公开(公告)号：US06927389B2

公开(公告)日：2005-08-09

申请号：US10309465

申请日：2002-12-03

申请人： Bo U. Curry ,  Jayati Ghosh ,  Kenneth L. Staton

发明人： Bo U. Curry ,  Jayati Ghosh ,  Kenneth L. Staton

IPC分类号： G01N21/64 ,  G02B7/08 ,  H01J3/14 ,  H01J5/16 ,  H01J40/14

CPC分类号： G01N21/6452 ,  G02B7/08

摘要： Optical scanner system approaches are described in which novel focusing approaches are provided. A control algorithm accounts for geometric variation of successive scans in opposite directions across a microarray slide or substrate in order to provide optimized focus. The feedback approach taught may involve PI or PID terms. In either type of control approach, a projected slope of the slide is calculated and followed back and forth outside a scan region of the array in exiting and entering fully adaptive focusing zones, respectively. During turn-around, the system may track a setpoint between the periods of following the extrapolated slope. Also provided are methods of using the subject system in a biopolymer array based application, including genomic and proteomic applications.

摘要翻译： 描述了提供新颖的聚焦方法的光学扫描器系统方法。 控制算法考虑了跨微阵列载玻片或基底的相反方向的连续扫描的几何变化，以便提供优化的焦点。 所教导的反馈方法可能涉及PI或PID术语。 在任一类型的控制方法中，计算滑块的投影斜率并分别在阵列的扫描区域之间来回并进入完全自适应聚焦区域。 在回转期间，系统可以追踪在外推斜率之后的周期之间的设定值。 还提供了在基于生物聚合物阵列的应用中使用主题系统的方法，包括基因组和蛋白质组学应用。

公开(公告)号：US07067783B2

公开(公告)日：2006-06-27

申请号：US10261359

申请日：2002-09-30

申请人： Bo U. Curry ,  Andreas N. Dorsel ,  Jayati Ghosh ,  Kenneth L. Staton

发明人： Bo U. Curry ,  Andreas N. Dorsel ,  Jayati Ghosh ,  Kenneth L. Staton

IPC分类号： G02B7/04

CPC分类号： G02B7/36 ,  G01N21/6428 ,  G01N21/6452 ,  G01N21/6456 ,  G01N2021/6419 ,  G01N2021/6421

摘要： Automated methods and systems for determining an in-focus-distance for a position on the surface of a molecular array substrate using a molecular array scanner are provided. A signal from a first position of an array substrate is detected and noise is filtered out of the detected signal using a symmetrical filter to produce an in-focus-distance. In one embodiment, the in-focus-distance is utilized as an estimated in-focus-distance at a second position of the array substrate. The method finds use in maintaining the focus of a light source while scanning the array by the scanner. Also provided are methods of assaying a sample using the methods and systems of the invention, and kits for performing the invention. The subject invention finds use in a variety of different applications, including both genomics and proteomics applications.

摘要翻译： 提供了使用分子阵列扫描仪来确定分子阵列衬底表面上的位置的对焦距离的自动化方法和系统。 检测来自阵列基板的第一位置的信号，并使用对称滤波器将噪声从检测信号中滤出，以产生对焦距离。 在一个实施例中，将聚焦距离用作阵列基板的第二位置处的估计的对焦距离。 该方法用于在扫描仪扫描阵列时保持光源的焦点。 还提供了使用本发明的方法和系统测定样品的方法以及用于实施本发明的试剂盒。 本发明可用于各种不同的应用，包括基因组学和蛋白质组学应用。

公开(公告)号：US08321138B2

公开(公告)日：2012-11-27

申请号：US11193912

申请日：2005-07-29

申请人： Bo U. Curry ,  Jayati Ghosh

发明人： Bo U. Curry ,  Jayati Ghosh

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

CPC分类号： G06F19/20

摘要： Methods, systems, and computer readable media for determining the quality of a CGH array, including calculating a spread of the derivative of log ratio value differences between consecutive probes representing consecutive positions along a chromosome, wherein ratio values are calculated from probe signals from a CGH array.

