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1. 发明授权

US07222059B2 Electrophoretic trace simulator 失效
标题翻译：电泳痕迹模拟器
公开(公告)号：US07222059B2
公开(公告)日：2007-05-22
申请号：US10295964
申请日：2002-11-15
申请人： Alexandre M. Izmailov , Thomas Yager
发明人： Alexandre M. Izmailov , Thomas Yager
IPC分类号： G06F17/50 , C12Q1/68
CPC分类号： G01N27/44717 , G01N27/44721
摘要： A simulated electrophoretic trace is prepared by first obtaining an input file containing an input base sequence comprising a string of letters (A, C, G and/or T) in an order corresponding to the input base sequence, and then modifying the input file using one or more functions to take into account perturbations associated with (1) changes in peak intensity as a function of base number; (2) peak shape as a function of base number; (3) peak skew; (4) spacing between peaks; (5) background; (6) noise; (7) spectral cross-talk; (8) instrumental effects and/or (9) gel electrophoresis effects to produce a modified file representing a simulated electrophoretic trace. The method may be performed using a specially adapted apparatus.
摘要翻译：通过首先以与输入的基本序列相对应的顺序获得包含字母串（A，C，G和/或T）的输入基序列的输入文件，然后使用考虑与（1）峰值强度变化作为基数的函数相关的扰动的一个或多个功能; （2）峰值形状作为基数的函数; （3）峰偏; （4）峰之间的间距; （5）背景; （6）噪音; （7）频谱串扰; （8）仪器效应和/或（9）凝胶电泳效应以产生表示模拟电泳迹线的修改文件。该方法可以使用特别适配的装置来执行。

2. 发明申请

US20080306696A1 Methods for Resolving Convoluted Peaks in a Chromatogram 有权
标题翻译：解决色谱峰的方法
公开(公告)号：US20080306696A1
公开(公告)日：2008-12-11
申请号：US12159213
申请日：2007-02-06
申请人： Alexandre M. Izmailov , Murugathas Yuwaraj
发明人： Alexandre M. Izmailov , Murugathas Yuwaraj
IPC分类号： G06F19/00
CPC分类号： G01N30/8624 , G01N30/8631
摘要： The present invention relates to methods for resolving convoluted peaks in a chromatogram into one or more constituent peaks using peak resolution values. The peaks methods of the invention determine empirical peak resolution values of “well-defined” or “isolated” peaks in the data, then extrapolate these empirical resolution values to peaks in neighboring regions to predict the number of constituent peaks at a given peak position. Predicted peak resolution values are compared to observed peak resolution values of low-resolution or convoluted peaks to determine the number of constituent peaks in the convoluted peaks. These methods enable extension of the region of data that can used for identifying nucleotide sequences, and increase base-calling accuracy in the low-resolution region (end region) of data.
摘要翻译：本发明涉及使用峰值分辨率将色谱图中的卷曲峰分解成一个或多个组成峰的方法。本发明的峰方法确定数据中“明确”或“隔离”峰的经验峰分辨率值，然后将这些经验分辨率值推算到相邻区域中的峰值，以预测在给定峰位置处的构成峰的数量。将预测的峰值分辨率值与观察到的低分辨率或卷积峰值的峰值分辨率进行比较，以确定卷积峰值中的组成峰数。这些方法能够扩展可用于识别核苷酸序列的数据区域，并增加数据的低分辨率区域（结束区域）中的基本呼叫精度。

