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1. 发明申请

WO02070731A2 METHODS AND PRIMERS FOR EVALUATING HIV-1 MUTATIONS 审中-公开
标题翻译：用于评估HIV-1突变的方法和准则
公开(公告)号：WO02070731A2
公开(公告)日：2002-09-12
申请号：PCT/US0206632
申请日：2002-03-05
申请人： VISIBLE GENETICS INC , LLOYD ROBERT M JR , UZGIRIS AREJAS , HUONG JOE TZONG-JYH
发明人： LLOYD ROBERT M JR , UZGIRIS AREJAS , HUONG JOE TZONG-JYH
IPC分类号： G01N33/53 , C12N15/09 , C12Q1/68 , C12Q1/70 , G01N33/566 , C12Q
CPC分类号： C12Q1/703
摘要： Primer sequences and a method of using such sequences for the genotyping of HIV-1-containing samples, particularly those which have failed genotyping analysis are provided using primer sequences designed for analysis of Group B subtype of the Group M type virus. For example, a combination of primers, including at least one species of forward primer and at least one species of reverse primer where the forward primer(s) can be represented by the degenerate sequence: RARRARGGGCTGYTGGARATGTS (Seq. ID No. 9) and the reverse primer(s) can be represented by the degenerate sequence: BCHTYACYTTRATCCCSGVRTARATYTGACT (Seq. ID No.: 10) or BCHTYACYTTRATCCCSGVRTARATYTGAC (Seq. ID No. 12) are suitably employed. The selected primers, one or more from each group, can be used as reverse transcription, amplification and sequencing primers and are suitably packaged in a genotyping kit. Such a kit may include reagents in addition to the primers, such as an RNase inhibitor, a reverse transcriptase, a polymerase, and/or dNTP and ddNTP feedstocks.
摘要翻译：使用设计用于分析组M型病毒的B组亚型的引物序列，提供引物序列和使用这些序列用于基因分型含HIV-1的样品，特别是那些基因分型失败的基因分型的方法。例如，包括至少一种正向引物和至少一种反向引物的引物的组合，其中正向引物可以由简并序列表示：RARRARGGGCTGYTGGARATGTS（Seq.ID No.9）和反向引物可以由简并序列表示：BCHTYACYTTRATCCCSGVRTARATYTGACT（Seq.ID No .: 10）或BCHTYACYTTRATCCCSGVRTARATYTGAC（Seq.ID No.12）。所选择的引物，每个组中的一个或多个可用作逆转录，扩增和测序引物，并且适当地包装在基因分型试剂盒中。这样的试剂盒可以包括除了引物外的试剂，例如RNA酶抑制剂，逆转录酶，聚合酶和/或dNTP和ddNTP原料。

2. 发明申请

WO9841650A3 METHOD AND KIT FOR QUANTITATION AND NUCLEIC ACID SEQUENCING OF NUCLEIC ACID ANALYTES IN A SAMPLE 审中-公开
标题翻译：核酸分析仪在样品中的定量和核酸序列的方法和工具
公开(公告)号：WO9841650A3
公开(公告)日：1999-01-14
申请号：PCT/CA9800240
申请日：1998-03-18
申请人： VISIBLE GENETICS INC , LACROIX JEAN MICHEL , DUNN JAMES M
发明人： LACROIX JEAN-MICHEL , DUNN JAMES M
IPC分类号： C12Q1/68 , C12Q1/70
CPC分类号： C12Q1/6851 , C12Q1/703
摘要： A method for quantitative and qualitative analysis of a nucleic acid analyte in a sample suspected to contain the nucleic acid analyte first combines the sample with a control nucleic acid, and two primer pairs, a first primer pair effective to amplify a conserved region of the nucleic acid analyte if present in the sample to produce a conserved fragment having a first length and to amplify the control nucleic acid to produce a control fragment having a second length different from the first length, and a second primer pair effective to amplify a second region of the nucleic acid analyte to produce a sequencing fragment. One member of the first primer pair is labeled with a detectable label, and one member of the second primer pair may be labeled with a label such as biotin effective to permit capture of the primer. The combined mixture is then processed to amplify the sample and control nucleic acid using the fist and second primer pairs to produce an amplification product mixture containing conserved fragments, sequencing fragments and control fragments when the nucleic acid analyte is present in the sample, and only control fragment when the nucleic acid analyte is not present in the sample. This product mixture is analyzed to determine the relative amounts of conserved fragments and control fragments in the amplification product mixture to quantify the amount of nucleic acid analyte in the sample and used as a starting point for a reaction to determine the sequence of the sequencing fragment.