摘要翻译： 用于确定CGH阵列质量的方法，系统和计算机可读介质，包括计算代表沿着染色体的连续位置的连续探针之间的对数比值差的导数的扩展，其中根据CGH的探测信号计算比值 数组。

公开(公告)号：US20080102453A1

公开(公告)日：2008-05-01

申请号：US11591222

申请日：2006-10-31

申请人： Jayati Ghosh ,  Bo U. Curry

发明人： Jayati Ghosh ,  Bo U. Curry

IPC分类号： C12Q1/68 ,  G06F19/00

CPC分类号： G16B25/00

摘要： Methods, systems and computer readable media for analysis of comparative genomic hybridization data analysis, including creating a centralization curve from log ratio data values for DNA copy numbers of a genome of a test sample relative to a genome of a reference sample, wherein the reference sample has a known ploidy, and the test sample has a same copy number as the reference sample in normal, non-aberrant genomic regions; identifying a peak corresponding to regions of normal copy number in the centralization curve; centralizing the log ratio data so that the peak corresponding to regions of normal copy number is centered at a log ratio value of zero; calculating a mathematical measurement that is a function of the width of the peak corresponding to regions of normal copy number; calculating a tolerance value as a function of the mathematical measurement; and outputting the tolerance value. Methods, systems and computer readable media are provided to create a centralization curve from log ratio data values for DNA copy numbers of a genome of a test sample relative to a genome of a reference sample, wherein the reference sample has a known ploidy, and the test sample has a same copy number as the reference sample in normal, non-aberrant genomic regions; identify peaks in the centralization curve; assign copy numbers to the identified peaks; plot expected ratios, based on the assigned copy numbers, of the peaks versus observed ratios of the peaks calculated from the log ratio data values; conclude that the assigned copy numbers are correct if the plot of the expected ratios versus the observed ratios is substantially linear; and output at least one of the plot of expected ratios versus observed ratios, and a conclusion as to whether the plot is substantially linear.

摘要翻译： 用于分析比较基因组杂交数据分析的方法，系统和计算机可读介质，包括从参考样品的基因组的测试样品的基因组的DNA拷贝数的对数比数据值创建中心化曲线，其中参考样品 具有已知的倍性，测试样品与正常非异常基因组区域中的参考样品具有相同的拷贝数; 识别对应于集中曲线中正常拷贝数的区域的峰值; 集中对数比数据使得对应于正常拷贝数的区域的峰值以对数比值为零为中心; 计算作为与正常拷贝数的区域对应的峰值的宽度的函数的数学测量; 计算公差值作为数学测量的函数; 并输出公差值。 提供方法，系统和计算机可读介质以从测试样品的基因组的DNA拷贝数的对数比数据值相对于参照样品的基因组产生中心化曲线，其中参考样品具有已知的倍性， 测试样品与正常非异常基因组区域中的参考样品具有相同的拷贝数; 识别中心曲线中的峰值; 将复制号码分配给识别的峰; 根据分配的拷贝数，从对数比数据值计算的峰与观察到的峰的比率的预期比率; 得出结论，如果预期比率与观察到的比率的曲线基本上是线性的，则分配的拷贝数是正确的; 并输出预期比率与观察到的比率的曲线中的至少一个，以及关于该曲线是否基本上是线性的结论。

公开(公告)号：US08043867B2

公开(公告)日：2011-10-25

申请号：US12409871

申请日：2009-03-24

申请人： Patrick T. Petruno ,  John F. Petrilla ,  Michael J. Brosnan ,  Rong Zhou ,  Daniel B. Roitman ,  Bo U. Curry

发明人： Patrick T. Petruno ,  John F. Petrilla ,  Michael J. Brosnan ,  Rong Zhou ,  Daniel B. Roitman ,  Bo U. Curry

IPC分类号： G01N33/53

CPC分类号： G01N33/54386 ,  G01N21/17 ,  G01N21/274 ,  G01N21/6428 ,  G01N21/8483 ,  G01N33/558 ,  G01N2021/6439 ,  G01N2201/062 ,  G01N2201/067 ,  Y10S435/805 ,  Y10S435/823 ,  Y10S436/807 ,  Y10S436/809 ,  Y10S436/81 ,  Y10S436/823 ,  Y10T436/25125

摘要： An assay test strip includes a flow path, a sample receiving zone, a label, a detection zone that includes a region of interest, and at least one position marker. The at least one position marker is aligned with respect to the region of interest such that location of the at least one position marker indicates a position of the region of interest. A diagnostic test system includes a reader that obtains light intensity measurement from exposed regions of the test strip, and a data analyzer that performs at least one of (a) identifying ones of the light intensity measurements obtained from the test region based on at least one measurement obtained from the at least one reference feature, and (b) generating a control signal modifying at least one operational parameter of the reader based on at least one measurement obtained from the at least one reference feature.

