公开(公告)号：US12259323B2

公开(公告)日：2025-03-25

申请号：US17862297

申请日：2022-07-11

Applicant: Quantum-Si Incorporated

Inventor： Jonathan M. Rothberg ,  Ali Kabiri ,  Gerard Schmid ,  Keith G. Fife ,  James Beach ,  Jason W. Sickler ,  Lawrence C. West ,  Paul E. Glenn ,  Kyle Preston ,  Farshid Ghasemi ,  Benjamin Cipriany ,  Jeremy Lackey

IPC: G01N21/64 ,  C12Q1/6869 ,  C12Q1/6874 ,  G01N21/77 ,  G01N33/543

Abstract: System and methods for analyzing single molecules and performing nucleic acid sequencing. An integrated device may include multiple pixels with sample wells configured to receive a sample, which when excited, emits radiation. The integrated device includes a surface having a trench region recessed from a portion of the surface and an array of sample wells, disposed in the trench region. The integrated device also includes a waveguide configured to couple excitation energy to at least one sample well in the array and positioned at a first distance from a surface of the trench region and at a second distance from the surface in a region separate from the trench region. The first distance is smaller than the second distance. 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.

公开(公告)号：US12179204B2

公开(公告)日：2024-12-31

申请号：US16580877

申请日：2019-09-24

Applicant: Quantum-Si Incorporated

Inventor： Guojun Chen ,  James Beach ,  Kathren Fink Croce ,  Jeremy Lackey ,  Gerard Schmid

IPC: G02B6/136 ,  B01L3/00 ,  G02B6/132 ,  G02B6/12

Abstract: A method of forming an integrated device includes forming a sample well within a cladding layer of a substrate; forming a sacrificial spacer layer over the substrate and into the sample well; performing a directional etch of the sacrificial spacer layer so as to form a sacrificial sidewall spacer on sidewalls of the sample well; forming, over the substrate and into the sample well, a functional layer that provides a location for attachment of a biomolecule; and removing the sacrificial spacer material.

公开(公告)号：US20240068027A1

公开(公告)日：2024-02-29

申请号：US18188122

申请日：2023-03-22

Applicant: Quantum-Si Incorporated

Inventor： Jonathan M. Rothberg ,  Jeremy Lackey ,  Brian Reed ,  Xinghua Shi ,  Haidong Huang ,  David Dodd

IPC: C12Q1/6876 ,  C07H19/073 ,  C07H19/173 ,  C07H21/04 ,  C12Q1/6806 ,  C12Q1/6816

CPC classification number: C12Q1/6876 ,  C07H19/073 ,  C07H19/173 ,  C07H21/04 ,  C12Q1/6806 ,  C12Q1/6816 ,  C12Q1/6869

Abstract: Compositions useful for the detection of single molecules in a sample are provided. In some aspects, the disclosure provides a nucleic acid connected to a nucleotide and two or more luminescent labels. In some embodiments, the nucleic acids described herein comprise one or more structural features that provide enhanced fluorescence intensity. In some aspects, methods of sequencing using the labeled nucleotides of the disclosure are provided.

公开(公告)号：US20230375475A1

公开(公告)日：2023-11-23

申请号：US18356150

申请日：2023-07-20

Applicant: Quantum-Si Incorporated

Inventor： Jonathan M. Rothberg ,  Ali Kabiri ,  Gerard Schmid ,  Keith G. Fife ,  James Beach ,  Jason W. Sickler ,  Lawrence C. West ,  Paul E. Glenn ,  Kyle Preston ,  Farshid Ghasemi ,  Benjamin Cipriany ,  Jeremy Lackey

IPC: G01N21/64 ,  C12Q1/6869 ,  C12Q1/6874 ,  G01N21/77 ,  G01N33/543

CPC classification number: G01N21/6428 ,  G01N21/648 ,  C12Q1/6869 ,  C12Q1/6874 ,  G01N21/6408 ,  G01N21/6454 ,  G01N21/6486 ,  G01N21/7743 ,  G01N33/54373 ,  G01N2021/6421 ,  G01N2021/6419

Abstract: System and methods for analyzing single molecules and performing nucleic acid sequencing. An integrated device may include multiple pixels with sample wells configured to receive a sample, which when excited, emits radiation. The integrated device includes a surface having a trench region recessed from a portion of the surface and an array of sample wells, disposed in the trench region. The integrated device also includes a waveguide configured to couple excitation energy to at least one sample well in the array and positioned at a first distance from a surface of the trench region and at a second distance from the surface in a region separate from the trench region. The first distance is smaller than the second distance. 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.

