公开(公告)号：US09727032B2

公开(公告)日：2017-08-08

申请号：US13994661

申请日：2011-12-06

Applicant: Yerramalli Subramaniam ,  Puneet Suri ,  Sylvia Chang ,  Chengyong Yang

Inventor： Yerramalli Subramaniam ,  Puneet Suri ,  Sylvia Chang ,  Chengyong Yang

IPC: G05B11/01 ,  G06F19/22

CPC classification number: B24B41/062 ,  B24B5/04 ,  B24B41/065 ,  G05B11/01 ,  G06F19/22

Abstract: Systems and methods of providing run-time quality control and monitoring of a single or multiple sequencing runs are provided herein. In some embodiments, the run-time system includes or is in communication with a processor capable of determining various types of run-time information relating to the quality, progress, etc. of various sequencing runs. In some embodiments, the system can also be in communication with a user interface, for example, a GUI, capable of representing and communicating various types of information to a user regarding the quality of the individual or multiple runs, the functioning of the instrument, an error event, etc. Additionally, the system can capable of receiving actionable information from a user via the GUI thereby allowing the user to terminate or repeat various sequencing steps in a particular run, terminate a entire run, terminate all runs, allow a run to proceed, etc.

公开(公告)号：US20110105345A1

公开(公告)日：2011-05-05

申请号：US12848967

申请日：2010-08-02

Applicant: Francis T. Cheng ,  Chengyong Yang ,  Casey R. McFarland ,  Ying Wang

Inventor： Francis T. Cheng ,  Chengyong Yang ,  Casey R. McFarland ,  Ying Wang

IPC: C40B30/02

CPC classification number: G16B30/00 ,  C12Q1/6816 ,  C12Q1/6827 ,  G01N21/6428 ,  G01N25/04 ,  G01N2021/6439 ,  G16B40/00 ,  C12Q2527/107 ,  C12Q2537/165

Abstract: The present application provides for various embodiments of methods for the analysis of high resolution melt (HRM) curve data; where statistical assay variations in melt curve data may result from system noise in an analysis system. Such system noise may arise from various sources, such as the thermal non-uniformity of a thermocycler block in a thermal cycler apparatus, a detection system, etc. Additionally, various methods for the analysis of HRM curve data may provide an identification of a sample without the need for a user inputted information.

Abstract translation: 本申请提供了用于分析高分辨率熔体（HRM）曲线数据的方法的各种实施方案; 其中熔体曲线数据的统计测定变化可能由分析系统中的系统噪声引起。 这种系统噪声可能来自各种来源，例如热循环仪装置中的热循环器块的热不均匀性，检测系统等。另外，用于分析HRM曲线数据的各种方法可以提供样品的鉴定 而不需要用户输入的信息。

公开(公告)号：US20130316918A1

公开(公告)日：2013-11-28

申请号：US13989026

申请日：2011-11-22

Applicant: Ming Jiang ,  Chengyong Yang ,  Eugene Wang

Inventor： Ming Jiang ,  Chengyong Yang ,  Eugene Wang

IPC: C12Q1/68

CPC classification number: C12Q1/6874 ,  G16B25/00

Abstract: A method for improving color calls or base calls utilizes current and prior cycle multi-channel intensity data from a sequencing run to model residual cycle buildup. The model is applied to correct the multi-cycle channel intensity for the current cycle. The corrected multi-cycle channel intensity is used for color calls or base calls for the current cycle.

Abstract translation: 用于改进颜色调用或基本调用的方法利用来自测序运行的模型残余循环积累的当前和先前循环多通道强度数据。 该模型用于校正当前周期的多周期通道强度。 校正的多周期信道强度用于当前周期的彩色呼叫或基本呼叫。

公开(公告)号：US20130331992A1

公开(公告)日：2013-12-12

申请号：US13994661

申请日：2011-12-06

Applicant: Yerramalli Subramaniam ,  Puneet Suri ,  Sylvia Chang ,  Chengyong Yang

Inventor： Yerramalli Subramaniam ,  Puneet Suri ,  Sylvia Chang ,  Chengyong Yang

IPC: G05B11/01

CPC classification number: B24B41/062 ,  B24B5/04 ,  B24B41/065 ,  G05B11/01 ,  G06F19/22

Abstract: Systems and methods of providing run-time quality control and monitoring of a single or multiple sequencing runs are provided herein. In some embodiments, the run-time system includes or is in communication with a processor capable of determining various types of run-time information relating to the quality, progress, etc. of various sequencing runs. In some embodiments, the system can also be in communication with a user interface, for example, a GUI, capable of representing and communicating various types of information to a user regarding the quality of the individual or multiple runs, the functioning of the instrument, an error event, etc. Additionally, the system can capable of receiving actionable information from a user via the GUI thereby allowing the user to terminate or repeat various sequencing steps in a particular run, terminate a entire run, terminate all runs, allow a run to proceed, etc.

