公开(公告)号：US20240201088A1

公开(公告)日：2024-06-20

申请号：US18417995

申请日：2024-01-19

申请人： Element Biosciences, Inc.

发明人： Arash GHORBANI ,  Russell HUDYMA ,  John BAILEY ,  Michael PREVITE

IPC分类号： G01N21/64 ,  C12Q1/6869

CPC分类号： G01N21/6428 ,  C12Q1/6869 ,  G01N21/6458 ,  G01N2021/6439

摘要： 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 fields-of-view, improved imaging system duty cycle and a more compact system, and thus enable higher throughput image acquisition and analysis for genomics and other imaging applications at a lower cost.

公开(公告)号：US20240191278A1

公开(公告)日：2024-06-13

申请号：US18510487

申请日：2023-11-15

申请人： Element Biosciences, Inc.

发明人： Sinan ARSLAN ,  Junhua ZHAO ,  Molly HE ,  Samantha SNOW ,  William LIGHT ,  Matthew KELLINGER ,  Michael PREVITE ,  Michael KIM ,  Hua YU ,  Yu-Hsien HWANG-FU ,  Marco TJIOE ,  Andrew BODDICKER ,  Mark AMBROSO ,  Tyler LOPEZ ,  Michael KLEIN ,  Virginia SAADE

IPC分类号： C12Q1/6806 ,  C12Q1/6834 ,  C12Q1/6853 ,  C12Q1/6874 ,  G01N21/64

CPC分类号： C12Q1/6806 ,  C12Q1/6834 ,  C12Q1/6853 ,  C12Q1/6874 ,  G01N21/6428 ,  G01N21/6458 ,  C12Q2600/158

摘要： The present disclosure provides compositions and methods that employ the compositions for conducting pairwise sequencing and for generating concatemer template molecules for pairwise sequencing. The concatemers can be generated using a rolling circle amplification reaction which is conducted either on-support, or conducted in-solution and then distributed onto a support. The rolling circle amplification reaction generates concatemers containing tandem copies of a sequence of interest and at least one universal adaptor sequence. An increase in the number of tandem copies in a given concatemer increases the number of sites along the concatemer for hybridizing to multiple sequencing primers which serve as multiple initiation sites for polymerase-catalyzed sequencing reactions. When the sequencing reaction employs detectably labeled nucleotides and/or detectably labeled multivalent molecules (e.g., having nucleotide units), the signals emitted by the nucleotides or nucleotide units that participate in the parallel sequencing reactions along the concatemer yields an increased signal intensity for each concatemer.

公开(公告)号：US20240011022A1

公开(公告)日：2024-01-11

申请号：US18347440

申请日：2023-07-05

申请人： Element Biosciences, Inc.

发明人： Junhua ZHAO ,  Xiaodong QI ,  Shawn LEVY

IPC分类号： C12N15/10

CPC分类号： C12N15/1065

摘要： The present disclosure provides compositions comprising nucleic acid double-stranded splint adaptors, including kits, and methods that employ the double-stranded splint adaptors, e.g., PCR-free workflows. The double-stranded splint adaptors (200) can be used in a one-pot, multi-enzyme reaction to introduce one or more new adaptor sequences into a library molecule. The double-stranded splint adaptor (200) comprises a first splint strand (long splint strand (300)) and a second splint strand (short splint strand (400)), where the first and second splint strands are hybridized together to form the double-stranded splint adaptor (200) having a double-stranded region and two flanking single-stranded regions. The second splint strand (400) carries the new adaptor sequence(s) to be introduced, such as for example a universal binding sequence and/or an index sequence.

公开(公告)号：US20230326065A1

公开(公告)日：2023-10-12

申请号：US18078820

申请日：2022-12-09

申请人： Element Biosciences, Inc.

