公开(公告)号：US20200371034A1

公开(公告)日：2020-11-26

申请号：US16900008

申请日：2020-06-12

Applicant: Quantum-Si Incorporated

Inventor： Jonathan M. Rothberg ,  Ali Kabiri ,  Jason W. Sickler ,  Brett J. Gyarfas ,  Jeremy Lackey ,  Gerard Schmid

IPC: G01N21/64 ,  C12Q1/6874 ,  G01N21/77 ,  B01L3/00 ,  C12Q1/6869

Abstract: An active-source-pixel, integrated device capable of performing biomolecule detection and/or analysis, such as single-molecule nucleic acid sequencing, is described. An active pixel of the integrated device includes a sample well into which a sample to be analyzed may diffuse, an excitation source for providing excitation energy to the sample well, and a sensor configured to detect emission from the sample. The sensor may comprise two or more segments that produce a set of signals that are analyzed to differentiate between and identify tags that are attached to, or associated with, the sample. Tag differentiation may be spectral and/or temporal based. Identification of the tags may be used to detect, analyze, and/or sequence the biomolecule.

公开(公告)号：US10711299B2

公开(公告)日：2020-07-14

申请号：US15611573

申请日：2017-06-01

Applicant: Quantum-Si Incorporated

Inventor： Jonathan M. Rothberg ,  Craig Wenger ,  Mel Davey ,  Keith G. Fife ,  Jimmy Jia ,  Brian Reed ,  Brett J. Gyarfas

IPC: C12Q1/6869 ,  G16B30/00 ,  G01N21/64

Abstract: System and methods for identifying nucleotides based on data acquired from a sensor during sequencing of nucleic acids. The method may include obtaining characteristics of light detected from luminescent labels associated with the nucleotides during nucleotide incorporation events. The characteristics may include, for each nucleotide incorporation event, a temporal characteristic the light and an intensity characteristic of the light. The temporal characteristic representing a speed of decay of a probability of photon emission by a luminescent label after excitation. The method may further include grouping points representing the characteristics of the nucleotide incorporation events into groups of points. The individual points may represent at least the temporal characteristic and the intensity characteristic for a corresponding nucleotide incorporation event. The method may further include assigning the groups of points to individual nucleotides.

公开(公告)号：US20190383739A1

公开(公告)日：2019-12-19

申请号：US16442861

申请日：2019-06-17

Applicant: Quantum-Si Incorporated

Inventor： Jonathan M. Rothberg ,  Ali Kabiri ,  Jason W. Sickler ,  Brett J. Gyarfas ,  Jeremy Lackey ,  Gerard Schmid ,  Paul E. Glenn ,  Lawrence C. West ,  Benjamin Cipriany ,  Keith G. Fife

IPC: G01N21/64 ,  C12Q1/6874

Abstract: Apparatus and methods for analyzing single molecules and performing nucleic acid sequencing. An apparatus can include an assay chip that includes multiple pixels with sample wells configured to receive a sample, which, when excited, emits emission energy; at least one element for directing the emission energy in a particular direction; and a light path along which the emission energy travels from the sample well toward a sensor. The apparatus also includes an instrument that interfaces with the assay chip. The instrument includes an excitation light source for exciting the sample in each sample well; a plurality of sensors corresponding the sample wells. Each sensor may detect emission energy from a sample in a respective sample well. The instrument includes at least one optical element that directs the emission energy from each sample well towards a respective sensor of the plurality of sensors.

公开(公告)号：US20180120229A1

公开(公告)日：2018-05-03

申请号：US15845996

申请日：2017-12-18

Applicant: Quantum-Si Incorporated

Inventor： Jonathan M. Rothberg ,  Ali Kabiri ,  Jason W. Sickler ,  Brett J. Gyarfas ,  Jeremy Lackey ,  Gerard Schmid ,  Lawrence C. West ,  Keith G. Fife ,  Benjamin Cipriany ,  Farshid Ghasemi

IPC: G01N21/64

CPC classification number: G01N21/6408 ,  C12Q1/6869 ,  C12Q1/6874 ,  G01N21/6428 ,  G01N21/6454 ,  G01N21/648 ,  G01N2021/6419 ,  G01N2021/6421 ,  G01N2021/6439 ,  G01N2021/6463 ,  G01N2201/0696 ,  G01N2201/08 ,  G01N2201/12

