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    Spectral calibration of fluorescent polynucleotide separation apparatus
    2.
    发明授权
    Spectral calibration of fluorescent polynucleotide separation apparatus 有权

    公开(公告)号：US06821402B1

    公开(公告)日：2004-11-23

    申请号：US09154178

    申请日：1998-09-16

    申请人： Muhammad A. Sharaf ,  Maria C. Roque-Biewer

    发明人： Muhammad A. Sharaf ,  Maria C. Roque-Biewer

    IPC分类号： G01N2726

    CPC分类号： G01N27/44726 ,  Y10T436/10

    摘要： The invention relates to methods, compositions, and systems for calibrating a fluorescent polynucleotide separation apparatus. One aspect of the invention is multiple color calibration standards and their use. A multiple color calibration standard is a mixture of at least two polynucleotides of different length, wherein each of the polynucleotides is labeled with a spectrally distinct fluorescent dye. Another aspect of the invention is to produce total emission temporal profiles of multiple color calibration standards for use in calibrating fluorescent polynucleotide separation apparatus. The peaks corresponding to the fluorescently labeled polynucleotides in the total emission temporal profile may be detected using a peak detector that is driven by changes in the slopes of the total emission temporal profile. Calibration of fluorescent polynucleotide separation apparatus, with various embodiments of the methods of the invention, includes the step of identification of the labeled polynucleotides of the multiple color calibration standards. The process of spectral calibration of a fluorescent polynucleotide separation apparatus using a multiple color calibration standard may include the step of the estimating (extracting) of the dyes' reference spectra, using information from the peak detection process performed on the total emission temporal profile. Other aspects of the invention include systems for separating and detecting fluorescently labeled polynucleotides, wherein the system is designed for spectral calibration in accordance with the subject calibration methods employing multiple color calibration standards. Another aspect of the invention is methods and compositions for detecting the flow of electrical current through a separation channel of a fluorescent polynucleotide separation apparatus. These methods and compositions employ monitoring dyes. Monitoring dyes are fluorescent dyes that are spectrally distinct from the dye on the polynucleotide intended to convey genetic information, e.g., fluorescent polynucleotide sequencing reaction products.

    Spectral calibration of fluorescent polynucleotide separation apparatus
    6.
    发明授权
    Spectral calibration of fluorescent polynucleotide separation apparatus 有权

    公开(公告)号：US06991712B2

    公开(公告)日：2006-01-31

    申请号：US09927791

    申请日：2001-08-10

    申请人： Muhammad A. Sharaf ,  Maria C. Roque-Biewer

    发明人： Muhammad A. Sharaf ,  Maria C. Roque-Biewer

    IPC分类号： C07K1/26 ,  B01D59/42

    CPC分类号： G01N27/44726 ,  Y10T436/10

    摘要： The invention relates to methods, compositions, and systems for calibrating a fluorescent polynucleotide separation apparatus. One aspect of the invention is multiple color calibration standards and their use. A multiple color calibration standard is a mixture of at least two polynucleotides of different length, wherein each of the polynucleotides is labeled with a spectrally distinct fluorescent dye. Another aspect of the invention is to produce total emission temporal profiles of multiple color calibration standards for use in calibrating fluorescent polynucleotide separation apparatus. The peaks corresponding to the fluorescently labeled polynucleotides in the total emission temporal profile may be detected using a peak detector that is driven by changes in the slopes of the total emission temporal profile. Calibration of fluorescent polynucleotide separation apparatus, with various embodiments of the methods of the invention, includes the step of identification of the labeled polynucleotides of the multiple color calibration standards. The process of spectral calibration of a fluorescent polynucleotide separation apparatus using a multiple color calibration standard may include the step of the estimating (extracting) of the dyes' reference spectra, using information from the peak detection process performed on the total emission temporal profile. Other aspects of the invention include systems for separating and detecting fluorescently labeled polynucleotides, wherein the system is designed for spectral calibration in accordance with the subject calibration methods employing multiple color calibration standards. Another aspect of the invention is methods and compositions for detecting the flow of electrical current through a separation channel of a fluorescent polynucleotide separation apparatus. These methods and compositions employ monitoring dyes. Monitoring dyes are fluorescent dyes that are spectrally distinct from the dye on the polynucleotide intended to convey genetic information, e.g., fluorescent polynucleotide sequencing reaction products.

