Patents by Inventor Shengrong Lin

Shengrong Lin has filed for patents to protect the following inventions. This listing includes patent applications that are pending as well as patents that have already been granted by the United States Patent and Trademark Office (USPTO).

  • Patent number: 11060135
    Abstract: A method includes forming a patterned substrate including a plurality of base pads, using a nano-imprint lithography process. A capture substance is attached to each of the plurality of base pads, optionally through a linker, the capture substance being adapted to promote capture of a target molecule.
    Type: Grant
    Filed: August 30, 2018
    Date of Patent: July 13, 2021
    Assignee: Illumina, Inc.
    Inventors: M. Shane Bowen, Kevin L. Gunderson, Shengrong Lin, Maria Candelaria Rogert Bacigalupo, Kandaswamy Vijayan, Yir-Shyuan Wu, Bala Murali Venkatesan, James Tsay, John M. Beierle, Lorenzo Berti, Sang Ryul Park
  • Publication number: 20210108258
    Abstract: A method includes forming a patterned substrate including a plurality of base pads, using a nano-imprint lithography process. A capture substance is attached to each of the plurality of base pads, optionally through a linker, the capture substance being adapted to promote capture of a target molecule.
    Type: Application
    Filed: December 7, 2020
    Publication date: April 15, 2021
    Inventors: M. Shane Bowen, Kevin L. Gunderson, Shengrong Lin, Maria Candelaria Rogert Bacigalupo, Kandaswamy Vijayan, Yir-Shyuan Wu, Bala Murali Venkatesan, James Tsay, John M. Beierle, Lorenzo Berti, Sang Ryul Park
  • Publication number: 20210002716
    Abstract: In some aspects, the present disclosure provides methods for enriching amplicons, or amplification products, comprising a concatemer of at least two or more copies of a target polynucleotide. In some embodiments, a method comprises sequencing the amplicons comprising at least two or more copies of a target polynucleotide. In some embodiments, the target polynucleotides comprise sequences resulting from chromosome rearrangement, including but not limited to point mutations, single nucleotide polymorphisms, insertions, deletions, and translocations including fusion genes. In some aspects, the present disclosure provides compositions and reaction mixtures useful in the described methods.
    Type: Application
    Filed: July 13, 2020
    Publication date: January 7, 2021
    Inventors: Li WENG, Shengrong LIN, Ling Fung TANG
  • Publication number: 20200399684
    Abstract: Provided is a surface having metal regions and an interstitial region having a composition that differs from the metal regions, wherein a continuous gel layer coats the surface across the metal regions and the interstitial regions. Nucleic acids or other analytes can be attached to the continuous gel layer such that a greater amount is attached over the metal regions than over the interstitial region. Also provided are methods for making such surfaces. Methods are also provided for making an array of nucleic acids or other analytes using such surfaces.
    Type: Application
    Filed: September 2, 2020
    Publication date: December 24, 2020
    Applicant: ILLUMINA, INC.
    Inventors: Shengrong LIN, Yir-Shyuan WU, Kevin GUNDERSON, John A. MOON
  • Patent number: 10865444
    Abstract: The present disclosure relates to the field of molecular biology and more specifically to methods for capturing, amplifying and sequencing target polynucleotides on a solid surface.
    Type: Grant
    Filed: March 26, 2018
    Date of Patent: December 15, 2020
    Assignee: Illumina, Inc.
    Inventors: Hongxia Xu, Alex Aravanis, Shengrong Lin
  • Patent number: 10787698
    Abstract: Provided is a surface having metal regions and an interstitial region having a composition that differs from the metal regions, wherein a continuous gel layer coats the surface across the metal regions and the interstitial regions. Nucleic acids or other analytes can be attached to the continuous gel layer such that a greater amount is attached over the metal regions than over the interstitial region. Also provided are methods for making such surfaces. Methods are also provided for making an array of nucleic acids or other analytes using such surfaces.
    Type: Grant
    Filed: June 13, 2014
    Date of Patent: September 29, 2020
    Assignee: ILLUMINA, INC.
    Inventors: Shengrong Lin, Yir-Shyuan Wu, Kevin Gunderson, John A. Moon
  • Patent number: 10767222
    Abstract: In some aspects, the present disclosure provides methods for identifying sequence variants in a nucleic acid sample. In some embodiments, a method comprises identifying sequence differences between sequencing reads and a reference sequence, and calling a sequence difference that occurs in at least two different circular polynucleotides, such as two circular polynucleotides having different junctions, as the sequence variant. In some aspects, the present disclosure provides compositions and systems useful in the described methods.
    Type: Grant
    Filed: December 11, 2014
    Date of Patent: September 8, 2020
    Assignee: ACCURAGEN HOLDINGS LIMITED
    Inventors: Shengrong Lin, Zhaohui Sun, Grace Qizhi Zhao, Paul Ling-Fung Tang
  • Patent number: 10752942
    Abstract: In some aspects, the present disclosure provides methods for enriching amplicons, or amplification products, comprising a concatemer of at least two or more copies of a target polynucleotide. In some embodiments, a method comprises sequencing the amplicons comprising at least two or more copies of a target polynucleotide. In some embodiments, the target polynucleotides comprise sequences resulting from chromosome rearrangement, including but not limited to point mutations, single nucleotide polymorphisms, insertions, deletions, and translocations including fusion genes. In some aspects, the present disclosure provides compositions and reaction mixtures useful in the described methods.