Abstract: System and methods for analyzing single molecules and performing nucleic acid sequencing. An integrated device includes multiple pixels with sample wells configured to receive a sample, which when excited, emits radiation. The integrated device includes at least one waveguide configured to propagate excitation energy to the sample wells from a region of the integrated device configured to couple with an excitation energy source. A pixel may also include at least one element for directing the emission energy towards a sensor within the pixel. The system also includes an instrument that interfaces with the integrated device. The instrument may include an excitation energy source for providing excitation energy to the integrated device by coupling to an excitation energy coupling region of the integrated device. One of multiple markers distinguishable by temporal parameters of the emission energy may label the sample and configuration of the sensor within a pixel may allow for detection of a temporal parameter associated with the marker labeling the sample.

公开(公告)号：US20160370291A1

公开(公告)日：2016-12-22

申请号：US15255245

申请日：2016-09-02

Applicant: Quantum-Si Incorporated

Inventor： Jonathan M. Rothberg ,  Ali Kabiri ,  Jason W. Sickler ,  Brett J. Gyarfas ,  Jeremy Lackey ,  Gerard Schmid ,  Lawrence C. West ,  Keith G. Fife ,  Benjamin Cipriany ,  Farshid Ghasemi

IPC: G01N21/64 ,  C12Q1/68

CPC classification number: G01N21/6408 ,  C12Q1/6869 ,  C12Q1/6874 ,  G01N21/6428 ,  G01N21/6454 ,  G01N21/648 ,  G01N2021/6419 ,  G01N2021/6421 ,  G01N2021/6439 ,  G01N2021/6463 ,  G01N2201/0696 ,  G01N2201/08 ,  G01N2201/12

Abstract: System and methods for analyzing single molecules and performing nucleic acid sequencing. An integrated device includes multiple pixels with sample wells configured to receive a sample, which when excited, emits radiation. The integrated device includes at least one waveguide configured to propagate excitation energy to the sample wells from a region of the integrated device configured to couple with an excitation energy source. A pixel may also include at least one element for directing the emission energy towards a sensor within the pixel. The system also includes an instrument that interfaces with the integrated device. The instrument may include an excitation energy source for providing excitation energy to the integrated device by coupling to an excitation energy coupling region of the integrated device. One of multiple markers distinguishable by temporal parameters of the emission energy may label the sample and configuration of the sensor within a pixel may allow for detection of a temporal parameter associated with the marker labeling the sample.

公开(公告)号：US20150177150A1

公开(公告)日：2015-06-25

申请号：US14543867

申请日：2014-11-17

Applicant: Quantum-Si Incorporated

Inventor： Jonathan M. Rothberg ,  Ali Kabiri ,  Jason W. Sickler ,  Brett J. Gyarfas ,  Jeremy Lackey ,  Gerard Schmid ,  Benjamin Cipriany ,  Jack Jewell ,  Lawrence West ,  Michael Ferrigno ,  Paul E. Glenn ,  Adam E. Cohen ,  Anthony Bellofiore

IPC: G01N21/64

CPC classification number: G01N21/6486 ,  B01L3/5085 ,  B01L2200/12 ,  B01L2300/0829 ,  B01L2300/0887 ,  B01L2300/0893 ,  B01L2300/168 ,  C12Q1/6869 ,  C12Q1/6874 ,  C12Q2521/101 ,  C12Q2537/157 ,  C12Q2563/107 ,  C12Q2565/607 ,  G01N21/64 ,  G01N21/645 ,  G01N21/6452 ,  G01N21/648 ,  G01N21/7743 ,  G01N21/7746 ,  G01N2021/6419 ,  G01N2021/6441 ,  G01N2021/6478 ,  G01N2201/02 ,  G01N2201/06113 ,  G01N2201/0612 ,  G01N2201/062 ,  G01N2201/068 ,  G01N2201/125 ,  Y10T29/49016 ,  C12Q2525/101

Abstract: Apparatus and methods for analyzing single molecule and performing nucleic acid sequencing. An apparatus can include an assay chip that includes multiple pixels with sample wells configured to receive a sample, which, when excited, emits emission energy; at least one element for directing the emission energy in a particular direction; and a light path along which the emission energy travels from the sample well toward a sensor. The apparatus also includes an instrument that interfaces with the assay chip. The instrument includes an excitation light source for exciting the sample in each sample well; a plurality of sensors corresponding the sample wells. Each sensor may detect emission energy from a sample in a respective sample well. The instrument includes at least one optical element that directs the emission energy from each sample well towards a respective sensor of the plurality of sensors.

