公开(公告)号：WO2010138187A1

公开(公告)日：2010-12-02

申请号：PCT/US2010/001549

申请日：2010-05-27

Applicant: ION TORRENT SYSTEMS INCORPORATED ,  HINZ, Wolfgang ,  LEAMON, John H. ,  LIGHT, David ,  ROTHBERG, Jonathan M.

Inventor： HINZ, Wolfgang ,  LEAMON, John H. ,  LIGHT, David ,  ROTHBERG, Jonathan M.

IPC: C07H21/00 ,  G01N33/48

CPC classification number: C12N15/1093 ,  C12Q1/6806 ,  C12Q1/6834 ,  C12Q1/6853 ,  C12Q2535/122 ,  C12Q2563/155 ,  C12Q2563/159 ,  C12Q2565/607 ,  C12Q2565/537 ,  C12Q2565/629

Abstract: The invention provides particle compositions having applications in nucleic acid analysis. Nucleic acid polymer particles of the invention allow polynucleotides to be attached throughout their volumes for higher loading capacities than those achievable solely with surface attachment. In one aspect, nucleic acid polymer particles of the invention comprise polyacrylamide particles with uniform size distributions having low coefficients of variations, which result in reduced particle-to-particle variation in analytical assays. Such particle compositions are used in various amplification reactions to make amplicon libraries from nucleic acid fragment libraries.

Abstract translation: 本发明提供了在核酸分析中具有应用的颗粒组合物。 本发明的核酸聚合物颗粒允许多核苷酸在其整个体积中被连接，以便比仅通过表面附着可实现的更高的负载能力。 在一个方面，本发明的核酸聚合物颗粒包含具有低变异系数的具有均匀尺寸分布的聚丙烯酰胺颗粒，这导致分析测定中颗粒 - 颗粒变化的降低。 这种颗粒组合物用于各种扩增反应以制备来自核酸片段文库的扩增子文库。

公开(公告)号：WO2010138182A2

公开(公告)日：2010-12-02

申请号：PCT/US2010001543

申请日：2010-05-27

Applicant: ION TORRENT SYSTEMS INC ,  ROTHBERG JONATHAN M ,  HINZ WOLFGANG ,  DAVIDSON JOHN F ,  VAN OIJEN ANTOINE M ,  LEAMON JOHN H ,  HUBER MARTIN ,  BUSTILLO JAMES M ,  MILGREW MARK JAMES ,  SCHULTZ JONATHAN ,  MARRAN DAVID ,  REARICK TODD ,  JOHNSON KIM L

Inventor： ROTHBERG JONATHAN M ,  HINZ WOLFGANG ,  DAVIDSON JOHN F ,  VAN OIJEN ANTOINE M ,  LEAMON JOHN H ,  HUBER MARTIN ,  BUSTILLO JAMES M ,  MILGREW MARK JAMES ,  SCHULTZ JONATHAN ,  MARRAN DAVID ,  REARICK TODD ,  JOHNSON KIM L

IPC: C40B20/00 ,  C12P19/34 ,  C12Q1/68 ,  C40B40/06 ,  C40B60/10

CPC classification number: G01N27/4145 ,  C12Q1/6869 ,  C12Q1/6874 ,  G01N27/27 ,  G01N27/414 ,  Y10T29/49002

Abstract: Methods and apparatus relating to FET arrays including large FET arrays for monitoring chemical and/or biological reactions such as nucleic acid sequencing-by- synthesis reactions. Some methods provided herein relate to improving signal (and also signal-to-noise ratio) from released hydrogen ions during nucleic acid sequencing reactions.

Abstract translation: 涉及FET阵列的方法和装置，包括用于监测化学和/或生物反应的大型FET阵列，例如通过合成反应的核酸测序。 本文提供的一些方法涉及在核酸测序反应期间从释放的氢离子改进信号（以及信噪比）。

公开(公告)号：WO2010047804A8

公开(公告)日：2010-04-29

申请号：PCT/US2009/005745

申请日：2009-10-22

Applicant: LIFE TECHNOLOGIES CORPORATION ,  ROTHBERG, Jonathan, M. ,  SCHULTZ, Jonathan, C. ,  JOHNSON, Kim, L. ,  REARICK, Todd, M. ,  MILGREW, Mark, James ,  MARRAN, David ,  BUSTILLO, James, M.

