Abstract: Methods and systems for image analysis are provided, and in particular for identifying a set of base-calling locations in a flow cell for DNA sequencing. These include capturing flow cell images after each sequencing step performed on the flow cell, and identifying candidate cluster centers in at least one of the flow cell images. Intensities are determined for each candidate cluster center in a set of flow cell images. Purities are determined for each candidate cluster center based on the intensities. Each candidate cluster center with a purity greater than the purity of the surrounding candidate cluster centers within a distance threshold is added to a template set of base-calling locations.
Type:
Grant
Filed:
March 31, 2021
Date of Patent:
December 14, 2021
Assignee:
Element Biosciences, Inc.
Inventors:
Chunhong Zhou, Semyon Kruglyak, Francisco Garcia, Minghao Guo, Haosen Wang, Ryan Kelly
Abstract: Methods and systems for sequencing a nucleic acid molecule are described that comprise imaging a first surface and an axially-displaced second surface using a compensation-free optical system, the system comprising an objective lens and at least one image sensor, wherein said optical system has a numerical aperture (NA) of less than 0.6 and a field-of-view (FOV) of greater than 1.0 mm2; and) processing the images of the first surface and the axially-displaced second surface to correct for optical aberration such that the images of the first surface and the axially-displaced second surface have substantially the same optical resolution.
Type:
Grant
Filed:
September 9, 2020
Date of Patent:
July 13, 2021
Assignee:
ELEMENT BIOSCIENCES, INC.
Inventors:
Steve Xiangling Chen, Minghao Guo, Michael Previte, Chunhong Zhou, Derek Fuller
Abstract: Fluorescence imaging system designs are described that provide larger fields-of-view, increased spatial resolution, improved modulation transfer and image quality, higher spatial sampling frequency, faster transitions between image capture when repositioning the sample plane to capture a series of images (e.g., of different fields-of-view), and improved imaging system duty cycle, and thus enable higher throughput image acquisition and analysis for genomics and other imaging applications.
Type:
Grant
Filed:
September 9, 2020
Date of Patent:
July 6, 2021
Assignee:
ELEMENT BIOSCIENCES, INC.
Inventors:
Steve Xiangling Chen, Minghao Guo, Michael Previte, Chunhong Zhou, Derek Fuller
Abstract: Multivalent binding compositions including a particle-nucleotide conjugate having a plurality of copies of a nucleotide attached to the particle are described. The multivalent binding compositions allow one to localize detectable signals to active regions of biochemical interaction, e.g., sites of protein-protein interaction, protein-nucleic acid interaction, nucleic acid hybridization, or enzymatic reaction, and can be used to identify sites of base incorporation in elongating nucleic acid chains during polymerase reactions and to provide improved base discrimination for sequencing and array based applications.
Type:
Grant
Filed:
April 22, 2020
Date of Patent:
April 20, 2021
Assignee:
ELEMENT BIOSCIENCES, INC.
Inventors:
Sinan Arslan, Chunhong Zhou, Molly Min He, Matthew Kellinger, Adeline Huizhen Mah, Michael Previte, Lei Sun
Abstract: Methods and formulations for preparing low non-specific binding surfaces are described, and the prepared surface can provide improved performance for nucleic acid detection and base calling applications. The surface provides more accurate nucleic acid detection, enhanced contrast to noise ratio, and better data collection.
Type:
Grant
Filed:
January 10, 2020
Date of Patent:
December 29, 2020
Assignee:
ELEMENT BIOSCIENCES, INC.
Inventors:
Chunhong Zhou, Sinan Arslan, Molly Min He, Matthew Kellinger, Adeline Huizhen Mah, Michael Previte, Lei Sun
Abstract: Multivalent binding compositions including a particle-nucleotide conjugate having a plurality of copies of a nucleotide attached to the particle are described. The multivalent binding compositions allow one to localize detectable signals to active regions of biochemical interaction, e.g., sites of protein-protein interaction, protein-nucleic acid interaction, nucleic acid hybridization, or enzymatic reaction, and can be used to identify sites of base incorporation in elongating nucleic acid chains during polymerase reactions and to provide improved base discrimination for sequencing and array based applications.
Type:
Grant
Filed:
September 23, 2019
Date of Patent:
September 8, 2020
Assignee:
ELEMENT BIOSCIENCES, INC.
Inventors:
Sinan Arslan, Molly He, Matthew Kellinger, Jake Levieux, Michael Previte, Junhua Zhao, Su Zhang
Abstract: Multivalent binding compositions including a particle-nucleotide conjugate having a plurality of copies of a nucleotide attached to the particle are described. The multivalent binding compositions allow one to localize detectable signals to active regions of biochemical interaction, e.g., sites of protein-protein interaction, protein-nucleic acid interaction, nucleic acid hybridization, or enzymatic reaction, and can be used to identify sites of base incorporation in elongating nucleic acid chains during polymerase reactions and to provide improved base discrimination for sequencing and array based applications.
Type:
Grant
Filed:
January 10, 2020
Date of Patent:
July 7, 2020
Assignee:
ELEMENT BIOSCIENCES, INC.
Inventors:
Sinan Arslan, Chunhong Zhou, Molly Min He, Matthew Kellinger, Adeline Huizhen Mah, Michael Previte, Lei Sun