Abstract translation: 用于分析单分子和进行核酸测序的装置和方法。 装置可以包括测定芯片，其包括多个像素，其中样品阱被配置为接收样品，当被激发时，样品阱发射发射能量; 用于在特定方向上引导发射能量的至少一个元件; 以及发光能量从样品阱向传感器行进的光路。 该装置还包括与测定芯片接口的仪器。 仪器包括用于激发每个样品井中的样品的激发光源; 多个传感器对应于样品孔。 每个传感器可以检测来自相应样品阱中的样品的发射能量。 仪器包括至少一个光学元件，其将来自每个样品的发射能量引向多个传感器中的相应传感器。

公开(公告)号：US20150141268A1

公开(公告)日：2015-05-21

申请号：US14543888

申请日：2014-11-17

Applicant: Quantum-Si Incorporated

Inventor： Jonathan M. Rothberg ,  Ali Kabiri ,  Jason W. Sickler ,  Brett J. Gyarfas ,  Jeremy Lackey ,  Gerard Schmid

IPC: C12Q1/68 ,  G01N21/64

CPC classification number: G01N21/6486 ,  B01L3/5085 ,  B01L2200/12 ,  B01L2300/0829 ,  B01L2300/0887 ,  B01L2300/0893 ,  B01L2300/168 ,  C12Q1/6869 ,  C12Q1/6874 ,  C12Q2521/101 ,  C12Q2537/157 ,  C12Q2563/107 ,  C12Q2565/607 ,  G01N21/64 ,  G01N21/645 ,  G01N21/6452 ,  G01N21/648 ,  G01N21/7743 ,  G01N21/7746 ,  G01N2021/6419 ,  G01N2021/6441 ,  G01N2021/6478 ,  G01N2201/02 ,  G01N2201/06113 ,  G01N2201/0612 ,  G01N2201/062 ,  G01N2201/068 ,  G01N2201/125 ,  Y10T29/49016 ,  C12Q2525/101

Abstract: An active-source-pixel, integrated device capable of performing biomolecule detection and/or analysis, such as single-molecule nucleic acid sequencing, is described. An active pixel of the integrated device includes a sample well into which a sample to be analyzed may diffuse, an excitation source for providing excitation energy to the sample well, and a sensor configured to detect emission from the sample. The sensor may comprise two or more segments that produce a set of signals that are analyzed to differentiate between and identify tags that are attached to, or associated with, the sample. Tag differentiation may be spectral and/or temporal based. Identification of the tags may be used to detect, analyze, and/or sequence the biomolecule.

Abstract translation: 描述了能够进行生物分子检测和/或分析的活性源像素集成器件，例如单分子核酸测序。 集成器件的有源像素包括样本阱，待分析的样本可以扩散到其中，用于向样本阱提供激发能量的激发源以及被配置为检测来自样本的发射的传感器。 传感器可以包括产生一组信号的两个或更多个片段，所述一组信号被分析以区分和识别附加到样本或与样本相关联的标签。 标签分化可以是基于频谱和/或时间的。 标签的识别可用于检测，分析和/或序列生物分子。

公开(公告)号：US20150141267A1

公开(公告)日：2015-05-21

申请号：US14543865

申请日：2014-11-17

Applicant: Quantum-Si Incorporated

Inventor： Jonathan M. Rothberg ,  Ali Kabiri ,  Jason W. Sickler ,  Brett J. Gyarfas ,  Jeremy Lackey ,  Gerard Schmid ,  Benjamin Cipriany ,  Jack Jewell ,  Lawrence West ,  Michael Ferrigno ,  Paul E. Glenn ,  Anthony Bellofiore