Abstract translation: 本文提供了提供单次或多次测序运行的运行时质量控制和监控的系统和方法。 在一些实施例中，运行时系统包括或正在与能够确定与各种排序运行的质量，进度等相关的各种运行时信息的处理器通信。 在一些实施例中，系统还可以与用户接口（例如，GUI）通信，该用户接口能够向用户表示和传达关于个人或多个运行的质量，仪器的功能的各种类型的信息， 错误事件等。另外，系统能够经由GUI从用户接收可操作的信息，从而允许用户终止或重复特定运行中的各种排序步骤，终止整个运行，终止所有运行，允许运行 继续等

公开(公告)号：US20110096975A1

公开(公告)日：2011-04-28

申请号：US12878943

申请日：2010-09-09

Applicant: Chengyong YANG ,  Robert BEAUDOIN ,  Curtis GEHMAN ,  Andrew SHERIDAN

Inventor： Chengyong YANG ,  Robert BEAUDOIN ,  Curtis GEHMAN ,  Andrew SHERIDAN

IPC: G06K9/00

CPC classification number: C12Q1/6869 ,  C12Q2563/149 ,  C12Q2535/101

Abstract: Disclosed are systems and methods for identifying microparticles or features arranged in high density arrays. Using the techniques of the present teachings allow for effective discrimination and characterization of microparticles such as sequencing beads or features having densities of about 39×106 particles/cm2 or more. In certain embodiments, such identification can be achieved via use of two or more images corresponding to respective subsets of the microparticles or features. In certain embodiments, microparticles in each such subset can be configured with a target that hybridizes with a labeled probe, thereby resulting in the corresponding image having lower density of objects to identify.

Abstract translation: 公开了用于识别以高密度阵列排列的微粒或特征的系统和方法。 使用本教导的技术允许有效地区分和表征微粒，例如测量珠粒或具有约39×10 6个/ cm 2或更大密度的特征。 在某些实施例中，可以通过使用对应于微粒或特征的相应子集的两个或多个图像来实现这种识别。 在某些实施方案中，每个这样的子集中的微粒可以配置有与标记的探针杂交的靶，从而导致相应的图像具有较低密度的物体以识别。

公开(公告)号：US20080201103A1

公开(公告)日：2008-08-21

申请号：US12021032

申请日：2008-01-28

Applicant: Chengyong Yang ,  David C. Woo

Inventor： Chengyong Yang ,  David C. Woo

IPC: G06F17/18 ,  G01N33/48 ,  G01D18/00

CPC classification number: G06F17/18 ,  G01D1/14 ,  G01N21/6428 ,  G01N2021/6439

Abstract: The present teachings comprise systems and methods for calibrating the background or baseline signal in a PCR or other reaction. The background signal derived from detected emissions of sample wells can be subjected to a normalized statistical metric, and be compared to a threshold or other standard to discard outlier cycles or other extraneous data. According to various embodiments, a relative standard deviation (relativeSTD) for the background component can be generated by dividing the standard deviation by the median of differences across all wells, where the difference is defined as the difference between maximum and minimum pixel values of a well. The relativeSTD as a metric is not sensitive to machine-dependent variations in absolute signal output that can be caused by different gain settings, different LED draw currents, different optical paths, or other instrumental variations. More accurate background characterization can be achieved.

Abstract translation: 本教导包括用于在PCR或其他反应中校准背景或基线信号的系统和方法。 从检测到的样本井的排放导出的背景信号可以经受归一化的统计度量，并与阈值或其他标准进行比较以丢弃异常周期或其他无关数据。 根据各种实施例，可以通过将标准偏差除以所有孔的差异中值来产生背景分量的相对标准偏差（relativeSTD），其中差被定义为井的最大和最小像素值之间的差 。 作为度量的relativeSTD对于可能由不同的增益设置，不同的LED绘制电流，不同的光路或其他工具变化引起的绝对信号输出的机器相关变化不敏感。 可以获得更准确的背景特征。