3. 发明授权

US06397150B1 Method and apparatus for sequencing of DNA using an internal calibrant 失效
标题翻译：使用内部校准物测序DNA的方法和装置
公开(公告)号：US06397150B1
公开(公告)日：2002-05-28
申请号：US09628736
申请日：2000-07-27
申请人： Alexandre M. Izmailov
发明人： Alexandre M. Izmailov
IPC分类号： C12Q168
CPC分类号： G06F19/22 , C12Q1/6869 , C12Q2545/101
摘要： For evaluation of a target DNA sequence, a sample mixture is prepared containing one or more sets of sequencing polynucleotide fragments, each set containing fragments having lengths indicative of the positions of at least one base within the target DNA sequence. These sequencing fragment sets are each labeled with a different type of label (for example fluorescent labels). The sample mixture also includes a set of calibrant polynucleotide fragments having a plurality of known fragment lengths. The calibrant polynucleotide fragments are labeled with a spectroscopically-distinguishable calibrant label. The sample mixture is then electrophoretically separated to separate the polynucleotide fragments as a function of fragment length. Real-time detection is used to detect the label(s) on the set(s) of sequencing fragments and the calibrant label as they migrate in a common lane of the separation medium to produce a sequencing data trace and a calibrant data trace. The calibrant peaks are then used to define a set of coefficients for linearizing the sequencing data trace from each lane to a common corrected time scale in which the peaks from each lane are evenly spaced. The linearized sequencing data traces are then aligned by assigning base position numbers to each peak in the sequencing data traces, and these aligned traces are used for base calling.
摘要翻译：为了评估靶DNA序列，制备含有一组或多组测序多聚核苷酸片段的样品混合物，每组测序多核苷酸片段含有长度指示靶DNA序列中至少一个碱基的位置的片段。这些测序片段组各自用不同类型的标记（例如荧光标记）标记。样品混合物还包括一组具有多个已知片段长度的校准多核苷酸片段。校准的多核苷酸片段用光谱可区分的校准物标记物标记。然后将样品混合物电泳分离，以分离作为片段长度的函数的多核苷酸片段。使用实时检测来检测序列片段和校准物标签集合上的标签，因为它们在分离介质的共同通道中迁移，以产生测序数据跟踪和校准数据跟踪。然后使用校准峰来定义用于将来自每个通道的测序数据轨迹线性化到公共校正时间标度的一组系数，其中来自每个通道的峰均匀间隔。然后通过为测序数据轨迹中的每个峰分配基本位置编号来对齐线性化的测序数据轨迹，并且这些对齐的轨迹用于基本调用。

4. 发明授权

US06110339A Nanofabricated separation matrix for analysis of biopolymers and methods of making and using same 失效
标题翻译：用于生物聚合物分析的纳米分离基质及其制备和使用方法
公开(公告)号：US06110339A
公开(公告)日：2000-08-29
申请号：US973932
申请日：1997-12-16
申请人： Thomas D. Yager , Paul Waterhouse , Alexandre M. Izmailov , Bruno Maruzzo , John K. Stevens , Marina T. Larson
发明人： Thomas D. Yager , Paul Waterhouse , Alexandre M. Izmailov , Bruno Maruzzo , John K. Stevens , Marina T. Larson
IPC分类号： G01N27/447
CPC分类号： G01N27/44704 , G01N27/44773 , G01N27/44791 , Y10T436/143333
摘要： Separation matrices useful in the formation of solid-state mm- to cm-scale devices for the rapid, high-resolution separation of single-stranded DNA ladder bands generated by the Sanger dideoxy- or Maxam/Gilbert chemical DNA sequencing procedures are formed from a solid support (1) having a plurality of posts (4) disposed on a first major surface thereof to form an obstacle course of posts (4) and pores (5). The posts are arranged in a regular X, Y array and are separated one from another by a distance of 100 nm or less, preferably 10 to 30 nm, and are optionally separated into lanes 2. The separation matrix can be manufactured by first forming a mold, preferably a reusable mold using lithography techniques. The mold is the reverse of the desired pattern of posts and pores of the obstacle course, and is used for casting the obstacle course. The cast obstacle course is then fused to a solid support and separated from the mold. Alternatively, the separation matrix can be formed from a polymer which undergoes specific and quantifiable swelling in the presence of a selected chemical compound. In this case, the matrix is cast on a mold in a conventional manner with a spacing between posts greater than the desired final spacing of 100 nm or less. For use, a buffer solution saturated with the specific chemical agent that controls swelling is added, causing the posts to swell to a defined amount to achieve the desired separation.
摘要翻译： PCT No.PCT / US96 / 09999 Sec。 371日期：1997年12月16日 102（e）日期1997年12月16日PCT提交1996年6月7日PCT公布。出版物WO96 / 42012 PCT 日期1996年12月27日用于形成固态mm至cm尺度装置的分离基质用于快速，高分辨率分离由Sanger双脱氧或Maxam / Gilbert化学DNA测序产生的单链DNA梯形带步骤由具有设置在其第一主表面上的多个柱（4）的固体支撑件（1）形成，以形成柱（4）和孔（5）的障碍物路线。柱以规则的X，Y阵列布置，并且彼此分离一个距离为100nm或更小，优选为10至30nm，并且任选地分离成通道2.分离基体可以通过首先形成模具，优选使用光刻技术的可重复使用的模具。模具与障碍物路线的柱和孔的期望图案相反，并且用于铸造障碍物路线。然后将铸造的障碍物道路融合到固体支撑物并与模具分离。或者，分离基质可以由在所选择的化合物存在下经历特异性和可定量溶胀的聚合物形成。在这种情况下，基体以常规方式在模具上铸造，柱之间的间距大于期望的最终间距为100nm或更小。为了使用，加入饱和了特定化学试剂的缓冲溶液以控制溶胀，导致柱膨胀至规定的量以达到所需的分离。