IPC: C12Q1/68 ,  G01N21/64

CPC classification number: G01N21/6486 ,  B01L3/5085 ,  B01L2200/12 ,  B01L2300/0829 ,  B01L2300/0887 ,  B01L2300/0893 ,  B01L2300/168 ,  C12Q1/6869 ,  C12Q1/6874 ,  C12Q2521/101 ,  C12Q2537/157 ,  C12Q2563/107 ,  C12Q2565/607 ,  G01N21/64 ,  G01N21/645 ,  G01N21/6452 ,  G01N21/648 ,  G01N21/7743 ,  G01N21/7746 ,  G01N2021/6419 ,  G01N2021/6441 ,  G01N2021/6478 ,  G01N2201/02 ,  G01N2201/06113 ,  G01N2201/0612 ,  G01N2201/062 ,  G01N2201/068 ,  G01N2201/125 ,  Y10T29/49016 ,  C12Q2525/101

Abstract: Apparatus and methods for analyzing single molecule and performing nucleic acid sequencing. An integrated device includes multiple pixels with sample wells configured to receive a sample, which, when excited, emits radiation; at least one element for directing the emission radiation in a particular direction; and a light path along which the emission radiation travels from the sample well toward a sensor. The apparatus also includes an instrument that interfaces with the integrated device. Each sensor may detect emission radiation from a sample in a respective sample well. The instrument includes an excitation light source for exciting the sample in each sample well.

Abstract translation: 用于分析单分子和进行核酸测序的装置和方法。 集成器件包括多个像素，其中样品阱被配置为接收样品，当被激发时，样品阱发射辐射; 用于在特定方向上引导发射辐射的至少一个元件; 以及发射辐射从样品阱向传感器行进的光路。 该装置还包括与集成装置接口的仪器。 每个传感器可以检测来自相应样品阱中的样品的发射辐射。 该仪器包括用于激发每个样品孔中的样品的激发光源。

公开(公告)号：US20240068943A1

公开(公告)日：2024-02-29

申请号：US18500999

申请日：2023-11-02

Applicant: Quantum-Si Incorporated

Inventor： Jonathan M. Rothberg ,  Benjamin Cipriany ,  Faisal R. Ahmad ,  Joseph D. Clark ,  Daniel B. Frier ,  Michael Ferrigno ,  Mel Davey ,  Thomas Raymond Thurston ,  Brett J. Gyarfas ,  Todd Rearick ,  Jeremy Christopher Jordan

IPC: G01N21/64 ,  G06F1/08

CPC classification number: G01N21/6402 ,  G01N21/6486 ,  G06F1/08 ,  G01N2021/6495 ,  G01N2201/125 ,  G01N2201/126

Abstract: Instrument control and data acquisition in advanced analytic systems that utilize optical pulses for sample analysis are described. Clocking signals for data acquisition, data processing, communication, and/or other data handling functionalities can be derived from an on-board pulsed optical source, such as a passively mode-locked laser. The derived clocking signals can operate in combination with one or more clocking signals from a stable oscillator, so that instrument operation and data handling can tolerate interruptions in operation of the pulsed optical source.

公开(公告)号：US11808700B2

公开(公告)日：2023-11-07

申请号：US16442206

申请日：2019-06-14

Applicant: Quantum-Si Incorporated

Inventor： Jonathan M. Rothberg ,  Benjamin Cipriany ,  Faisal R. Ahmad ,  Joseph D. Clark ,  Daniel B. Frier ,  Michael Ferrigno ,  Mel Davey ,  Tom Thurston ,  Brett J. Gyarfas ,  Todd Rearick ,  Jeremy Christopher Jordan

IPC: G01N21/64 ,  G06F1/08

CPC classification number: G01N21/6402 ,  G01N21/6486 ,  G06F1/08 ,  G01N2021/6495 ,  G01N2201/125 ,  G01N2201/126

Abstract: Instrument control and data acquisition in advanced analytic systems that utilize optical pulses for sample analysis are described. Clocking signals for data acquisition, data processing, communication, and/or other data handling functionalities can be derived from an on-board pulsed optical source, such as a passively mode-locked laser. The derived clocking signals can operate in combination with one or more clocking signals from a stable oscillator, so that instrument operation and data handling can tolerate interruptions in operation of the pulsed optical source.