公开(公告)号：US06303303B1

公开(公告)日：2001-10-16

申请号：US09190756

申请日：1998-11-12

申请人： Ronald J. Green ,  Vrijmoed Chi ,  Rodney D. Gilchrist ,  Gregory Dee ,  John K. Stevens

发明人： Ronald J. Green ,  Vrijmoed Chi ,  Rodney D. Gilchrist ,  Gregory Dee ,  John K. Stevens

IPC分类号： C12Q168

CPC分类号： G01N27/44721 ,  G01N27/44717 ,  G06F19/18 ,  G06F19/22 ,  Y10T436/143333

摘要： Normalization of experimental fragment patterns for nucleic acid polymers having putatively known sequences starts with obtaining at least one raw fragment pattern for the experimental sample. The raw fragment pattern represents the positions of a selected nucleic acid base within the polymer as a function of migration time or distance. This raw fragment pattern is conditioned using conventional baseline correction and noise reduction technique to yield a clean fragment pattern. The clean fragment pattern is then evaluated to determine one or more “normalization coefficients.” These normalization coefficients reflect the displacement, stretching or shrinking, and rate of stretching or shrinking of the clean fragment, or segments thereof, which are necessary to obtain a suitably high degree of correlation between the clean fragment pattern and a standard fragment pattern which represents the positions of the selected nucleic acid base within a standard polymer actually having the known sequence as a function of migration time or distance. The normalization coefficients are then applied to the clean fragment pattern to produce a normalized fragment pattern which is used for base-calling in a conventional manner. This method may be implemented in an apparatus comprising a computer processor programmed to determine normalization coefficients for an experimental fragment pattern. This computer may be separate from the electrophoresis apparatus, or part of an integrated unit.

摘要翻译： 具有推定已知序列的核酸聚合物的实验片段模式的归一化从获得实验样品的至少一个原始片段图案开始。 原始片段图案表示聚合物内所选择的核酸碱基作为迁移时间或距离的函数的位置。 使用常规的基线校正和降噪技术调节该原始片段模式以产生干净的片段模式。 然后评估干净的片段模式以确定一个或多个“归一化系数”。 这些归一化系数反映了清洁片段或其片段的位移，拉伸或缩小以及拉伸或收缩速率，这些片段或片段是清洁片段图案与标示片段图案之间适当高程度的相关性所必需的， 实际上具有已知序列的标准聚合物内所选核酸碱基的位置作为迁移时间或距离的函数。 然后将归一化系数应用于干净的片段模式以产生用于以常规方式的基本呼叫的归一化的片段模式。 该方法可以在包括被编程为确定实验片段模式的归一化系数的计算机处理器的装置中实现。 该计算机可以与电泳装置或集成单元的一部分分开。

公开(公告)号：US5853979A

公开(公告)日：1998-12-29

申请号：US497202

申请日：1995-06-30

申请人： Ronald J. Green ,  Vrijmoed Chi ,  Rodney D. Gilchrist ,  Gregory Dee ,  John K. Stevens

发明人： Ronald J. Green ,  Vrijmoed Chi ,  Rodney D. Gilchrist ,  Gregory Dee ,  John K. Stevens

IPC分类号： C12Q1/68 ,  G01N27/447 ,  C12Q1/70 ,  G01N33/48 ,  G06K9/00

CPC分类号： G01N27/44721 ,  G01N27/44717 ,  G06F19/18 ,  G06F19/22 ,  Y10T436/143333

摘要： Normalization of experimental fragment patterns for nucleic acid polymers having putatively known sequences starts with obtaining at least one raw fragment pattern for the experimental sample. The raw fragment pattern represents the positions of a selected nucleic acid base within the polymer as a function of migration time or distance. This raw fragment pattern is conditioned using conventional baseline correction and noise reduction technique to yield a clean fragment pattern. The clean fragment pattern is then evaluated to determine one or more "normalization coefficients." These normalization coefficients reflect the displacement, stretching or shrinking, and rate of stretching or shrinking of the clean fragment, or segments thereof, which are necessary to obtain a suitably high degree of correlation between the clean fragment pattern and a standard fragment pattern which represents the positions of the selected nucleic acid base within a standard polymer actually having the known sequence as a function of migration time or distance. The normalization coefficients are then applied to the clean fragment pattern to produce a normalized fragment pattern which is used for base-calling in a conventional manner. This method may be implemented in an apparatus comprising a computer processor programmed to determine normalization coefficients for an experimental fragment pattern. This computer may be separate from the electrophoresis apparatus, or part of an integrated unit.