3. 发明申请

WO1998011259A2 COMPOSITION, METHOD AND KIT FOR DETECTION AND IDENTIFICATION OF SEXUALLY TRANSMITTED DISEASE MICROORGANISMS 审中-公开
标题翻译：用于检测和鉴定性传播疾病微生物的组合物，方法和试剂盒
公开(公告)号：WO1998011259A2
公开(公告)日：1998-03-19
申请号：PCT/CA1997000660
申请日：1997-09-09
申请人： VISIBLE GENETICS INC. , CHERNESKY, Max , LUINSTRA, Kathleen , JANG, Dan , CHONG, Sylvia , MAHONY, James, B. , DUNN, James, M.
发明人： VISIBLE GENETICS INC.
IPC分类号： C12Q01/70
CPC分类号： C12Q1/689 , C12Q2600/16
摘要： Co-amplification and detection of at least three sexually transmitted disease pathogens in DNA isolated from a patient sample are achieved by combining the isolated DNA with at least first, second and third oligonucleotide primer pairs for amplification of a gene fragments from first, second and third different sexually transmitted disease pathogens. One of the primers in each primer pair is labeled with a detectable label. The first, second and third oligonucleotide primer pairs are reacted with the isolated DNA in an amplification reaction to generate an amplification product mixture that contains amplified gene fragments from either or both of the first and second sexually transmitted disease pathogens, depending on whether or not the first and second sexually transmitted disease pathogens are present in the patient sample. Amplified gene fragments in the amplification product mixture are then evaluated, for example by gel electrophoresis to determine whether amplified gene fragments from the first, second or third sexually transmitted disease pathogen are present.
摘要翻译：分离的DNA中至少三种性传播疾病病原体的偶联扩增和检测在取自患者的样品中进行，将分离的DNA与至少第一，第二和第三用于扩增来自不同于性传播疾病的第一，第二和第三病原体的基因片段的一对寡核苷酸引物。每对引物的引物之一用可检测标记进行标记。第一对，第二对和第三对寡核苷酸引物在扩增反应中与分离的DNA反应以产生扩增产物混合物，所述扩增产物混合物含有第一或第二（或两者）性传播疾病病原体，取决于样品中是否存在第一和第二性传播疾病病原体。然后在扩增产物混合物中评估扩增的基因片段，例如通过凝胶电泳，以确定是否存在性传播疾病的第一，第二或第三病原体的扩增基因片段。

4. 发明申请

WO1998000708A1 METHOD AND APPARATUS FOR ALIGNMENT OF SIGNALS FOR USE IN DNA BASE-CALLING 审中-公开
标题翻译：用于DNA基因检测中使用信号的方法和装置
公开(公告)号：WO1998000708A1
公开(公告)日：1998-01-08
申请号：PCT/CA1997000463
申请日：1997-06-26
申请人： VISIBLE GENETICS INC. , GILCHRIST, Rodney, D. , CHI, Vrijmoed
发明人： VISIBLE GENETICS INC.
IPC分类号： 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; 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。

5. 发明申请

WO1997041257A1 METHOD, COMPOSITIONS AND KIT FOR DETECTION AND IDENTIFICATION OF MICROORGANISMS 审中-公开
标题翻译：方法，组合物和试剂盒检测和鉴定微生物
公开(公告)号：WO1997041257A1
公开(公告)日：1997-11-06
申请号：PCT/US1997007133
申请日：1997-04-29
申请人： VISIBLE GENETICS INC. , LACROIX, Jean-Michel , LEUSHNER, James , HUI, May , DUNN, James, M. , LARSON, Marina, T.
发明人： VISIBLE GENETICS INC.
IPC分类号： C12Q01/68
CPC分类号： B01L7/525 , B01L7/52 , C12Q1/6841 , C12Q1/6858 , C12Q1/6869 , C12Q1/6881 , C12Q1/689 , C12Q1/703 , C12Q2600/156 , G01N2035/00237
摘要： Evaluation of a sample for the presence and qualitative nature of a microorganism can be performed in a single vessel by combining a natural abundance DNA sample with a sequencing mixture containing a primer pair, a thermally stable polymerase such as ThermoSequenase which incorporates dideoxynucleotides into an extending nucleic acid polymer at a rate which is no less than about 0.4 times the rate of incorporation of deoxynucleotides, nucleotide triphosphate feedstocks, and a chain terminating nucleotide triphosphate. The mixture is processed through multiple thermal cycles for annealing, extension and denaturation to produce a product mixture which is analyzed by electrophoresis.
摘要翻译：通过将天然丰度DNA样品与含有引物对的测序混合物，热稳定聚合酶如ThermoSequenase TM组合，可以在单个容器中评价样品的存在和定性性质，其将二脱氧核苷酸掺入延伸的核酸聚合物的速度不低于脱氧核苷酸，核苷酸三磷酸酯原料和链终止核苷酸三磷酸的引入速率的约0.4倍。通过多个热循环处理混合物进行退火，延伸和变性以产生通过电泳分析的产物混合物。

