公开(公告)号：US09957558B2

公开(公告)日：2018-05-01

申请号：US13458739

申请日：2012-04-27

Applicant: John Leamon ,  Mark Andersen ,  Michael Thornton

Inventor： John Leamon ,  Mark Andersen ,  Michael Thornton

IPC: C12Q1/68 ,  C12N15/10

CPC classification number: C12Q1/686 ,  C12N15/1065 ,  C12Q1/6806 ,  C12Q1/6855 ,  C12Q1/6874 ,  C12Q1/6886 ,  C12Q2600/16 ,  C12Q2521/307 ,  C12Q2525/101 ,  C12Q2525/191 ,  C12Q2537/143

Abstract: The present invention provides methods, compositions, kits, systems and apparatus that are useful for multiplex PCR of one or more nucleic acids present in a sample. In particular, various target-specific primers are provided that allow for the selective amplification of one or more target sequences. In one aspect, the invention relates to target-specific primers useful for the selective amplification of one or more target sequences associated with cancer or inherited disease. In some aspects, amplified target sequences obtained using the disclosed methods, kits, systems and apparatuses can be used in various downstream processes including nucleic acid sequencing and used to detect the presence of genetic variants.

公开(公告)号：US09322055B2

公开(公告)日：2016-04-26

申请号：US14009304

申请日：2012-03-30

Applicant: Gordon A. Janaway ,  Mark Andersen ,  Kornelija Zgonc ,  Michael Pallas ,  Marcin Sikora ,  Casey McFarland ,  Ferrier N. Le ,  Haopeng Wang ,  Jian Gong ,  Gothami Padmabandu

Inventor： Gordon A. Janaway ,  Mark Andersen ,  Kornelija Zgonc ,  Michael Pallas ,  Marcin Sikora ,  Casey McFarland ,  Ferrier N. Le ,  Haopeng Wang ,  Jian Gong ,  Gothami Padmabandu

IPC: C12Q1/68 ,  C12P19/34

CPC classification number: C12Q1/6886 ,  C12Q1/686 ,  C12Q2600/158 ,  C12Q2600/178 ,  G01N21/6486 ,  C12Q2537/16 ,  C12Q2563/143 ,  C12Q2563/159 ,  C12Q2565/626

Abstract: Methods and systems for quantification of a target nucleic acid in a sample are provided. The method includes forming a plurality of discrete sample portions. Each of the plurality of discrete sample portions comprising a portion of the sample, and a reaction mixture. The method further includes amplifying the plurality of discrete sample portions to form a plurality of discrete processed sample portions. At least one discrete processed sample portion containing nucleic acid amplification reaction products. Fluorescence signals are detected from the at least one of the plurality of discrete processed sample portions to determine a presence of the at least one target nucleic acid. The method also includes determining the respective volumes of the plurality of the plurality of discrete processed sample portions, and estimating the number of copies-per-unit-volume of the at least one target nucleic acid in the sample. Estimating the number of copies-per-unit-volume is based on the number of discrete processed sample portions determined to contain the at least one target nucleic acid therein.

Abstract translation: 提供了用于定量样品中靶核酸的方法和系统。 该方法包括形成多个离散的样本部分。 多个离散样品部分中的每一个包含样品的一部分和反应混合物。 该方法还包括放大多个离散样本部分以形成多个离散处理的样本部分。 至少一个离散加工的样品部分含有核酸扩增反应产物。 从所述多个离散处理样品部分中的至少一个检测荧光信号以确定所述至少一种靶核酸的存在。 该方法还包括确定多个多个离散处理的样本部分的相应体积，以及估计样品中至少一个靶核酸的每单位体积的拷贝数。 估计每单位体积的拷贝数是基于确定为在其中含有至少一种靶核酸的离散加工样品部分的数量。