Inventor： ROTHBERG, Jonathan, M. ,  SCHULTZ, Jonathan, C. ,  JOHNSON, Kim, L. ,  REARICK, Todd, M. ,  MILGREW, Mark, James ,  MARRAN, David ,  BUSTILLO, James, M.

IPC: G01N27/416 ,  C12M1/34

Abstract: The invention is directed to apparatus and chips comprising a large scale chemical field effect transistor arrays that include an array of sample-retaining regions capable of retaining a chemical or biological sample from a sample fluid for analysis. In one aspect such transistor arrays have a pitch of 10 μm or less and each sample-retaining region is positioned on at least one chemical field effect transistor which is configured to generate at least one output signal related to a characteristic of a chemical or biological sample in such sample-retaining region. In one embodiment, the characteristic of said chemical or biological sample is a concentration of a charged species and wherein each of said chemical field effect transistors is an ion-sensitive field effect transistor having a floating gate with a dielectric layer on a surface thereof, the dielectric layer contacting said sample fluid and being capable of accumulating charge in proportion to a concentration of the charged species in said sample fluid. In one embodiment such charged species is a hydrogen ion such that the sensors measure changes in pH of the sample fluid in or adjacent to the sample-retaining region thereof. Apparatus and chips of the invention may be adapted for large scale pH-based DNA sequencing and other bioscience and biomedical applications.

公开(公告)号：WO2009158006A2

公开(公告)日：2009-12-30

申请号：PCT/US2009/003797

申请日：2009-06-26

Applicant: ION TORRENT SYSTEMS INCORPORATED ,  ROTHBERG, Jonathan, M.

Inventor： ROTHBERG, Jonathan, M.

IPC: G01N27/414 ,  C12Q1/68 ,  H01L29/786 ,  H01L29/06 ,  G01N27/416

CPC classification number: G01N27/4145 ,  G01N27/4148

Abstract: Methods and apparatuses relating to large scale FET arrays for analyte detection and measurement are provided. ChemFET (e.g., ISFET) arrays may be fabricated using conventional CMOS processing techniques based on improved FET pixel and array designs that increase measurement sensitivity and accuracy, and at the same time facilitate significantly small pixel sizes and dense arrays. Improved array control techniques provide for rapid data acquisition from large and dense arrays. Such arrays may be employed to detect a presence and/or concentration changes of various analyte types in a wide variety of chemical and/or biological processes.

Abstract translation: 提供了与用于分析物检测和测量的大规模FET阵列相关的方法和装置。 可以使用基于提高测量灵敏度和精度的改进的FET像素和阵列设计的传统CMOS处理技术来制造ChemFET（例如，ISFET）阵列，并且同时促进显着小的像素尺寸和致密阵列。 改进的阵列控制技术提供了从大型和密集阵列的快速数据采集。 可以使用这样的阵列来检测各种化学和/或生物过程中各种分析物类型的存在和/或浓度变化。

公开(公告)号：WO2007133710A3

公开(公告)日：2007-11-22

申请号：PCT/US2007/011462

申请日：2007-05-11

Applicant: RAINDANCE TECHNOLOGIES, INC. ,  LINK, Darren, R. ,  WEINER, Michael ,  MARREN, David ,  ROTHBERG, Jonathan, M.

Inventor： LINK, Darren, R. ,  WEINER, Michael ,  MARREN, David ,  ROTHBERG, Jonathan, M.

IPC: B01F13/00 ,  B01J19/00 ,  B01L3/00 ,  G01N15/14 ,  G01N33/50

Abstract: The present invention provides novel microfluidic substrates and methods that are useful for performing biological, chemical and diagnostic assays. The substrates can include a plurality of electrically addressable, channel bearing fluidic modules integrally arranged such that a continuous channel is provided for flow of immiscible fluids.

