公开(公告)号：US20230326064A1

公开(公告)日：2023-10-12

申请号：US18078797

申请日：2022-12-09

Applicant: Element Biosciences, Inc.

Inventor： Chunhong ZHOU ,  Semyon KRUGLYAK ,  Francisco GARCIA ,  Minghao GUO ,  Haosen WANG ,  Ryan KELLY

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

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

Abstract: Image data analysis, particularly identifying cluster locations for performing base-calling in a digital flow cell image during DNA sequencing, is described. Each nucleic acid template molecule immobilized on a support may include an insert sequence and a sample index sequence. The sample index sequence may include a k-mer sequence. A sequencing system may conduct k cycles of sequencing reactions of the k-mer sequence before conducting one or more cycles of the insert sequence sequencing reactions and generate a first plurality of flow cell images. Pixel intensities may be determined for pixels of the first plurality of flow cell images. A base calling template may be determined and include base calling locations based on the pixel intensities and respective color purities of the pixel intensities. The base calling template may register a second plurality of flow cell images of the support in one or more cycles subsequent to the k cycles.

公开(公告)号：US20230392144A1

公开(公告)日：2023-12-07

申请号：US18328650

申请日：2023-06-02

Applicant: Element Biosciences, Inc.

Inventor： Andrew PRICE ,  Junhua ZHAO ,  Semyon KRUGLYAK ,  Kelly BLEASE ,  Hua YU ,  Andrew ALTOMARE ,  Ryan KELLEY ,  Juan MORENO

IPC: C12N15/10 ,  C12Q1/6834

CPC classification number: C12N15/1093 ,  C12Q1/6834

Abstract: The present disclosure provides compositions comprising reagents employed in a nucleic acid library preparation workflow for removing deaminated bases, and methods for using the reagents. The compositions and methods described herein reduce base call errors, such as C:G to T:A transitions, in nucleic acid sequencing workflows.

公开(公告)号：US20220101039A1

公开(公告)日：2022-03-31

申请号：US17547602

申请日：2021-12-10

Applicant: Element Biosciences, Inc.

Inventor： Chunhong ZHOU ,  Semyon KRUGLYAK ,  Francisco GARCIA ,  Minghao GUO ,  Haosen WANG ,  Ryan KELLY

IPC: G06K9/62 ,  G06K9/00 ,  G06T7/30

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.

公开(公告)号：US20220405523A1

公开(公告)日：2022-12-22

申请号：US17854042

申请日：2022-06-30

Applicant: Element Biosciences, Inc.

Inventor： Chunhong ZHOU ,  Semyon KRUGLYAK ,  Francisco GARCIA ,  Minghao GUO ,  Haosen WANG ,  Ryan KELLY

IPC: G06K9/62 ,  G06T7/30 ,  G06V10/75 ,  G06V20/69

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.

公开(公告)号：US20230326065A1

公开(公告)日：2023-10-12

申请号：US18078820

申请日：2022-12-09

Applicant: Element Biosciences, Inc.

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

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

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

Abstract: 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：US20230295692A1

公开(公告)日：2023-09-21

申请号：US18161581

申请日：2023-01-30

Applicant: ELEMENT BIOSCIENCES, INC.

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

IPC: C12Q1/6816 ,  C12Q1/6855

CPC classification number: C12Q1/6816 ,  C12Q1/6855

Abstract: 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.