公开(公告)号：US20060234252A1

公开(公告)日：2006-10-19

申请号：US11173569

申请日：2005-07-01

Applicant: Mark Andersen

Inventor： Mark Andersen

IPC: C12Q1/68

CPC classification number: C12Q1/683 ,  C12Q2523/125 ,  C12Q2521/501

Abstract: Methods for determining the methylation state of at least one target nucleotide that employ a reaction catalyzed by a structure-specific nuclease, typically coupled with a ligation reaction are disclosed. By detecting the cleaved flap, a ligation product, a ligation product surrogate, a hybridization complex, or combinations thereof, one can infer the degree to which the corresponding target nucleotide is methylated. Certain of the disclosed methods are particularly useful for evaluating bisulfite-treated target sequences and determining the degree of target nucleotide methylation. The disclosed methods are well suited for rapidly analyzing a large number of target sequences, typically in one or more multiplex reactions. Kits for performing coupled nuclease and ligase methylation detection assays are also disclosed.

Abstract translation: 公开了确定通过结合特异性核酸酶催化的反应的至少一种靶核苷酸的甲基化状态的方法，通常与连接反应偶联。 通过检测切割的瓣，连接产物，连接产物替代物，杂交复合物或其组合，可以推断相应的靶核苷酸被甲基化的程度。 某些所公开的方法对于评估亚硫酸氢盐处理的靶序列和确定靶核苷酸甲基化程度特别有用。 所公开的方法非常适合于通常在一个或多个多重反应中快速分析大量目标序列。 还公开了用于进行偶联核酸酶和连接酶甲基化检测测定的试剂盒。

公开(公告)号：US20060019288A1

公开(公告)日：2006-01-26

申请号：US11173112

申请日：2005-06-30

Applicant: Mark Andersen ,  H. Wenz ,  Caifu Chen ,  Achim Karger

Inventor： Mark Andersen ,  H. Wenz ,  Caifu Chen ,  Achim Karger

IPC: C12Q1/68 ,  C12P19/34

CPC classification number: C12Q1/6855 ,  C12P19/34

Abstract: The present teachings pertain to methods, reaction mixtures, and kits for ligating polynucleotides. In some embodiments, a heat-activatable ligation agent, a phosphorylation agent, and a decontamination agent are included in the same ligation reaction mixture with at least one probe set, at least one linker set, and at least one target polynucleotide. A reaction at a first temperature results in hybridization of the probes to the target, phosphorylation of the probes, and decontamination of unwanted reaction components. A reaction at a second temperature results in the ligation of the probes together. In some embodiments, the present teachings are applied in highly multi-plexed ligation reactions in which a plurality of single nucleotide polymorphisms in a plurality of target polynucleotides are queried, and eventually detected using a mobility dependent analysis technique.

Abstract translation: 本教导涉及用于连接多核苷酸的方法，反应混合物和试剂盒。 在一些实施方案中，与至少一个探针组，至少一个接头组和至少一个靶多核苷酸在相同的连接反应混合物中包括可热激活的连接剂，磷酸化剂和去污剂。 在第一温度下的反应导致探针与靶的杂交，探针的磷酸化，以及不期望的反应组分的去污。 在第二温度下的反应导致探头连接在一起。 在一些实施方案中，本教导应用于高多重连接的连接反应中，其中查询多个目标多核苷酸中的多个单核苷酸多态性，并且最终使用迁移率依赖性分析技术检测。

公开(公告)号：US20050266458A1

公开(公告)日：2005-12-01

申请号：US11119985

申请日：2005-05-02

Applicant: Mark Andersen ,  Jer-Kang Chen ,  Michael Hunkapiller ,  Steven Menchen

Inventor： Mark Andersen ,  Jer-Kang Chen ,  Michael Hunkapiller ,  Steven Menchen

IPC: C12Q1/68

CPC classification number: C12Q1/68 ,  C12Q1/6827 ,  C12Q1/6862 ,  C12Q2537/164 ,  C12Q2521/501

Abstract: Ligation-based methods and kits are disclosed for determining the degree of methylation of one or more target nucleotides. In certain embodiments, the methylation status of one or more target nucleotides is determined by generating misligation products. In certain embodiments, at least one target nucleotide is amplified prior to the ligation reaction. In certain embodiments, at least one ligation product, at least one ligation product surrogate, at least one misligation product, at least one misligation product surrogate, or combinations thereof are amplified. In certain embodiments, one or more ligation probes comprise at least one nucleotide analog, at least one Modification, at least one mismatched nucleotide, or combinations thereof.