6. 发明申请

WO1997021996A1 ELECTROPHORESIS GELS AND GEL HOLDERS HAVING ADHESIVE AFFIXED FIBER SPACERS AND METHOD OF MAKING SAME 审中-公开
标题翻译：具有粘合纤维纤维间隔物的电泳胶凝胶和凝胶保持器及其制造方法
公开(公告)号：WO1997021996A1
公开(公告)日：1997-06-19
申请号：PCT/CA1996000833
申请日：1996-12-12
申请人： VISIBLE GENETICS INC. , IZMAILOV, Alexandre , ZALESKI, Henryk , WATERHOUSE, Paul
发明人： VISIBLE GENETICS INC.
IPC分类号： G01N27/447
CPC分类号： G01N27/44704
摘要： Gel holders for electrophoresis gels are made using fibers, particularly glass fibers, which are affixed to the substrates forming the gel holder using an adhesive. These gel holders can be made by placing a plurality of adhesive-coated fibers between a first planar substrate and a second planar substrate; and applying pressure to the outside of the substrates to adhere the fibers to the first and second substrates. This forms a gel chamber between the first and second substrates which has a thickness defined by diameter of the fibers. Alternatively, uncoated fibers may be laid down in pairs, with a line of adhesive disposed between each fiber of the pair. When the adhesive is cured, it binds the fibers in position as spacers. At the same time, the fibers isolate the adhesive from the gel compartment. In this way, interference of components of the adhesive with the polymerization of the gel in the gel chamber can be avoided. Gel holders formed using either of these methods 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：用于电泳凝胶的凝胶保持器使用纤维，特别是玻璃纤维制成，其使用粘合剂固定到形成凝胶保持器的基材上。这些凝胶保持器可以通过在第一平面基板和第二平面基板之间放置多个粘合剂涂覆的纤维来制造; 并向衬底外部施加压力以将纤维粘附到第一和第二衬底上。这在第一和第二基底之间形成凝胶室，其具有由纤维的直径限定的厚度。或者，未涂覆的纤维可以成对铺设，一对粘合剂布置在该对的每个纤维之间。当粘合剂固化时，其将纤维作为间隔物结合在适当位置。同时，纤维将胶粘剂与凝胶隔离隔离。以这种方式，可以避免粘合剂组分与凝胶室中的凝胶聚合的干扰。使用这些方法之一形成的凝胶容器可以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。

7. 发明申请

WO1997008344A3 METHOD FOR IDENTIFICATION OF MUTATIONS USING LIGATION OF MULTIPLE OLIGONUCLEOTIDE PROBES 审中-公开
公开(公告)号：WO1997008344A3
公开(公告)日：1997-03-06
申请号：PCT/US1996014020
申请日：1996-08-28
申请人： VISIBLE GENETICS INC. , YAGER, Thomas, D. , DUNN, James, M.
发明人： VISIBLE GENETICS INC.
IPC分类号： C12Q01/68

8. 发明申请

WO1997002488A1 METHOD AND SYSTEM FOR DNA SEQUENCE DETERMINATION AND MUTATION DETECTION 审中-公开
标题翻译：用于DNA序列测定和突变检测的方法和系统
公开(公告)号：WO1997002488A1
公开(公告)日：1997-01-23
申请号：PCT/US1996011130
申请日：1996-06-28
申请人： VISIBLE GENETICS INC. , GREEN, Ronald, J. , CHI, Vrijmoed , GILCHRIST, Rodney, D. , DEE, Gregory , STEVENS, John, K.
发明人： VISIBLE GENETICS INC.
IPC分类号： G01N27/447
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 timeor 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 serapate 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。该计算机可以从电泳装置或集成单元的一部分塞来。