5. 发明申请

US20080306694A1 Methods for Detecting Peaks in a Nucleic Acid Data Trace 审中-公开
标题翻译：检测核酸数据痕迹中的峰的方法
公开(公告)号：US20080306694A1
公开(公告)日：2008-12-11
申请号：US12158766
申请日：2007-02-06
申请人： Alexandre M. Izmailov , Murugathas Yuwaraj
发明人： Alexandre M. Izmailov , Murugathas Yuwaraj
IPC分类号： C12Q1/68 , G06F19/00
CPC分类号： G16B30/00 , C12Q1/6869
摘要： The present invention relates to methods and apparatus for detecting peaks in a sample nucleic acid data trace derived from a sample polynucleotide by (a) receiving a sequence signature of a reference polynucleotide, wherein the sequence signature comprises a profile of peak height at one or more peak position of a nucleic acid sequence data trace of one or more of reference polynucleotides; (b) receiving a sample nucleic acid sequence data trace of a sample polynucleotide corresponding to the reference polynucleotide, wherein the sample nucleic acid sequence data trace comprises a value of peak height at one or more peak position corresponding to the peak positions of the sequence signature; and (c) detecting peaks in the sample nucleic acid data trace having a peak height that correlates with the profile of peak height of the sequence signature at a corresponding peak position.
摘要翻译：本发明涉及用于通过（a）接收参考多核苷酸的序列特征来检测衍生自样品多核苷酸的样品核酸数据曲线中的峰的方法和装置，其中序列特征包括在一个或多个一个或多个参考多核苷酸的核酸序列数据痕迹的峰位置; （b）接收对应于所述参照多核苷酸的样品多核苷酸的样品核酸序列数据迹线，其中所述样品核酸序列数据迹线包括对应于所述序列签名的峰位置的一个或多个峰位置处的峰高值值 ; 和（c）检测样品核酸数据迹线中具有与相应峰位置处的序列特征峰高度分布相关的峰高的峰。

