted to a set of noise detectors whose individual results or decisions are polled or weighted to determine the presence of noise in the baseline or other region. In embodiments, a second derivative analysis on the baseline region can be performed.

Abstract translation: 根据本教导的实施例的系统和方法包含一组可能的信号变换，其可用于检查噪声的放大轮廓的基线区域。 在实施方式中，可以执行差异时间序列分析以确定在PCR的早期周期或其他反应中的中值差异时间序列幅度上的检测到的荧光或其他信号强度的偏差。 在实施例中，可以在产生多分辨率分析的不同跳段大小上执行差异时间序列分析或其他检测技术。 在实施例中，可以将放大曲线传送到一组噪声检测器，其中对各个结果或决定进行轮询或加权以确定基线或其他区域中存在噪声。 在实施例中，可以执行对基线区域的二阶导数分析。

公开(公告)号：WO2012174119A3

公开(公告)日：2013-04-11

申请号：PCT/US2012042263

申请日：2012-06-13

Applicant: LIFE TECHNOLOGIES CORP ,  JI YONGMEI ,  SHIH SHEUNG-MEI RITA ,  DEGORICIJA LOVORKA ,  ZHOU ZHAOHUI ,  CUMMINGS CRAIG ,  FURTADO MANOHAR ,  BRZOSKA PIUS ,  BURRELL ANGELA ,  LEONG HARRISON ,  FANG XINGWANG ,  BOUNPHENG MANGKEY ,  SHAH ROHAN

Inventor： JI YONGMEI ,  SHIH SHEUNG-MEI RITA ,  DEGORICIJA LOVORKA ,  ZHOU ZHAOHUI ,  CUMMINGS CRAIG ,  FURTADO MANOHAR ,  BRZOSKA PIUS ,  BURRELL ANGELA ,  LEONG HARRISON ,  FANG XINGWANG ,  BOUNPHENG MANGKEY ,  SHAH ROHAN

IPC: C12Q1/68

CPC classification number: C12Q1/689 ,  C12R1/01

Abstract: Disclosed are genomic sequences for nine strains of Cronobacter spp. (C. sakazakii - 696, 701, 680; C. malonaticus - 507, 681; C. turicensis - 564; C. muytjensii - 530; C. dublinensis - 582; C. genomospl - 581) and compositions, methods, and kits for detecting, identifying and distinguishing Cronobacter spp. strains from each other and from non-Cronobacter spp. strains. Some embodiments describe isolated nucleic acid compositions unique to certain Cronobacter strains as well as compositions that are specific to all Cronobacter spp. Primer and probe compositions and methods of use of primers and probes are also provided. Kits for identification of Cronobacter spp. are also described. Some embodiments relate to computer software methods for setting a control based threshold for analysis of PCR

Abstract translation: 公开了九个克罗杆菌属菌株的基因组序列。 （C. sakazakii-696,701,680; C. malonaticus-507,681; C. turicensis-564; C. muytjensii-530; C.dublinensis-582; C.基因组蛋白-58）和组合物，方法和试剂盒 用于检测，识别和鉴别克罗杆菌属。 菌株彼此和非克罗杆菌属。 株。 一些实施方案描述了某些克罗杆菌菌株特有的分离的核酸组合物以及对所有克罗杆菌属特异性的组合物。 还提供引物和探针组合物以及引物和探针的使用方法。 克隆杆菌属鉴定试剂盒 也被描述。 一些实施例涉及用于设置用于PCR分析的基于控制的阈值的计算机软件方法

公开(公告)号：WO2012174119A2

公开(公告)日：2012-12-20

申请号：PCT/US2012/042263

申请日：2012-06-13

Applicant: LIFE TECHNOLOGIES CORPORATION ,  JI, Yongmei ,  SHIH, Sheung-Mei ("Rita") ,  DEGORICIJA, Lovorka ,  ZHOU, Zhaohui ,  CUMMINGS, Craig ,  FURTADO, Manohar ,  BRZOSKA, Pius ,  BURRELL, Angela ,  LEONG, Harrison ,  FANG, Xingwang ,  BOUNPHENG, Mangkey ,  SHAH, Rohan