摘要翻译： 具有推定已知序列的核酸聚合物的实验片段模式的归一化从获得实验样品的至少一个原始片段图案开始。 原始片段图案表示聚合物内所选择的核酸碱基作为迁移时间或距离的函数的位置。 使用常规的基线校正和降噪技术调节该原始片段模式以产生干净的片段模式。 然后评估干净的片段模式以确定一个或多个“归一化系数”。 这些归一化系数反映了清洁片段或其片段的位移，拉伸或缩小以及拉伸或收缩速率，这些片段或片段是清洁片段图案与标示片段图案之间适当高程度的相关性所必需的， 实际上具有已知序列的标准聚合物内所选核酸碱基的位置作为迁移时间或距离的函数。 然后将归一化系数应用于干净的片段模式以产生用于以常规方式的基本呼叫的归一化的片段模式。 该方法可以在包括被编程为确定实验片段模式的归一化系数的计算机处理器的装置中实现。 该计算机可以与电泳装置或集成单元的一部分分开。

公开(公告)号：US06554987B1

公开(公告)日：2003-04-29

申请号：US09147916

申请日：1999-11-04

申请人： Rodney D. Gilchrist ,  Vrijmoed Chi

发明人： Rodney D. Gilchrist ,  Vrijmoed Chi

IPC分类号： G01N27447

CPC分类号： G06K9/00543 ,  G01N27/44717 ,  G01N27/44721 ,  G06F19/18 ,  G06F19/22

摘要： Data traces from four channels of an automated electrophoresis detection apparatus are aligned by identifying peaks in each of the four data traces; optionally normalizing the data traces to achieve a uniform peak height; combining the four data traces in an initial alignment; and determining coefficients of shift and stretch for selected data points within each data trace. The coefficients are determined by optimizing a cost function which reflects the extent of overlap of peaks in the combined normalized data traces to which the coefficients have been applied. The cost function is optimized when the extent of overlap is at a minimum. The coefficients are then used to generate a warp function for each data trace. These warp functions are applied to their respective data traces to produce four warped data traces which are aligned to form an aligned data set. The aligned data set may be displayed on a video screen of a sequencing apparatus, or may be used as the data set for a base-calling process.

摘要翻译： 通过识别四个数据迹线中的每一个中的峰值来对齐自动电泳检测装置的四个通道的数据迹线; 可选地归一化数据轨迹以实现均匀的峰高; 在初始对齐中组合四条数据轨迹; 并确定每个数据轨迹内所选数据点的偏移和拉伸系数。 通过优化成本函数来确定系数，该成本函数反映了已经应用系数的组合归一化数据轨迹中的峰的重叠程度。 当重叠程度最小时，优化成本函数。 然后，系数用于为每个数据跟踪生成warp函数。 这些翘曲函数被应用于它们各自的数据迹线以产生四个翘曲的数据迹线，其被对准以形成对准的数据集。 对准的数据集可以显示在排序装置的视频屏幕上，或者可以用作基本呼叫处理的数据集。

公开(公告)号：US5916747A

公开(公告)日：1999-06-29

申请号：US670534

申请日：1996-06-27

申请人： Rodney D. Gilchrist ,  Vrijmoed Chi

发明人： Rodney D. Gilchrist ,  Vrijmoed Chi

IPC分类号： C12Q1/68 ,  G01N27/447

CPC分类号： G06K9/00543 ,  G01N27/44717 ,  G01N27/44721 ,  G06F19/18 ,  G06F19/22

摘要： Data traces from four channels of an automated electrophoresis detection apparatus are aligned by identifying peaks in each of the four data traces; normalizing the heights of the peaks in each of the data traces to a common value to generate four normalized data traces; combining the four normalized data traces in an initial alignment; and determining coefficients of shift and stretch for selected data points within each normalized data trace. The coefficients are determined by optimizing a cost function which reflects the extent of overlap of peaks in the combined normalized data traces to which the coefficients have been applied. The cost function is optimized when the extent of overlap is at a minimum. The coefficients are then used to generate a warp function for each normalized data trace. These warp function are applied to their respective data traces to produce four warped data traces which are aligned to form an aligned data set. The aligned data set may be displayed on a video screen of a sequencing apparatus, or may be used as the data set for a base-calling process.