发明人： Connor THOMPSON ,  Tsung-li LIU ,  Semyon KRUGLYAK ,  Minghao GUO

IPC分类号： G06T7/66 ,  G06T7/30 ,  G06V10/75 ,  G06V20/69 ,  G06F18/232 ,  G06V10/762

CPC分类号： G06T7/66 ,  G06T7/30 ,  G06V10/751 ,  G06V20/693 ,  G06V20/695 ,  G06F18/232 ,  G06V10/763 ,  G06V20/69 ,  G06V2201/04

摘要： Image data analysis, and particularly identifying cluster or polony locations for performing base-calling in a digital image of a flow cell during DNA sequencing is described. A method may include generating a first plurality of flow cell images of a cellular sample immobilized on a support by conducting one or more cycles of sequencing reactions. The cellular sample may include a plurality of concatemer molecules therewithin. For the first plurality of flow cell image, pixel intensities, and a respective color purity of each of the pixel intensities may be determined. A base calling template may include base calling locations based on the pixel intensities and the respective color purity of the pixel intensities. The base calling template may be for registering a second plurality of flow cell images of the support in one or more subsequent cycles of the one or more cycles.

公开(公告)号：US11781185B2

公开(公告)日：2023-10-10

申请号：US17947984

申请日：2022-09-19

申请人： Element Biosciences, Inc.

发明人： Sinan Arslan ,  Molly He ,  Michael Previte ,  Ramreddy Tippana ,  Hua Yu ,  William Light ,  Junhua Zhao

IPC分类号： C12Q1/68 ,  C12Q1/6874 ,  C12Q1/6806

CPC分类号： C12Q1/6874 ,  C12Q1/6806

摘要： Provided herein are fluorescently-labeled nucleotide conjugates for nucleic acid analysis. Also provided are reagents used for forming binding complexes between a fluorescently-labeled nucleotide conjugate and a target nucleic acid sequence in the presence of one or more reagents disclosed herein. Binding complexes can be detected in the presence of the one or more reagents. For example, the one or more reagents may contain a photobleaching reducing agent configured to reduce photobleaching resulting from use of the fluorescently-labeled nucleotide conjugate to form the binding complex in a nucleic acid analysis. Such nucleic acid analysis may be used to identify sites of nucleobase binding or incorporation between the target nucleic acid sequence and one or more nucleotide moieties of the fluorescently-labeled nucleotide conjugate in a nucleic acid sequence reaction.

公开(公告)号：US20230295692A1

公开(公告)日：2023-09-21

申请号：US18161581

申请日：2023-01-30

申请人： ELEMENT BIOSCIENCES, INC.

发明人： Lorenzo BERTI ,  Semyon KRUGLYAK ,  Matthew KELLINGER ,  Molly HE ,  Sinan ARSLAN ,  Junhua ZHAO ,  Michael PREVITE

IPC分类号： C12Q1/6816 ,  C12Q1/6855

CPC分类号： C12Q1/6816 ,  C12Q1/6855

摘要： Methods and systems for detecting the presence of a target nucleic acid sequence in one or more samples of a plurality of samples are described. The methods may comprise the use of linear barcoded nucleic acid probes that, upon hybridization to a target nucleic acid sequence, may be ligated to circularize the probe molecule, amplified, and sequenced. The use of a probe-specific barcode integrated into the nucleic acid probe molecule, and sample-specific barcodes that may be incorporated into the nucleic acid probe molecule or added during the amplification step, enable large-scale multiplexed assay and sample processing.

公开(公告)号：US20230203564A1

公开(公告)日：2023-06-29

申请号：US18166429

申请日：2023-02-08

申请人： Element Biosciences, Inc.

发明人： Sinan ARSLAN ,  Junhua ZHAO ,  Molly HE ,  Samantha SNOW ,  William LIGHT ,  Matthew KELLINGER ,  Michael PREVITE ,  Michael KIM ,  Hua YU ,  Yu-Hsien HWANG-FU ,  Marco TJIOE ,  Andrew BODDICKER ,  Mark AMBROSO ,  Tyler LOPEZ ,  Michael KLEIN ,  Virginia SAADE