Abstract translation: 公开了基于连接的方法和试剂盒以确定一个或多个靶核苷酸的甲基化程度。 在某些实施方案中，通过产生错误产物来确定一个或多个靶核苷酸的甲基化状态。 在某些实施方案中，在连接反应之前扩增至少一种靶核苷酸。 在某些实施方案中，扩增至少一种连接产物，至少一种连接产物替代物，至少一种错误产物，至少一种错误产物替代物或其组合。 在某些实施方案中，一个或多个连接探针包含至少一个核苷酸类似物，至少一个修饰，至少一个错配核苷酸或其组合。

公开(公告)号：US08925461B2

公开(公告)日：2015-01-06

申请号：US13472027

申请日：2012-05-15

Applicant: Mark Andersen ,  Steve Brandon ,  Jim Ferraro ,  James Kelley ,  Grant Tollefson

Inventor： Mark Andersen ,  Steve Brandon ,  Jim Ferraro ,  James Kelley ,  Grant Tollefson

IPC: F42B3/103 ,  F42B3/12

CPC classification number: F23Q2/48 ,  F42B3/127

Abstract: An igniter includes a housing having a first end with an opening, a second end opposite the first end, a longitudinal axis extending from the first end to the second end, and a top surface with a weakened area. The igniter may further include a pyrotechnic material disposed within the housing, a header having a first end and a second end opposite the first end, and a bridge element provided on the first end of the header and having lead wires on the second end of the header. The first end of the header may be inserted into the opening of the housing in a first direction so as to force the header against the pyrotechnic material. Flow of current through the bridge element heats the bridge element and ignites the pyrotechnic material, which causes the weakened area to rupture.

Abstract translation: 点火器包括壳体，其具有带有开口的第一端，与第一端相对的第二端，从第一端延伸到第二端的纵向轴线以及具有弱化区域的顶面。 点火器还可以包括设置在壳体内的烟火材料，具有第一端和与第一端相对的第二端的集管，以及设置在集管的第一端上的桥接元件，并且在第二端上具有引线 标题。 集管的第一端可以沿着第一方向插入壳体的开口中，以便将集管压在烟火材料上。 通过桥梁元件的电流流动加热桥接元件并点燃烟火材料，导致弱化区域破裂。

公开(公告)号：US08728728B2

公开(公告)日：2014-05-20

申请号：US13619815

申请日：2012-09-14

Applicant: John Leamon ,  Mark Andersen ,  Michael Thornton

Inventor： John Leamon ,  Mark Andersen ,  Michael Thornton

IPC: C12Q1/68 ,  C12P19/34 ,  C07H21/02 ,  C07H21/04

CPC classification number: C12Q1/686 ,  C12N15/1065 ,  C12Q1/6806 ,  C12Q1/6855 ,  C12Q1/6874 ,  C12Q1/6886 ,  C12Q2600/16 ,  C12Q2521/307 ,  C12Q2525/101 ,  C12Q2525/191 ,  C12Q2537/143

Abstract: The present invention provides methods, compositions, kits, systems and apparatus that are useful for multiplex PCR of one or more nucleic acids present in a sample. In particular, various target-specific primers are provided that allow for the selective amplification of one or more target sequences. In one aspect, the invention relates to target-specific primers useful for the selective amplification of one or more target sequences associated with cancer or inherited disease. In some aspects, amplified target sequences obtained using the disclosed methods, kits, systems and apparatuses can be used in various downstream processes including nucleic acid sequencing and used to detect the presence of genetic variants.

