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：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：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：US06914229B2

公开(公告)日：2005-07-05

申请号：US10086658

申请日：2002-02-28

申请人： John F. Corson ,  Debra A. Sillman ,  Jayati Ghosh ,  Kenneth L. Staton

发明人： John F. Corson ,  Debra A. Sillman ,  Jayati Ghosh ,  Kenneth L. Staton

IPC分类号： G01N21/27 ,  G01N21/64 ,  H01J40/14

CPC分类号： G01N21/6452 ,  G01N21/6428 ,  G01N2021/6421

摘要： A method and system for preventing signal clipping in a molecular array scanner by adding an offset signal to the signal generated by the photodetectors and initial stages of signal processing within a molecular array scanner in order to promote the signal above the level where signal information is lost during analog-to-digital signal conversion and/or digital signal integration. A portion of the offset is then subtracted from the digital signal or integrated digital signals, leaving a smaller, constant offset that is reported to the user, stored in a data file, or otherwise made available for further correction during later molecular array data processing.

摘要翻译： 一种用于在分子阵列扫描器中防止信号限幅的方法和系统，该方法和系统通过将偏移信号加到由光电检测器产生的信号和分子阵列扫描器内的信号处理的初始阶段，以便将信号提升到信号信息丢失的水平之上 在模数转换和/或数字信号集成期间。 然后从数字信号或集成的数字信号中减去偏移的一部分，留下一个较小的恒定偏移，报告给用户，存储在数据文件中，或者在以后的分子阵列数据处理中可用于进一步校正。

公开(公告)号：US20090012732A1

公开(公告)日：2009-01-08

申请号：US12231517

申请日：2008-09-02

申请人： John Frederick Corson ,  Jayati Ghosh ,  Svetlana Shchegrova

发明人： John Frederick Corson ,  Jayati Ghosh ,  Svetlana Shchegrova

IPC分类号： G06F17/10

CPC分类号： G06F19/20

摘要： Methods, systems and computer readable media for removing trends in signal intensity values from features on a chemical array. Inputted signal values from features on the array are surface fitted to calculate a surface approximation. The surface approximation is normalized and used to de-trend the signal intensity values from the features.

摘要翻译： 用于从化学阵列上的特征消除信号强度值趋势的方法，系统和计算机可读介质。 来自阵列中特征的输入信号值进行表面拟合，以计算表面近似值。 表面近似被归一化并用于从特征中消除信号强度值。

公开(公告)号：US07437249B2

公开(公告)日：2008-10-14

申请号：US11479269

申请日：2006-06-30

申请人： John Frederick Corson ,  Jayati Ghosh ,  Svetlana Shchegrova

发明人： John Frederick Corson ,  Jayati Ghosh ,  Svetlana Shchegrova

IPC分类号： G06F19/00 ,  G01N33/50

CPC分类号： G06F19/20

摘要： Methods, systems and computer readable media for removing trends in signal intensity values from features on a chemical array. Inputted signal values from features on the array are surface fitted to calculate a surface approximation. The surface approximation is normalized and used to de-trend the signal intensity values from the features.

公开(公告)号：US20080120038A1

公开(公告)日：2008-05-22

申请号：US11492472

申请日：2006-07-24

申请人： Jayati Ghosh ,  Amir Ben-dor ,  Anya Tsalenko ,  Bo Curry

发明人： Jayati Ghosh ,  Amir Ben-dor ,  Anya Tsalenko ,  Bo Curry

IPC分类号： G06F19/00

CPC分类号： G06F19/20 ,  G06F19/24 ,  G06F19/26

摘要： Embodiments of the present invention include methods and systems for analysis of comparative genomic hybridization (“CGH”) data, including CGH data obtained from microarray experiments.

摘要翻译： 本发明的实施方案包括用于分析比较基因组杂交（“CGH”）数据的方法和系统，包括从微阵列实验获得的CGH数据。

公开(公告)号：US20080004824A1

公开(公告)日：2008-01-03

申请号：US11479269

申请日：2006-06-30

申请人： John Corson ,  Jayati Ghosh ,  Svetlana Shchegrova

发明人： John Corson ,  Jayati Ghosh ,  Svetlana Shchegrova

IPC分类号： G06F17/10 ,  G06F19/00 ,  G06F17/40

CPC分类号： G06F19/20

摘要： Methods, systems and computer readable media for removing trends in signal intensity values from features on a chemical array. Inputted signal values from features on the array are surface fitted to calculate a surface approximation. The surface approximation is normalized and used to de-trend the signal intensity values from the features.

摘要翻译： 用于从化学阵列上的特征消除信号强度值趋势的方法，系统和计算机可读介质。 来自阵列中特征的输入信号值进行表面拟合，以计算表面近似值。 表面近似被归一化并用于从特征中消除信号强度值。

公开(公告)号：US07877213B2

公开(公告)日：2011-01-25

申请号：US11233560

申请日：2005-09-22

申请人： Jayati Ghosh ,  Charles D. Troup ,  Xiangyang Zhou

发明人： Jayati Ghosh ,  Charles D. Troup ,  Xiangyang Zhou

IPC分类号： G01N33/48

CPC分类号： G06F19/20

摘要： A system and method of operating a data processing system to provide feature extraction from an image obtained from a plurality of chemical arrays is disclosed. The method includes bifurcating processing of the image by performing image processing and post-processing. The image processing includes processing parts of the image, each part corresponding to a different one of the arrays, in an automated batch process, to produce image-processed outputs that are different from the image and contain information extracted from the image. The post-processing includes processing the image-processed outputs according to different post-processing protocols with respect to different ones of those parts of the image corresponding to at least two of the arrays, to produce post-processed outputs. The method includes outputting at least one of the image-processed outputs and/or at least one of the post-processed outputs.

摘要翻译： 公开了一种操作数据处理系统以从从多个化学阵列获得的图像中提取特征提取的系统和方法。 该方法包括通过执行图像处理和后处理来对图像进行分岔处理。 图像处理包括在自动批处理过程中处理图像的每个部分对应于不同的阵列的部分，以产生不同于图像的图像处理的输出并且包含从图像提取的信息。 后处理包括根据不同的后处理协议对相应于至少两个阵列的图像的那些部分中的不同的部分处理图像处理的输出，以产生后处理的输出。 该方法包括输出图像处理输出和/或至少一个后处理输出中的至少一个。