6. 发明授权

US06436641B1 Method and apparatus for DNA sequencing 失效
标题翻译：用于DNA测序的方法和装置
公开(公告)号：US06436641B1
公开(公告)日：2002-08-20
申请号：US09550467
申请日：2000-04-17
申请人： Alexandre M. Izmailov
发明人： Alexandre M. Izmailov
IPC分类号： C12O168
CPC分类号： G01N27/44726 , C12Q1/6869 , G01N27/44721 , C12Q2565/137 , C12Q2537/143 , C12Q2535/101
摘要： The sequence of a target DNA molecule is determined by preparing four chain termination reaction mixtures, one for each base type. The first set of fragments, indicative of the positions of a first type of base, are labeled with a first fluorescent label. The second set of fragments, indicative of the positions of a second type of base, are labeled with a second fluorescent label different from the first fluorescent label. The third set of fragments, indicative of the positions of a third type of base, are labeled with a third fluorescent label, different from the first and second fluorescent labels or with at least two labels, including at least one fluorescent label selected from among the first, second and third fluorescent labels. The fourth set of fragments, indicative of the positions of a fourth type of base, are labeled differently from the third set of chain-termination fragments and with at least two different species of labels including at least one fluorescent label selected from among the first, second and third fluorescent labels. Thus, a total of only three fluorescent labels are required to label the DNA sequencing fragments. The first, second, third and fourth sets of chain-termination fragments are loaded onto the same lane of an electrophoresis separation medium and separated in an electric field. The separated fragments are detected in real-time as they migrate in the electrophoresis separation medium by irradiating the separated fragments with an excitation beam and collecting light emitted by the fluorescent labels in three optical channels. The signals from three optical channels are evaluated to determine a DNA sequence for the target species. This evaluation can be done with a specifically programmed computer.
摘要翻译：靶DNA分子的序列通过制备四种链终止反应混合物来确定，每种碱基类型一种。指示第一类碱基位置的第一组片段用第一荧光标记标记。指示第二类碱基位置的第二组片段用不同于第一荧光标记的第二荧光标记进行标记。指示第三类碱基位置的第三组片段用不同于第一和第二荧光标记或至少两个标记的第三荧光标记进行标记，包括至少一种选自以下的荧光标记：第一，第二和第三荧光标记。指示第四类碱基的位置的第四组片段与第三组链终止片段不同地标记，并且与至少两种不同种类的标记物包括至少一种选自第一类型，第二和第三荧光标记。因此，需要总共只有三个荧光标记来标记DNA测序片段。将第一，第二，第三和第四组链终止片段加载到电泳分离介质的相同泳道上，并在电场中分离。分离的片段通过在电泳分离介质中迁移而被检测，通过用激发光束照射分离的片段并且收集由三个光学通道中的荧光标记发射的光。评估来自三个光学通道的信号以确定靶物种的DNA序列。该评估可以用专门编程的计算机完成。

7. 发明授权

US07386399B1 Method and apparatus for alignment of DNA sequencing data traces 失效
标题翻译：用于DNA测序数据追踪的方法和装置
公开(公告)号：US07386399B1
公开(公告)日：2008-06-10
申请号：US09827432
申请日：2001-04-06
申请人： Alexandre M. Izmailov , Thomas D. Yager
发明人： Alexandre M. Izmailov , Thomas D. Yager
IPC分类号： G01N33/48
CPC分类号： G06F19/22 , C12Q1/6869 , C12Q2545/101
摘要： The present invention is directed to a method for alignment of nucleic acid data traces. The method involves selecting reference alignment points from among internal peaks representing highly conserved bases, preferably consisting of heterogeneous multiplets. The alignment points may also optionally include the primer peak and/or the full-length peak. Reference position numbers are assigned to these alignment points reflecting the known relative position of the alignment point, a sequence position number is assigned to peaks in the data traces so as to maximize assigning the sequence position number and the reference position number to the same base. Optionally, the method may include the step of determining the average peak spacing interval between alignment points and assigning a sequence position number to peaks occurring at the intervals. The data traces are then aligned based on the assigned sequence position numbers.
摘要翻译：本发明涉及核酸数据踪迹的比对方法。该方法包括从表示高度保守的碱基的内部峰中选择参考比对点，优选由异质多重峰组成。对准点还可以任选地包括引物峰和/或全长峰。将参考位置编号分配给反映对准点的已知相对位置的这些对准点，将序列位置编号分配给数据轨迹中的峰值，以便最大程度地将序列位置编号和参考位置编号分配给同一基准。可选地，该方法可以包括确定对准点之间的平均峰间隔间隔并将序列位置编号分配给以间隔发生的峰值的步骤。然后基于分配的序列位置数对数据轨迹。