摘要翻译： 测定试片包括流路，样品接收区，标签，包括感兴趣区域的检测区和至少一个位置标记。 所述至少一个位置标记相对于所述感兴趣区域对齐，使得所述至少一个位置标记的位置指示所述感兴趣区域的位置。 诊断测试系统包括从测试条的暴露区域获得光强度测量的读取器，以及数据分析器，其执行以下至少一个：（a）基于至少一个（a）识别从测试区域获得的光强度测量中的一个 测量从所述至少一个参考特征获得的，以及（b）基于从所述至少一个参考特征获得的至少一个测量值生成修改所述读取器的至少一个操作参数的控制信号。

公开(公告)号：US20090325813A1

公开(公告)日：2009-12-31

申请号：US12215302

申请日：2008-06-26

申请人： Hui Wang ,  Bo U. Curry

发明人： Hui Wang ,  Bo U. Curry

IPC分类号： C40B30/04 ,  C40B40/06

CPC分类号： C12Q1/6837 ,  C12Q2545/113 ,  C12Q2525/207

摘要： Aspects of the disclosure are generally directed to methods, probes, probe compositions and kits for detecting or quantifying target oligonucleotides. In some embodiments, there are provided methods for determining the level of target oligonucleotides, such as a small RNA (e.g., miRNA), in a sample. In some embodiments, the methods comprise analyzing hybridization of target oligonucleotides to a test microarray; analyzing hybridization of a known amount of reference oligonucleotides (having the same sequences as the target oligonucleotides) to a calibration microarray; and determining the level of the target oligonucleotides in the sample by comparing the hybridization of the target oligonucleotides with the hybridization of the reference oligonucleotides.

摘要翻译： 本公开的方面通常涉及用于检测或定量靶寡核苷酸的方法，探针，探针组合物和试剂盒。 在一些实施方案中，提供了用于确定样品中靶寡核苷酸水平的方法，例如小RNA（例如miRNA）。 在一些实施方案中，所述方法包括分析靶寡核苷酸与测试微阵列的杂交; 分析已知量的参考寡核苷酸（具有与靶寡核苷酸相同的序列）与校准微阵列的杂交; 并通过比较靶寡核苷酸的杂交与参考寡核苷酸的杂交来确定样品中靶寡核苷酸的水平。

公开(公告)号：US20090180926A1

公开(公告)日：2009-07-16

申请号：US12409871

申请日：2009-03-24

申请人： Patrick T. Petruno ,  John F. Petrilla ,  Michael J. Brosnan ,  Rong Zhou ,  Daniel B. Roitman ,  Bo U. Curry

发明人： Patrick T. Petruno ,  John F. Petrilla ,  Michael J. Brosnan ,  Rong Zhou ,  Daniel B. Roitman ,  Bo U. Curry

IPC分类号： G01N31/22

CPC分类号： G01N33/54386 ,  G01N21/17 ,  G01N21/274 ,  G01N21/6428 ,  G01N21/8483 ,  G01N33/558 ,  G01N2021/6439 ,  G01N2201/062 ,  G01N2201/067 ,  Y10S435/805 ,  Y10S435/823 ,  Y10S436/807 ,  Y10S436/809 ,  Y10S436/81 ,  Y10S436/823 ,  Y10T436/25125

摘要： An assay test strip includes a flow path, a sample receiving zone, a label, a detection zone that includes a region of interest, and at least one position marker. The at least one position marker is aligned with respect to the region of interest such that location of the at least one position marker indicates a position of the region of interest. A diagnostic test system includes a reader that obtains light intensity measurement from exposed regions of the test strip, and a data analyzer that performs at least one of (a) identifying ones of the light intensity measurements obtained from the test region based on at least one measurement obtained from the at least one reference feature, and (b) generating a control signal modifying at least one operational parameter of the reader based on at least one measurement obtained from the at least one reference feature.