摘要翻译： 通过识别四个数据迹线中的每一个中的峰值来对齐自动电泳检测装置的四个通道的数据迹线; 将每个数据轨迹中的峰值的高度归一化为公共值，以生成四个标准化数据轨迹; 在初始对准中组合四个归一化数据轨迹; 并确定每个归一化数据轨迹内所选数据点的偏移和拉伸系数。 通过优化成本函数来确定系数，该成本函数反映了已经应用系数的组合归一化数据轨迹中的峰的重叠程度。 当重叠程度最小时，优化成本函数。 然后，系数用于为每个归一化数据轨迹生成翘曲函数。 这些翘曲函数被应用于它们各自的数据迹线以产生四个翘曲的数据迹线，其被对准以形成对齐的数据集。 对准的数据集可以显示在排序装置的视频屏幕上，或者可以用作基本呼叫处理的数据集。

公开(公告)号：US20110090846A1

公开(公告)日：2011-04-21

申请号：US12785154

申请日：2010-05-21

申请人： Thomas Hao ,  Tom Papadopoulos ,  Florin Tarcoci ,  Rodney D. Gilchrist ,  John K. Stevens ,  Christopher W. Verge ,  Paul Waterhouse ,  M. Jason August

发明人： Thomas Hao ,  Tom Papadopoulos ,  Florin Tarcoci ,  Rodney D. Gilchrist ,  John K. Stevens ,  Christopher W. Verge ,  Paul Waterhouse ,  M. Jason August

IPC分类号： H04W88/08

CPC分类号： G06Q10/087

摘要： A portable access point device is formed from a handheld computing device; an environmentally hardened case disposed around the computing device, and an access point module for reading and writing data to low frequency active radiating transceiver tags, such as RuBee® tags. The access point module is connected to the handheld computing device and the environmentally hardened case to provide a unitary handheld device, and the access point module transfers data between the handheld computing device and tags within communication range of the device.

摘要翻译： 便携式接入点设备由手持计算设备形成; 设置在计算设备周围的环境恶化的外壳，以及用于读取和写入数据到低频主动辐射收发器标签（例如RuBee标签）的接入点模块。 接入点模块连接到手持式计算设备和环境坚固的外壳以提供一体的手持设备，并且接入点模块在手持式计算设备和设备的通信范围内的标签之间传送数据。

公开(公告)号：US20080129456A1

公开(公告)日：2008-06-05

申请号：US11768328

申请日：2007-06-26

申请人： John K. Stevens ,  David Cramer ,  Tom Packert ,  Paul Waterhouse ,  James W. Cassidy ,  Rodney D. Gilchrist

发明人： John K. Stevens ,  David Cramer ,  Tom Packert ,  Paul Waterhouse ,  James W. Cassidy ,  Rodney D. Gilchrist

IPC分类号： H04Q5/22

CPC分类号： F02D41/0002 ,  Y02T10/42

摘要： A system has tags communicating by means of low frequency (below 1 megahertz) with routers which in turn communicate with nameservers. The tags have IP addresses, either explicitly programmed into the tags or associated in a virtual way with the tags. Lookups analogous to domain lookups permit human-friendly inquiries of tag status and location. Static (battery-backed) RAM in a tag permits great versatility in the localized function of the tag.

摘要翻译： 系统具有通过低频（低于1兆赫）进行通信的标签，路由器又与名称服务器进行通信。 这些标签具有IP地址，无论是明确地编入标签还是以虚拟方式与标签相关联。 类似于域查找的查找允许对标签状态和位置进行人性化的查询。 标签中的静态（电池供电）RAM允许标签的本地化功能具有很大的通用性。

公开(公告)号：US06404907B1

公开(公告)日：2002-06-11

申请号：US09345613

申请日：1999-06-25

申请人： Rodney D. Gilchrist ,  James M. Dunn

发明人： Rodney D. Gilchrist ,  James M. Dunn

IPC分类号： G06K900

CPC分类号： G06F19/22 ,  C12Q1/6869

摘要： Nucleic acid polymers are sequenced by obtaining forward and reverse data sets for forward and reverse strands of a sample nucleic acid polymer. The apparent base sequences of these forward and reverse sets are determined and the apparent sequences are compared to identify any deviations from perfect complementarity. Any such deviation presents a choice between two bases, only one of which is correct. A confidence algorithm is applied to the peaks in the data sets associated with a deviation to arrive at a numerical confidence value for each of the two base choices. These confidence values are compared to each other and to a predetermined threshold, and the base represented by the peak with the better confidence value is assigned as the “correct” base, provided that its confidence value is better than the threshold. The confidence value takes into account at least one, and preferably more than one of several specific characteristics of the peaks in the data set that were not complementary.