公开(公告)号：WO2007133710A2

公开(公告)日：2007-11-22

申请号：PCT/US2007011462

申请日：2007-05-11

Applicant: RAINDANCE TECHNOLOGIES INC ,  LINK DARREN R ,  WEINER MICHAEL ,  MARREN DAVID ,  ROTHBERG JONATHAN M

Inventor： LINK DARREN R ,  WEINER MICHAEL ,  MARREN DAVID ,  ROTHBERG JONATHAN M

IPC: B01F13/00 ,  B01J19/00 ,  B01L3/00 ,  G01N15/14 ,  G01N33/50

CPC classification number: B01F3/0807 ,  B01F13/0062 ,  B01J19/0093 ,  B01L3/502715 ,  B01L3/502746 ,  B01L3/502784 ,  B01L3/565 ,  B01L7/525 ,  B01L9/527 ,  B01L2200/027 ,  B01L2200/0636 ,  B01L2200/0647 ,  B01L2200/0673 ,  B01L2200/10 ,  B01L2300/0636 ,  B01L2300/0816 ,  B01L2300/0861 ,  B01L2300/0864 ,  B01L2300/0867 ,  B01L2300/165 ,  B01L2400/0415 ,  B01L2400/0424 ,  B01L2400/0487 ,  B01L2400/086 ,  B03C5/005 ,  B03C5/026 ,  C12N15/1068 ,  C12N15/1086 ,  C12Q1/00 ,  C12Q1/6806 ,  C12Q1/6837 ,  C12Q1/6844 ,  C12Q1/6855 ,  C12Q1/6869 ,  C12Q1/6874 ,  C12Q2565/628 ,  C12Q2565/629 ,  G01N15/147 ,  G01N21/05 ,  G01N21/64 ,  G01N27/3275 ,  G01N35/08 ,  G01N2021/0346 ,  G01N2035/00237 ,  G01N2035/00326 ,  G01N2201/024 ,  Y10T137/87571 ,  Y10T137/87619 ,  Y10T137/87652 ,  C12Q2525/191 ,  C12Q2563/159 ,  C12Q2535/101 ,  C12Q2563/149

Abstract: The present invention provides novel microfluidic substrates and methods that are useful for performing biological, chemical and diagnostic assays. The substrates can include a plurality of electrically addressable, channel bearing fluidic modules integrally arranged such that a continuous channel is provided for flow of immiscible fluids.

Abstract translation: 本发明提供了可用于进行生物学，化学和诊断测定的新型微流体底物和方法。 基板可以包括多个可电寻址的通道支承流体模块，其一体地布置成使得提供用于不混溶流体流动的连续通道。

公开(公告)号：WO2003004690A3

公开(公告)日：2003-01-16

申请号：PCT/US2002/021579

申请日：2002-07-08

Applicant: 454® CORPORATION ,  WEINER, Michael ,  ATTIYA, Said ,  CRENSHAW, Hugh ,  ROTHBERG, Jonathan, M. ,  MATSON, Steve

Inventor： WEINER, Michael ,  ATTIYA, Said ,  CRENSHAW, Hugh ,  ROTHBERG, Jonathan, M. ,  MATSON, Steve

IPC: G01N21/03

Abstract: The present invention relates to the field of fluid dynamics. More specifically, this invention relates to methods and apparatus for conducting densely packed, independent chemical reactions in parallel in a substantially two-dimensional array. Accordingly, this invention also focuses on the use of this array for applications such as DNA sequencing, most preferably pyrosequencing, and DNA amplification.