8. 发明授权

US06176990B1 Micro-electrophoresis chip for moving and separating nucleic acids and other charged molecules 失效
标题翻译：用于移动和分离核酸和其他带电分子的微电泳芯片
公开(公告)号：US06176990B1
公开(公告)日：2001-01-23
申请号：US08973933
申请日：1997-12-16
申请人： Thomas D. Yager , Paul Waterhouse , Alexandre M. Izmailov , Bruno C. Maruzzo , John K. Stevens , Marina T. Larson
发明人： Thomas D. Yager , Paul Waterhouse , Alexandre M. Izmailov , Bruno C. Maruzzo , John K. Stevens , Marina T. Larson
IPC分类号： G01N27453
CPC分类号： G01N27/44773 , G01N27/44704 , G01N27/44791
摘要： A microelectrophoresis chip comprises a substrate in which there are formed one or more channels, one channel for each sample to be evaluated. The channels extend for the length of the chip, a distance of generally around 1 cm, and are about 1 to 10 &mgr;m wide and 1 to 10 &mgr;m in depth. The channels are filled with a homogeneous separation matrix which acts as an obstacle to the electrophoretic migration of the charged molecules. Microelectrodes disposed in the channels are used to induce an electric field within the homogeneous separation medium. When a voltage is applied across two or more of the microelectrodes, the charged molecules are induced to move and separate according to the electric field density, the type of solvent film, and the charge, shape and size of the charged molecule. The chip may further comprise detectors, such as light polarization detectors, fluorescence emission detectors, biosensors, electrochemical sensors or other microcomponents which may include sites for enzymatic or chemical manipulation of the moved or separated charged molecules.
摘要翻译：微电泳芯片包括其中形成一个或多个通道的基底，每个待评估样品的通道一个通道。通道延长芯片的长度，通常约1厘米的距离，宽度约为1至10微米，深度为1至10毫米。通道充满均匀的分离基质，其作为电荷分子的电泳迁移的障碍。设置在通道中的微电极用于在均匀分离介质内诱发电场。当电压施加到两个或更多个微电极上时，根据电场密度，溶剂膜的类型和带电分子的电荷，形状和尺寸，诱导带电分子移动和分离。芯片还可以包括诸如光偏振检测器，荧光发射检测器，生物传感器，电化学传感器或其它微元件的检测器，其可以包括用于酶或分离带电分子的酶或化学操作的位点。