摘要翻译： 通过获得样品核酸聚合物的正向和反向链的正向和反向数据集来对核酸聚合物进行测序。 确定这些正向和反向集合的表观碱基序列，并比较表观序列以鉴定与完全互补性的任何偏差。 任何这样的偏差在两个基础之间作出选择，其中只有一个是正确的。 将置信算法应用于与偏差相关联的数据集中的峰值，以获得两个基本选择中的每一个的数值置信度值。 将这些置信度值彼此进行比较并达到预定阈值，并且将具有较好置信度值的峰值表示的基数分配为“正确”基数，条件是其置信度值优于阈值。 置信度值考虑了数据集中不相互补充的峰的至少一个，优选多于一个特征。

公开(公告)号：US5981186A

公开(公告)日：1999-11-09

申请号：US892003

申请日：1997-07-14

申请人： Chris Gabe ,  Rodney D. Gilchrist

发明人： Chris Gabe ,  Rodney D. Gilchrist

IPC分类号： C12Q1/68 ,  G01N27/447 ,  C12P19/34

CPC分类号： G01N27/44726 ,  C12Q1/6869

摘要： The sequence of a target nucleic acid polymer can be determined by (a) performing a first chain-extension sequencing reaction on the target nucleic acid polymer in a reaction mixture containing first and second chain-terminators to produce a first product mixture containing commonly-labeled polynucleotide fragments complementary to a first strand of the target nucleic acid polymer, each fragment in the mixture being terminated with the first or second chain-terminator; (b) performing a second chain extension sequencing reaction on the target nucleic acid polymer in a reaction mixture containing the first and a third chain-terminator to produce a second product mixture containing commonly-labeled polynucleotide fragments complementary to the first strand of the target nucleic acid polymer, each fragment in the mixture being terminated with the first or the third chain-terminator, said first, second and third chain-terminators each being different; and (c) evaluating the lengths of the polynucleotide fragments in the first and second product mixtures to determine the sequence of the target nucleic acid polymer. In the evaluation step, the first and second product mixtures can be evaluated in two separate lanes of a gel, in which case the labels employed in the two chain extension sequencing reactions can be the same. Alternatively, if the labels employed in the two chain extension reactions are different and spectroscopically distinguishable from one another, the first and second product mixtures can be combined before electrophoresis and the entire analysis can be performed in a single lane of a gel.

摘要翻译： 靶核酸聚合物的序列可以通过（a）在含有第一和第二链终止剂的反应混合物中对目标核酸聚合物进行第一链延伸测序反应来测定，以产生含有常规标记的第一产物混合物 与靶核酸聚合物的第一链互补的多核苷酸片段，混合物中的每个片段用第一或第二链终止子终止; （b）在含有第一和第三链终止子的反应混合物中对目标核酸聚合物进行第二链延伸测序反应以产生含有与靶核酸的第一链互补的通常标记的多核苷酸片段的第二产物混合物 所述混合物中的每个片段用第一或第三链终止剂终止，所述第一，第二和第三链终止剂各自不同; 和（c）评估第一和第二产物混合物中的多核苷酸片段的长度以确定靶核酸聚合物的序列。 在评估步骤中，第一和第二产物混合物可以在两个独立的凝胶通道中进行评估，在这种情况下，两个延伸测序反应中使用的标记可以相同。 或者，如果两个延伸反应中使用的标记是不同的并且在光谱上彼此区分，则可以在电泳之前组合第一和第二产物混合物，并且可以在凝胶的单一泳道中进行整个分析。

公开(公告)号：US6024854A

公开(公告)日：2000-02-15

申请号：US96227

申请日：1998-06-11

申请人： Rodney D. Gilchrist

发明人： Rodney D. Gilchrist

IPC分类号： G01N27/447 ,  G01N27/26

CPC分类号： G01N27/44743

摘要： Electrophoretic separation of an analyte species in a sample is achieved with increased resolution by loading the sample onto a loading site of an electrophoresis gel, said loading site having a gel/buffer interface and then applying a focusing electric field to a first pair of electrodes to cause the analyte species to migrate to a narrow region disposed at or near the loading site to produce a focused sample. Then a separation electric field is applied to cause the analyte species in the focused sample to migrate through the electrophoresis gel and to be separated into bands. This method is preferably performed in an electrophoresis apparatus that is particularly adapted to practicing the method by virtue of the a pair of focusing electrodes which are positioned to cause migration of sample to a narrow region near the buffer/gel interface within the sample loading site of the gel. This actual location of this narrow region may be in a buffer region over the gel, or just within the gel near the loading site, for example within 500 microns of the loading site.

摘要翻译： 通过将样品加载到电泳凝胶的加载位置上，通过提高分辨率来实现样品中分析物种的电泳分离，所述加载位点具有凝胶/缓冲液界面，然后将聚焦电场施加到第一对电极 使分析物种迁移到设置在装载位置处或附近的狭窄区域以产生聚焦样品。 然后施加分离电场以使聚焦样品中的分析物质迁移通过电泳凝胶并分离成条带。 该方法优选在电泳装置中进行，该电泳装置特别适于通过一对聚焦电极来实施该方法，所述聚焦电极被定位成使得样品迁移到样品加载位置内的缓冲液/凝胶界面附近的窄区域 凝胶。 该窄区域的该实际位置可以在凝胶上方的缓冲区域中，或者仅在加载位置附近的凝胶内，例如在装载位点的500微米内。