IPC分类号： C12Q1/6806 ,  C12Q1/6834 ,  C12Q1/6874 ,  G01N21/64 ,  C12Q1/6853

CPC分类号： C12Q1/6806 ,  C12Q1/6834 ,  C12Q1/6874 ,  G01N21/6428 ,  G01N21/6458 ,  C12Q1/6853 ,  C12Q2600/158

摘要： The present disclosure provides compositions and methods that employ the compositions for conducting pairwise sequencing and for generating concatemer template molecules for pairwise sequencing. The concatemers can be generated using a rolling circle amplification reaction which is conducted either on-support, or conducted in-solution and then distributed onto a support. The rolling circle amplification reaction generates concatemers containing tandem copies of a sequence of interest and at least one universal adaptor sequence. An increase in the number of tandem copies in a given concatemer increases the number of sites along the concatemer for hybridizing to multiple sequencing primers which serve as multiple initiation sites for polymerase-catalyzed sequencing reactions. When the sequencing reaction employs detectably labeled nucleotides and/or detectably labeled multivalent molecules (e.g., having nucleotide units), the signals emitted by the nucleotides or nucleotide units that participate in the parallel sequencing reactions along the concatemer yields an increased signal intensity for each concatemer.

公开(公告)号：US20230193354A1

公开(公告)日：2023-06-22

申请号：US17992564

申请日：2022-11-22

申请人： Element Biosciences, Inc.

发明人： Sinan ARSLAN ,  Junhua ZHAO ,  Molly HE ,  Samantha SNOW ,  William LIGHT ,  Matthew KELLINGER ,  Michael PREVITE ,  Michael KIM ,  Hua YU ,  Yu-Hsien HWANG-FU ,  Marco TJIOE ,  Andrew BODDICKER

IPC分类号： C12Q1/6806 ,  C12Q1/6834 ,  C12Q1/6874 ,  G01N21/64 ,  C12Q1/6853

CPC分类号： C12Q1/6806 ,  C12Q1/6834 ,  C12Q1/6874 ,  G01N21/6428 ,  G01N21/6458 ,  C12Q1/6853 ,  C12Q2600/158

摘要： The disclosure provides compositions and methods that employ the compositions for conducting pairwise sequencing and for generating concatemer template molecules for pairwise sequencing. The concatemers can be generated using a rolling circle amplification reaction which is conducted either on-support, or conducted in-solution and then distributed onto a support. The rolling circle amplification reaction generates concatemers containing tandem copies of a sequence of interest and at least one universal adaptor sequence. An increase in the number of tandem copies in a given concatemer increases the number of sites along the concatemer for hybridizing to multiple sequencing primers which serve as multiple initiation sites for polymerase-catalyzed sequencing reactions. When the sequencing reaction employs detectably labeled nucleotides and/or detectably labeled multivalent molecules (e.g., having nucleotide units), the signals emitted by the nucleotides or nucleotide units that participate in the parallel sequencing reactions along the concatemer yields an increased signal intensity for each concatemer.

公开(公告)号：US20230065693A1

公开(公告)日：2023-03-02

申请号：US17947984

申请日：2022-09-19

申请人： Element Biosciences, Inc.

发明人： Sinan ARSLAN ,  Molly HE ,  Michael PREVITE ,  Ramreddy TIPPANA ,  Hua YU ,  William LIGHT ,  Junhua ZHAO

IPC分类号： C12Q1/6874 ,  C12Q1/6806

摘要： The present disclosure provides compositions and methods that employ the compositions for conducting nucleic acid sequencing workflows, where the workflows include library preparation, immobilization and amplification of the library molecules to form immobilized template molecules, and sequencing the template molecules. In some embodiments, the compositions comprise reagents used to conduct nucleic acid sequencing workflows.

公开(公告)号：US11287422B2

公开(公告)日：2022-03-29

申请号：US17356929

申请日：2021-06-24

申请人： Element Biosciences, Inc.

发明人： Michael Previte ,  Molly Min He ,  Junhua Zhao ,  Hui Zhen Mah ,  Chunhong Zhou ,  Sinan Arslan ,  Matthew Kellinger ,  Lorenzo Berti ,  Steve Xiangling Chen

IPC分类号： G01N33/53 ,  G01N33/58 ,  C12Q1/68 ,  C12Q1/6874

摘要： 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.