    Multicomponent analysis method including the determination of a statistical confidence interval
    8.
    发明授权
    Multicomponent analysis method including the determination of a statistical confidence interval 失效
    多分量分析方法包括确定统计置信区间

    公开(公告)号：US6015667A

    公开(公告)日：2000-01-18

    申请号：US659115

    申请日：1996-06-03

    申请人： Muhammad A. Sharaf

    发明人： Muhammad A. Sharaf

    IPC分类号： C12N15/09 ,  C12Q1/68 ,  G01N21/27 ,  G01N21/64 ,  G01N27/416 ,  G01N27/42 ,  G01N27/447 ,  G01N30/74 ,  G01N30/86 ,  G01N33/50 ,  G06F17/00 ,  C12P19/34

    CPC分类号： G01N30/8665 ,  G01N2201/129

    摘要： A signal processing method in a processor is provided for performing a multicomponent analysis of a signal resulting from a spectral response of a mixture comprising a plurality of spectrally resolvable molecular species. The method provides both a determination of a concentration estimate and a statistical confidence interval for each species. In the method, a data vector d is received from a multichannel detector, data vector d having a length n.sub.c, n.sub.c being the number of detector channels being monitored. A calibration matrix K having n.sub.c rows and n.sub.p columns is provided wherein n.sub.c is larger than n.sub.p, n.sub.p being the number of spectrally resolvable molecular species. Next, a concentration estimate vector c having length n.sub.p is determined. Finally, a confidence interval CI.sub.i for each of the elements of the concentration estimate vector is determined according to the expressionCI.sub.i =c.sub.i .+-.(varcovar(c.sub.ii)).sup.1/2 Q.sub.(cl,nf)where Q is the critical value of a statistical distribution for a given level of confidence, cl, and a given number of degrees of freedom n.sub.f where n.sub.f =n.sub.c -n.sub.p. The invention further includes a program storage device embodying the method; a DNA sequencing process employing the method; and, an apparatus for carrying out the method.

    摘要翻译： 提供了一种处理器中的信号处理方法，用于对包含多个可光谱解析的分子物质的混合物的光谱响应产生的信号进行多组分分析。 该方法提供了每种物种的浓度估计和统计置信区间的确定。 在该方法中，从多通道检测器接收数据矢量d，数据矢量d的长度为nc，nc为被监视的检测器通道的数量。 提供了具有nc行和np列的校准矩阵K，其中nc大于np，np是可光谱解析的分子种类的数量。 接下来，确定长度为np的浓度估计矢量c。 最后，根据表达式Cii = ci +/-（varcovar（cii））+ E，fra 1/2 + EE Q（cl，nf）确定浓度估计向量的每个元素的置信区间CIi，其中Q是 nf = nc-np给定给定的置信度cl和给定数量的自由度nf的统计分布的临界值。 本发明还包括体现该方法的程序存储装置; 采用该方法的DNA测序方法; 以及用于执行该方法的装置。

    Quantitative Calibration Method and System for Genetic Analysis Instrumentation
    9.
    发明申请
    Quantitative Calibration Method and System for Genetic Analysis Instrumentation 审中-公开
    遗传分析仪器的定量校准方法和系统