公开(公告)号：WO0120039A3

公开(公告)日：2002-03-21

申请号：PCT/US0025290

申请日：2000-09-15

Applicant: CURAGEN CORP ,  ROTHBERG JONATHAN M ,  BADER JOEL S ,  DEWELL SCOTT B ,  MCDADE KEITH ,  SIMPSON JOHN W ,  BERKA JAN ,  COLANGELO CHRISTOPHER M

Inventor： ROTHBERG JONATHAN M ,  BADER JOEL S ,  DEWELL SCOTT B ,  MCDADE KEITH ,  SIMPSON JOHN W ,  BERKA JAN ,  COLANGELO CHRISTOPHER M

IPC: G01N33/50 ,  C12M1/00 ,  C12N15/09 ,  C12Q1/68 ,  G01N21/05 ,  G01N21/17 ,  G01N33/15 ,  G01N33/53 ,  G01N33/566 ,  H04N5/225 ,  B01J19/00

CPC classification number: C12Q1/6837 ,  C12Q1/6827 ,  C12Q1/6869 ,  C12Q1/6874 ,  C12Q2531/125 ,  C12Q2535/101 ,  C12Q2565/301

Abstract: Disclosed herein are methods and apparatuses for sequencing a nucleic acid. In one aspect, the method includes annealing a population of circular nucleic acid molecules to a plurality of anchor primers linked to a solid support, and amplifying those members of the population of circular nucleic acid molecules which anneal to the target nucleic acid, and then sequencing the amplified molecules by detecting the presence of a sequence by-product such as pyrophosphate.

Abstract translation: 本文公开了用于测序核酸的方法和装置。 一方面，该方法包括将多个环状核酸分子退火至与固体支持物连接的多个锚定引物，并扩增与靶核酸退火的环状核酸分子群体的那些成员，然后测序 通过检测序列副产物如焦磷酸盐的存在来扩增分子。

公开(公告)号：WO2020028257A2

公开(公告)日：2020-02-06

申请号：PCT/US2019/043927

申请日：2019-07-29

Applicant: HYPERFINE RESEARCH, INC. ,  WANG, Ziyi ,  KUNDU, Prantik ,  SACOLICK, Laura ,  SOFKA, Michal ,  ROTHBERG, Jonathan, M. ,  SCHLEMPER, Jo ,  MOSHEN SALEHI, Seyed, Sadegh ,  LAZARUS, Carole ,  DYVORNE, Hadrien, A. ,  O'HALLORAN, Rafael ,  4CATALYZER CORPORATION

Inventor： WANG, Ziyi ,  KUNDU, Prantik ,  SACOLICK, Laura ,  SOFKA, Michal ,  ROTHBERG, Jonathan, M. ,  SCHLEMPER, Jo ,  MOSHEN SALEHI, Seyed, Sadegh ,  LAZARUS, Carole ,  DYVORNE, Hadrien, A. ,  O'HALLORAN, Rafael

Abstract: A magnetic resonance imaging (MRI) system, comprising: a magnetics system comprising: a Bo magnet configured to provide a Bo field for the MRI system; gradient coils configured to provide gradient fields for the MRI system; and at least one RF coil configured to detect magnetic resonance (MR) signals; and a controller configured to: control the magnetics system to acquire MR spatial frequency data using non-Cartesian sampling; and generate an MR image from the acquired MR spatial frequency data using a neural network model comprising one or more neural network blocks including a first neural network block, wherein the first neural network block is configured to perform data consistency processing using a non-uniform Fourier transformation.

公开(公告)号：WO2018098141A1

公开(公告)日：2018-05-31

申请号：PCT/US2017/062763

申请日：2017-11-21

Applicant: HYPERFINE RESEARCH, INC. ,  SOFKA, Michal ,  ROTHBERG, Jonathan, M.

Inventor： SOFKA, Michal ,  ROTHBERG, Jonathan, M. ,  CHARVAT, Gregory, L. ,  RALSTON, Tyler, S.

IPC: G06T7/00

Abstract: Some aspects include a method of detecting change in degree of midline shift in a brain of a patient. While the patient remains positioned within the low-field magnetic resonance imaging device, acquiring first magnetic resonance (MR) image data and second MR image data of the patient's brain; providing the first and second MR data as input to a trained statistical classifier to obtain corresponding first and second output, identifying, from the first output, at least one initial location of at least one landmark associated with at least one midline structure of the patient's brain; identifying, from the second output, at least one updated location of the at least one landmark; and determining a degree of change in the midline shift using the at least one initial location of the at least one landmark and the at least one updated location of the at least one landmark.