公开(公告)号：US10001486B2

公开(公告)日：2018-06-19

申请号：US11500626

申请日：2006-08-08

申请人： Bo U. Curry ,  Rene P. Helbing

发明人： Bo U. Curry ,  Rene P. Helbing

IPC分类号： C12Q1/00 ,  C12Q1/68 ,  G06F19/00 ,  G01N33/58 ,  G01N33/558

CPC分类号： G01N33/582 ,  G01N33/558

摘要： A method to calibrate measurements of a test analyte in a test sample including measuring at least one test-light level responsive to reactions of at least one reagent group and at least one reactive test analyte in the test sample and measuring at least one control-light level responsive to reactions of at least one reagent group and at least one control analyte in a control sample. Each control analyte is a known amount of at least one reactive test analyte. The method further includes determining a presence of the reactive test analyte in the test sample based on the measured test-light levels and control-light levels. The reagent group and the reactive test analyte react by attaching to each other.

公开(公告)号：US20080038711A1

公开(公告)日：2008-02-14

申请号：US11500626

申请日：2006-08-08

申请人： Bo U. Curry ,  Rene P. Helbing

发明人： Bo U. Curry ,  Rene P. Helbing

IPC分类号： C12Q1/00 ,  C12Q1/68 ,  G06F19/00

CPC分类号： G01N33/582 ,  G01N33/558

摘要： A method to calibrate measurements of a test analyte in a test sample including measuring at least one test-light level responsive to reactions of at least one reagent group and at least one reactive test analyte in the test sample and measuring at least one control-light level responsive to reactions of at least one reagent group and at least one control analyte in a control sample. Each control analyte is a known amount of at least one reactive test analyte. The method further includes determining a presence of the reactive test analyte in the test sample based on the measured test-light levels and control-light levels. The reagent group and the reactive test analyte react by attaching to each other.

摘要翻译： 校准测试样品中测试分析物的测量的方法，包括测量响应于至少一种试剂组和至少一种反应性测试分析物在测试样品中的反应的至少一种测试光级，并测量至少一种对照光 响应于对照样品中至少一个试剂组和至少一个对照分析物的反应。 每个对照分析物是已知量的至少一种反应性测试分析物。 所述方法还包括基于测量的测试光水平和控制光水平来确定测试样品中反应性测试分析物的存在。 试剂组和反应性试验分析物通过彼此连接而反应。

公开(公告)号：US06870166B2

公开(公告)日：2005-03-22

申请号：US10087619

申请日：2002-02-28

申请人： Bo U. Curry ,  Andreas N. Dorsel ,  Kyle J. Schleifer ,  Debra A. Sillman

发明人： Bo U. Curry ,  Andreas N. Dorsel ,  Kyle J. Schleifer ,  Debra A. Sillman

IPC分类号： G01N21/64 ,  G01J1/20

CPC分类号： G01N21/6456 ,  G01N2021/6419 ,  G01N2021/6441 ,  G01N2021/6463 ,  G01N2021/6484

摘要： A maximum sensitivity optical scanning system is disclosed. It finds use in a variety of applications, including the reading of biopolymeric arrays. It operates by scanning sample at a setting selected to result in signal saturation for some, but not all available data. Subsequent scans of the same area are taken at lower sensitivity settings (in terms of detector gain and/or excitation light source gain or attenuation) and data from at least the previously saturated regions is obtained. If system sensitivity is set too low to produce useful results, optional features may adjust sensitivity upward and follow with an increased sensitivity scan as a remedial measure. Full signal sensitivity is better preserved as most needed in taking data for the weakest signals first with the high-level scan. Data for sample producing stronger signals that can better tolerate photobleaching is then taken in one way or another.

摘要翻译： 公开了一种最大灵敏度的光学扫描系统。 它可用于各种应用，包括读取生物聚合物阵列。 它通过在选定的设置上扫描样品来产生一些信号饱和而不是所有可用数据进行操作。 在较低的灵敏度设置（在检测器增益和/或激发光源增益或衰减方面）进行相同区域的后续扫描，并且获得来自至少先前饱和区域的数据。 如果系统灵敏度设置太低而无法产生有用的结果，可选功能可以向上调整灵敏度，并采用增加的灵敏度扫描作为补救措施。 完全的信号灵敏度更好地保留，因为首先采用高级扫描为最弱信号采集数据最为需要。 然后以一种或另一种方式获取产生更好的耐光漂白信号的样品的数据。