    公开(公告)号：US20100276580A1

    公开(公告)日：2010-11-04

    申请号：US12611892

    申请日：2009-11-03

    申请人： Muhammad A. Sharaf ,  Wanli Bi ,  Kenneth J. Livak

    发明人： Muhammad A. Sharaf ,  Wanli Bi ,  Kenneth J. Livak

    IPC分类号： G12B13/00 ,  G01N21/64 ,  G01N21/25

    CPC分类号： G01N21/274 ,  G01N21/278 ,  G01N21/6428 ,  G01N21/6452

    摘要： Aspects of the present invention provide a method and apparatus of generating a calibration matrix for a spectral detector instrument. A calibration plate contains one or more dye mixtures in each well of the calibration plate at known absolute concentration. From the calibration plate, aspects of the present invention are used to prepare a concentration matrix based on the dyes used in the assay and the different dye mixtures used in the calibration plate. An excitation source exposes the calibration plate causing the spectral species in each of the wells to fluoresce. The emission spectra for the different dye mixtures of dyes as gathered by the spectral detector instrument at different points in the range of spectra is used to generate a spectral matrix. Bilinear calibration is performed on the concentration matrix and the spectral matrix as to determine a calibration matrix relating spectra directly to absolute concentrations.

    摘要翻译： 本发明的方面提供了一种生成用于光谱检测器仪器的校准矩阵的方法和装置。 校准板在已知的绝对浓度下在校准板的每个孔中含有一种或多种染料混合物。 根据校准板，本发明的各方面用于制备基于测定中使用的染料和校准板中使用的不同染料混合物的浓度基质。 激发源暴露校准板，导致每个孔中的光谱物质发荧光。 由光谱检测仪器在光谱范围内的不同点收集的不同染料染料混合物的发射光谱用于产生光谱矩阵。 对浓度矩阵和光谱矩阵进行双线性校准，以确定直接将光谱与绝对浓度相关的校准矩阵。

    Alignment-based similarity scoring methods for quantifying the differences between related biopolymer sequences
    10.
    发明授权
    Alignment-based similarity scoring methods for quantifying the differences between related biopolymer sequences 失效
    用于量化相关生物聚合物序列之间的差异的基于对齐的相似性评分方法

    公开(公告)号：US5873052A

    公开(公告)日：1999-02-16

    申请号：US744490

    申请日：1996-11-06

    申请人： Muhammad A. Sharaf

    发明人： Muhammad A. Sharaf

    IPC分类号： C12N15/09 ,  C12Q1/68 ,  G01N33/50 ,  G06F17/30 ,  G06F19/22 ,  G06F19/00 ,  G06F17/00

    CPC分类号： G06F19/22

    摘要： Methods for assigning a quantitative score to the relatedness of aligned polymorphic biopolymer sequences such that small differences between otherwise identical sequences are highlighted are disclosed, including computer systems and program storage devices for carrying out the methods on a computer. Specifically, the methods of the invention comprise the steps of providing a test sequence and a basis set of sequences such that the test sequence and the basis set of sequences are aligned; determining the identity of a monomer unit at a position m in the test sequence; assigning a value of 1 to a local matching probability x.sub.m if the monomer unit at position m in the test sequence matches any members of the basis set at position m, or, assigning a value of between 0 and 1 to a local matching probability x.sub.m if the monomer unit at position m in the test sequence does not match any members of the basis set at position m. In a preferred embodiment, the above method is performed at a plurality of sequence locations and the local matching probabilities are multiplied together to provide a global matching probability.

    摘要翻译： 将定量分数分配给对准的多态性生物聚合物序列的相关性的方法，以便突出显示其他相同序列之间的小差异，包括用于在计算机上执行方法的计算机系统和程序存储装置。 具体地说，本发明的方法包括以下步骤：提供测试序列和基本的序列集合，使得测试序列和序列的基本组对齐; 确定测试序列中位置m处的单体单元的身份; 如果测试序列中位置m处的单体单元与位置m的基础集合中的任何成员匹配，或者将0和1之间的值分配给局部匹配概率xm，则将值1分配给局部匹配概率xm，if 测试顺序中位置m处的单体单元与位置m处的基础组的任何成员不匹配。 在优选实施例中，上述方法在多个序列位置执行，并且将局部匹配概率相乘以提供全局匹配概率。