9. 发明授权

US6054036A Electrophoresis gels and gel holders having fiber spacers and method of making same 失效
标题翻译：具有纤维间隔物的电泳凝胶和凝胶保持器及其制造方法
公开(公告)号：US6054036A
公开(公告)日：2000-04-25
申请号：US77304
申请日：1998-12-31
申请人： Alexandre M. Izmailov , Paul Waterhouse , Henryk Zaleski
发明人： Alexandre M. Izmailov , Paul Waterhouse , Henryk Zaleski
IPC分类号： G01N21/64 , G01N27/447 , G01N27/26
CPC分类号： G01N27/44721 , G01N27/44704
摘要： Gel holders for electrophoresis gels are made using clad fibers, particularly glass fibers as spacers between substrates. A plurality of fibers with a high-melting interior core and a low-melting external cladding are placed between a first planar substrate and a second planar substrate. The fibers are heated to a temperature sufficient to at least soften the exterior cladding of the fibers without softening the interior core of the fibers, and then cooled while they are in contact with the first and second substrates to solidify the exterior cladding. This adheres the fibers to the first and second substrates, and forms a gel chamber between said first and second substrates. The gel chamber has a thickness defined by interior core of the fibers. The fibers may be heated before or after the second substrate is placed over the top of the fibers. The gel holders thus formed may be filled immediately with a gel forming solution such as a polyacrylamide, or they may be stored indefinitely and used as needed.
摘要翻译： PCT No.PCT / CA96 / 00832 Sec。 371 1998年12月31日第 102（e）1998年12月31日PCT PCT 1996年12月12日PCT公布。 WO97 / 21995 PCT公开号日期1996年6月19日凝胶凝胶保持器使用包覆纤维制成，特别是作为衬底之间的间隔物的玻璃纤维。具有高熔点内芯和低熔点外包层的多根纤维被放置在第一平面基板和第二平面基板之间。纤维被加热到足以至少软化纤维的外包层的温度，而不软化纤维的内芯，然后在与第一和第二基底接触的同时冷却，以固化外包层。这将纤维粘附到第一和第二基底上，并在所述第一和第二基底之间形成凝胶室。凝胶室具有由纤维的内芯限定的厚度。纤维可以在将第二基底放置在纤维顶部之前或之后被加热。如此形成的凝胶保持器可立即用诸如聚丙烯酰胺的凝胶形成溶液填充，或者可以无限期地储存并根据需要使用。

10. 发明授权

US5897842A Method and apparatus for thermal cycling and for automated sample preparation with thermal cycling 失效
标题翻译：用于热循环的方法和设备以及用于热循环的自动化样品制备
公开(公告)号：US5897842A
公开(公告)日：1999-04-27
申请号：US703730
申请日：1996-08-27
申请人： James M. Dunn , James Leushner , John Renfrew , Paul Waterhouse , Alexandre M. Izmailov , Henryk Zaleski
发明人： James M. Dunn , James Leushner , John Renfrew , Paul Waterhouse , Alexandre M. Izmailov , Henryk Zaleski
IPC分类号： B01L7/00 , C12Q1/68 , C12Q1/70 , G01N35/00 , B01L9/00 , C12M3/02
CPC分类号： B01L7/52 , B01L7/525 , C12Q1/6841 , C12Q1/6881 , C12Q1/689 , C12Q1/703 , C12Q2600/156 , C12Q2600/16 , G01N2035/00237
摘要： An apparatus and method for thermally cycling a reaction mixture in a reaction vessel to expose the mixture to the varying temperatures necessary to, for example, achieve PCR amplification or the preparation of sequencing fragments using a cycle sequencing operation makes use of flow-through reaction vessels, such as capillary tubes, for the preparation and thermal cycling of reaction mixtures. In order to prevent loss of the reaction mixture from the vessels during heating, the thermal cycling apparatus of the invention provides means for sealing the proximal and distal end of each reaction vessel. The proximal ends can be sealed by coupling to a pump which permits movement of the samples within the reaction vessels. As to the distal ends, the reaction vessels can be sealed by pressing the distal end of each vessel against a sealing element with a conformable surface, or by immersing the distal end of each vessel in the reservoir of liquid, preferably of an oil, that is not miscible with the reaction mixture.
摘要翻译：在反应容器中热循环反应混合物以将混合物暴露于例如实现PCR扩增所需的变化温度或使用循环测序操作制备测序片段的装置和方法使用流通反应容器，如毛细管，用于反应混合物的制备和热循环。为了防止加热期间反应混合物从容器中的损失，本发明的热循环装置提供了用于密封每个反应容器的近端和远端的装置。近端可以通过联接到允许样品在反应容器内移动的泵来密封。对于远端，可以通过将每个容器的远端压靠具有适形表面的密封元件，或通过将每个容器的远端浸入液体储存器（优选油）中来密封反应容器，与反应混合物不混溶。

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