公开(公告)号：US20050196392A1

公开(公告)日：2005-09-08

申请号：US11061099

申请日：2005-02-18

Applicant: Mark Andersen

Inventor： Mark Andersen

IPC: A61K38/47 ,  C12Q1/68

CPC classification number: C12Q1/686 ,  C12N9/1252 ,  C12Q2527/149 ,  C12Q2521/101

Abstract: Compositions comprising at least two polymerases, including a lesion repair polymerase, are provided. Methods for producing primer extension products using at least two polymerases, including a lesion repair polymerase, are also provided. Kits for producing primer extension products comprising at least two polymerases, including a lesion repair polymerase, are also provided.

Abstract translation: 提供包含至少两种聚合酶（包括病变修复聚合酶）的组合物。 还提供了使用至少两种聚合酶（包括损伤修复聚合酶）产生引物延伸产物的方法。 还提供了用于生产包含至少两种聚合酶（包括病变修复聚合酶）的引物延伸产物的试剂盒。

公开(公告)号：US06924498B2

公开(公告)日：2005-08-02

申请号：US10861299

申请日：2004-06-04

Applicant: Philip T. Feldsine ,  Tim A. Kelly ,  Jim Christensen ,  Joseph B. Di Carlo ,  Mark Andersen ,  Anita Kressner

Inventor： Philip T. Feldsine ,  Tim A. Kelly ,  Jim Christensen ,  Joseph B. Di Carlo ,  Mark Andersen ,  Anita Kressner

IPC: G01N33/50 ,  G01N21/76 ,  G01N21/78 ,  G01N33/02 ,  G01N15/06

CPC classification number: G01N21/76

Abstract: Methods and apparatus for evaluating the quality of a sample of a product, an ingredient, an environment or a process by measuring multiple parameters thereof, including light emitted from a reacting sample containing ATP, ADP, alkaline phosphatase or other parameters such as pH, temperature, conductivity, oxidation reduction potential, dissolved gases, specific ions, and microbiological count. The apparatus comprises an integrated sample testing device used to collect a sample, mix reagents, react the sample, and collect it in a measurement chamber. The apparatus also comprises an instrument having a photon detection assembly for use with the sample testing device. The instrument can also comprise one or more sensing probes and a communication port to facilitate data collection, transfer and analysis. The method further comprises a mechanism for storing data, evaluating data, graphing data, and determining conformance to established criteria.

Abstract translation: 通过测量其多个参数，包括从含有ATP，ADP，碱性磷酸酶或其他参数如pH，温度的反应样品发射的光来评价产品，成分，环境或过程的样品的质量的方法和装置 ，电导率，氧化还原电位，溶解气体，特定离子和微生物数。 该装置包括用于收集样品，混合试剂，使样品反应并将其收集在测量室中的集成样品测试装置。 该装置还包括具有用于样品测试装置的光子检测组件的仪器。 仪器还可以包括一个或多个感测探头和通信端口，以便于数据收集，传输和分析。 该方法还包括用于存储数据，评估数据，绘制数据以及确定与已建立标准的一致性的机制。

公开(公告)号：US10156509B2

公开(公告)日：2018-12-18

申请号：US14127152

申请日：2012-06-13

Applicant: Mark Andersen ,  Michael C. Pallas ,  Haopeng Wang

Inventor： Mark Andersen ,  Michael C. Pallas ,  Haopeng Wang

IPC: C12Q1/68 ,  C12P19/34 ,  G01N15/04 ,  C12Q1/6816

Abstract: A method of aligning a plurality of targets is provided. The method includes generating a plurality of targets. A third phase includes the plurality of targets. The method further includes combining a first phase, a second phase, and the third phase in a volume. The first phase, the second phase, and the third phase are substantially immiscible, and the third phase is in fluid communication with the first phase and the second phase, and the first phase, the second phase, and the third phase are operable to be in a configuration of the third phase between the first phase and the second phase in the volume.