公开(公告)号：US11655504B2

公开(公告)日：2023-05-23

申请号：US16043547

申请日：2018-07-24

Applicant: Quantum-Si Incorporated

Inventor： Jonathan M. Rothberg ,  Jeremy Lackey ,  Brian Reed ,  Xinghua Shi ,  Haidong Huang ,  David Dodd

IPC: C12Q1/6876 ,  C12Q1/6816 ,  C12Q1/6806 ,  C07H19/073 ,  C07H21/04 ,  C07H19/173 ,  C12Q1/6869

CPC classification number: C12Q1/6876 ,  C07H19/073 ,  C07H19/173 ,  C07H21/04 ,  C12Q1/6806 ,  C12Q1/6816 ,  C12Q1/6869 ,  C12Q2525/185 ,  C12Q2525/197 ,  C12Q2525/313 ,  C12Q2563/103 ,  C12Q2600/16 ,  C12Q1/6869 ,  C12Q2525/197 ,  C12Q2563/103 ,  C12Q2565/102 ,  C12Q1/6869 ,  C12Q2525/197 ,  C12Q2563/107 ,  C12Q2565/102

Abstract: Compositions useful for the detection of single molecules in a sample are provided. In some aspects, the disclosure provides a nucleic acid connected to a nucleotide and two or more luminescent labels. In some embodiments, the nucleic acids described herein comprise one or more structural features that provide enhanced fluorescence intensity. In some aspects, methods of sequencing using the labeled nucleotides of the disclosure are provided.

公开(公告)号：US11613772B2

公开(公告)日：2023-03-28

申请号：US16751138

申请日：2020-01-23

Applicant: Quantum-Si Incorporated

Inventor： Jonathan M. Rothberg ,  Jeremy Lackey ,  Brian Reed ,  Xinghua Shi ,  Haidong Huang ,  David Dodd

IPC: C12Q1/68 ,  G01N21/64 ,  C12Q1/6818 ,  C12Q1/6869

Abstract: Compositions useful for the detection of single molecules in a sample are provided. In some aspects, the disclosure provides a nucleotide connected to a nucleic acid comprising a FRET label comprising at least three luminescent molecules. In some embodiments, the nucleic acids described herein comprise one or more structural features that provide enhanced fluorescence intensity. In some aspects, methods of sequencing using the labeled nucleotides of the disclosure are provided.

公开(公告)号：US20230058852A1

公开(公告)日：2023-02-23

申请号：US17690920

申请日：2022-03-09

Applicant: Quantum-Si Incorporated

Inventor： Brian Reed ,  Mohammad Wadud Bhuiya ,  Manjula Pandey ,  Jeremy Lackey ,  Jonathan M. Rothberg ,  Thomas Christian

IPC: C12N9/12 ,  C12Q1/6869 ,  C12P19/34 ,  C12N15/52

Abstract: Compositions comprising modified recombinant polymerizing enzymes are provided, along with nucleic acid molecules encoding the modified polymerizing enzymes. In some aspects, methods of using such polymerizing enzymes to synthesize a nucleic acid molecule or to sequence a nucleic acid template are provided.

公开(公告)号：US20220349823A1

公开(公告)日：2022-11-03

申请号：US17862297

申请日：2022-07-11

Applicant: Quantum-Si Incorporated

Inventor： Jonathan M. Rothberg ,  Ali Kabiri ,  Gerard Schmid ,  Keith G. Fife ,  James Beach ,  Jason W. Sickler ,  Lawrence C. West ,  Paul E. Glenn ,  Kyle Preston ,  Farshid Ghasemi ,  Benjamin Cipriany ,  Jeremy Lackey

IPC: G01N21/64 ,  C12Q1/6869 ,  C12Q1/6874 ,  G01N21/77 ,  G01N33/543

Abstract: System and methods for analyzing single molecules and performing nucleic acid sequencing. An integrated device may include multiple pixels with sample wells configured to receive a sample, which when excited, emits radiation. The integrated device includes a surface having a trench region recessed from a portion of the surface and an array of sample wells, disposed in the trench region. The integrated device also includes a waveguide configured to couple excitation energy to at least one sample well in the array and positioned at a first distance from a surface of the trench region and at a second distance from the surface in a region separate from the trench region. The first distance is smaller than the second distance. 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.

公开(公告)号：US11428635B2

公开(公告)日：2022-08-30

申请号：US16028159

申请日：2018-07-05

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 C. West ,  Michael Ferrigno ,  Paul E. Glenn ,  Anthony Bellofiore

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

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.

公开(公告)号：US20220099575A1

公开(公告)日：2022-03-31

申请号：US17497835

申请日：2021-10-08

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 ,  C12Q1/6874 ,  C12Q1/6869

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.