Inventor： JI, Yongmei ,  SHIH, Sheung-Mei ("Rita") ,  DEGORICIJA, Lovorka ,  ZHOU, Zhaohui ,  CUMMINGS, Craig ,  FURTADO, Manohar ,  BRZOSKA, Pius ,  BURRELL, Angela ,  LEONG, Harrison ,  FANG, Xingwang ,  BOUNPHENG, Mangkey ,  SHAH, Rohan

IPC: C12Q1/68

CPC classification number: C12Q1/689 ,  C12R1/01

Abstract: Disclosed are genomic sequences for nine strains of C ronobacter spp . (C. sakazakii - 696, 701, 680; C. malonaticus - 507, 681; C. turicensis - 564; C. muytjensii - 530; C. dublinensis - 582; C. genomospl - 581) and compositions, methods, and kits for detecting, identifying and distinguishing C ronobacter spp . strains from each other and from non-C ronobacter spp . strains. Some embodiments describe isolated nucleic acid compositions unique to certain C ronobacter strains as well as compositions that are specific to all C ronobacter spp . Primer and probe compositions and methods of use of primers and probes are also provided. Kits for identification of C ronobacter spp . are also described. Some embodiments relate to computer software methods for setting a control based threshold for analysis of PCR

Abstract translation: 公开了九个克罗杆菌属菌株的基因组序列。 （C. sakazakii-696,701,680; C. malonaticus-507,681; C. turicensis-564; C. muytjensii-530; C.dublinensis-582; C.基因组蛋白-58）和组合物，方法和试剂盒 用于检测，识别和鉴别克罗杆菌属。 菌株彼此和非克罗杆菌属。 株。 一些实施方案描述了某些克罗杆菌菌株特有的分离的核酸组合物以及对所有克罗杆菌属特异性的组合物。 还提供引物和探针组合物以及引物和探针的使用方法。 克隆杆菌属鉴定试剂盒 也被描述。 一些实施例涉及用于设置用于PCR分析的基于控制的阈值的计算机软件方法

公开(公告)号：WO2012068276A3

公开(公告)日：2012-07-19

申请号：PCT/US2011061034

申请日：2011-11-16

Applicant: LIFE TECHNOLOGIES CORP ,  LEONG HARRISON ,  MAJUMDAR NIVEDITA ,  SWARTZMAN ELANA

Inventor： LEONG HARRISON ,  MAJUMDAR NIVEDITA ,  SWARTZMAN ELANA

IPC: G06F19/24

CPC classification number: G06F19/18 ,  G06F19/24

Abstract: A proximity binding assay (PBA) is performed on at least one test sample, at least one reference sample, a background sample, and one or more calibration samples using a thermal cycler instrument. Ct values are determined for at least one set of test sample data and at least one set of reference sample data. Background corrected Ct values are calculated using a corresponding value in a background sample data set. A linear range is determined for the background corrected Ct values as a function of sample quantity. A linear regression line is calculated for each linear range. One or more parameter values of an exponential model (EM) fold change formula are estimated from the one or more sets of calibration sample data. A target protein quantity and associated confidence interval are calculated using the linear regression lines and the EM fold change formula.

Abstract translation: 使用热循环仪器在至少一个测试样品，至少一个参考样品，背景样品和一个或多个校准样品上进行接近结合测定（PBA）。 对至少一组测试样本数据和至少一组参考样本数据确定Ct值。 背景校正的Ct值是使用背景样本数据集中的对应值计算的。 根据样品数量确定背景校正Ct值的线性范围。 针对每个线性范围计算线性回归线。 根据一组或多组校准样本数据估计指数模型（EM）倍数变化公式的一个或多个参数值。 使用线性回归线和EM倍数变化公式计算目标蛋白质量和相关置信区间。