9. 发明申请

WO1996001909A1 METHOD, REAGENTS AND KIT FOR DIAGNOSIS AND TARGETED SCREENING FOR p53 MUTATIONS 审中-公开
标题翻译：用于p53突变的诊断和靶向筛选的方法，试剂和试剂盒
公开(公告)号：WO1996001909A1
公开(公告)日：1996-01-25
申请号：PCT/US1995008605
申请日：1995-07-07
申请人： VISIBLE GENETICS INC. , DIAMANDIS, Eleftherios , DUNN, James, M. , STEVENS, John, K.
发明人： VISIBLE GENETICS INC.
IPC分类号： C12Q01/68
CPC分类号： C12Q1/6827 , C12Q1/6858 , C12Q1/686 , C12Q1/6869 , C12Q1/6886 , C12Q2600/16
摘要： Rapid and cost effective diagnosis of p53 mutations of a sample of patients is achieved by employing a selected plurality of diagnostic tools, in a hierarchy of increasing accuracy and cost per tool, in which each tool detects essentially no false positives. Diagnostic tests that may be included among the plurality of tests selected include, in order of increasing accuracy and cost: (a) immunoassays; (b) analysis of DNA from a patient sample by quantitative amplification of p53 exons using amplification primers complementary to intron regions flanking each exon and examination of the length or quantity of each amplified fragment for nucleotide insertions or deletions relative to the normal p53 gene. Preferably, the amplification primers are multiplexed so that more than one DNA fragment is amplified in a single vessel, using sets of primers which provide gene fragments of distinctive lengths when used to amplify a normal p53 gene; and (c) analysis of DNA from a patient sample by DNA sequencing of the p53 gene beginning with the sequencing of those regions most likely to harbor point mutations, and proceeding to sequence regions less likely to harbor point mutations.
摘要翻译：通过采用所选择的多种诊断工具，以提高每个工具的精度和成本的等级来实现对患者样品的p53突变的快速和成本有效的诊断，其中每个工具基本上不检测到假阳性。可以包括在所选择的多个测试中的诊断测试包括：提高准确性和成本的顺序：（a）免疫测定; （b）使用与每个外显子侧翼互补的内含子区域的扩增引物以及相对于正常p53基因的核苷酸插入或缺失的每个扩增片段的长度或数量的检测，通过定量扩增p53外显子来分析来自患者样品的DNA。优选地，扩增引物被多重化，使得在单个容器中扩增多于一个DNA片段，使用提供用于扩增正常p53基因的特异长度的基因片段的引物组; 和（c）通过对最可能存在点突变的那些区域的测序开始的p53基因的DNA测序从患者样品中分析DNA，并且进行到不太可能存在点突变的序列区域。

10. 发明申请

WO0000637A3 METHOD FOR SEQUENCING NUCLEIC ACIDS WITH REDUCED ERRORS 审中-公开
标题翻译：用于测量具有减少误差的核酸的方法
公开(公告)号：WO0000637A3
公开(公告)日：2000-02-17
申请号：PCT/CA9900589
申请日：1999-06-25
申请人： VISIBLE GENETICS INC
发明人： GILCHRIST RODNEY D , DUNN JAMES M
IPC分类号： C12Q1/68 , G06F19/22 , G06F17/00
CPC分类号： G06F19/22 , C12Q1/6869
摘要： In accordance with the invention, nucleic acid polymers are sequenced in a method comprising the steps of: a) obtaining forward and reverse data sets for forward and reverse strands of the sample nucleic acid; b) determining the apparent sequence of bases for the forward and reverse data sets; c) comparing the apparent forward and reverse sequences of basis for perfect complementarity to identify any deviations from complementarity in the apparent sequence, any such deviation presenting a choice between two bases, only one of which is correct; d) applying a confidence algorithm to peaks in the data set associated with a deviation to arrive at a numerical confidence value; and e) comparing each numerical confidence value to a predetermined threshold and selecting as the correct base the base represented by the peak which has the better numerical confidence value, provided that the numerical confidence value is better than the threshold. The confidence algorithm takes into account at least one, and preferably more than one of several specific characteristics of the peaks in the data sets that were not complementary.
摘要翻译：根据本发明，核酸聚合物的方法包括以下步骤：a）获得样品核酸正向和反向链的正向和反向数据集; b）确定正向和反向数据集的基数的表观序列; c）比较完美互补性的明显正向和反向序列以识别表观序列中与互补性的任何偏差，任何这样的偏差表示两个碱基之间的选择，其中仅一个是正确的; d）将置信算法应用于与偏差相关联的数据集中的峰值以得到数值置信度值; 以及e）将每个数字置信度值与预定阈值进行比较，并且选择具有较好数值置信度值的峰表示的基数作为正确基数，条件是数值置信度值优于阈值。置信度算法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。

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