    Type: Grant
    Filed: April 6, 2018
    Date of Patent: August 25, 2020
    Assignee: ACCURAGEN HOLDINGS LIMITED
    Inventors: Li Weng, Shengrong Lin, Ling Fung Tang
  • Patent number: 10724088
    Abstract: In some aspects, the present disclosure provides methods for identifying sequence variants in a nucleic acid sample. In some embodiments, a method comprises identifying sequence differences between sequencing reads and a reference sequence, and calling a sequence difference that occurs in at least two different circular polynucleotides, such as two circular polynucleotides having different junctions, or two different sheared polynucleotides as the sequence variant. In some aspects, the present disclosure provides compositions and systems useful in the described method.
    Type: Grant
    Filed: October 26, 2018
    Date of Patent: July 28, 2020
    Assignee: ACCURAGEN HOLDINGS LIMITED
    Inventors: Li Weng, Zhaohui Sun, Shengrong Lin
  • Publication number: 20200080141
    Abstract: In some aspects, the present disclosure provides methods for enriching amplicons, or amplification products, comprising a concatemer of at least two or more copies of a target polynucleotide. In some embodiments, a method comprises sequencing the amplicons comprising at least two or more copies of a target polynucleotide. In some embodiments, the target polynucleotides comprise sequences resulting from chromosome rearrangement, including but not limited to point mutations, single nucleotide polymorphisms, insertions, deletions, and translocations including fusion genes. In some aspects, the present disclosure provides compositions and reaction mixtures useful in the described methods.
    Type: Application
    Filed: November 19, 2019
    Publication date: March 12, 2020
    Inventors: Li WENG, Shengrong LIN, Lin Fung TANG
  • Publication number: 20200010884
    Abstract: In some aspects, the present disclosure provides methods for identifying sequence variants, as well as methods of determining copy number of a genetic locus in a sample. Systems and kits for performing methods of the disclosure, as well as compositions produced by or useful in methods of the disclosure are also provided. In some embodiments, methods comprise extending 3? ends of polynucleotides by adding one or more pre-determined nucleotides. In some embodiments, methods comprise use of a strand-tagging sequence.
    Type: Application
    Filed: May 16, 2017
    Publication date: January 9, 2020
    Inventors: Malek FAHAM, Shengrong LIN, Ling Fung TANG, Yontao LU, Zhaohui SUN, Yingyu WANG, Li WENG
  • Publication number: 20200010883
    Abstract: In some aspects, the present disclosure provides methods for enriching amplicons, or amplification products, comprising a concatemer of at least two or more copies of a target polynucleotide. In some embodiments, a method comprises sequencing the amplicons comprising at least two or more copies of a target polynucleotide. In some embodiments, the target polynucleotides comprise sequences resulting from chromosome rearrangement, including but not limited to point mutations, single nucleotide polymorphisms, insertions, deletions, and translocations including fusion genes. In some aspects, the present disclosure provides compositions and reaction mixtures useful in the described methods.
    Type: Application
    Filed: June 7, 2019
    Publication date: January 9, 2020
    Inventors: Li WENG, Shengrong LIN, Lin Fung TANG
  • Publication number: 20190323073
    Abstract: The present disclosure provides cell-free nucleic acid standards comprising genomic polynucleotides and methods of using cell-free nucleic acid standards comprising genomic polynucleotides for developing, optimizing, and validating cell-free nucleic acid assays.
    Type: Application
    Filed: June 22, 2017
    Publication date: October 24, 2019
    Applicant: ACCURAGEN HOLDINGS LIMITED
    Inventors: Chia-hui LIN, Grace Qizhi ZHAO, Shengrong LIN, Li WENG
  • Patent number: 10280454
    Abstract: A microarray is designed capture one or more molecules of interest at each of a plurality of sites on a substrate. The sites comprise base pads, such as polymer base pads, that promote the attachment of the molecules at the sites. The microarray may be made by one or more patterning techniques to create a layout of base pads in a desired pattern. Further, the microarrays may include features to encourage clonality at the sites.
    Type: Grant
    Filed: March 27, 2017
    Date of Patent: May 7, 2019
    Assignee: ILLUMINA, INC.
    Inventors: M. Shane Bowen, Kevin L. Gunderson, Shengrong Lin, Maria Candelaria Rogert Bacigalupo, Kandaswamy Vijayan, Yir-Shyuan Wu, Bala Murali Venkatesan, James Tsay, John M. Beierle, Lorenzo Berti, Sang Ryul Park
  • Publication number: 20190119743
    Abstract: In some aspects, the present disclosure provides methods for identifying sequence variants in a nucleic acid sample. In some embodiments, a method comprises identifying sequence differences between sequencing reads and a reference sequence, and calling a sequence difference that occurs in at least two different circular polynucleotides, such as two circular polynucleotides having different junctions, or two different sheared polynucleotides as the sequence variant. In some aspects, the present disclosure provides compositions and systems useful in the described method.
    Type: Application
    Filed: October 26, 2018
    Publication date: April 25, 2019
    Inventors: Li Weng, Zhaohui Sun, Shengrong Lin
  • Publication number: 20180371535
    Abstract: A method includes forming a patterned substrate including a plurality of base pads, using a nano-imprint lithography process. A capture substance is attached to each of the plurality of base pads, optionally through a linker, the capture substance being adapted to promote capture of a target molecule.
    Type: Application
    Filed: August 30, 2018
    Publication date: December 27, 2018
    Inventors: M. Shane Bowen, Kevin L. Gunderson, Shengrong Lin, Maria Candelaria Rogert Bacigalupo, Kandaswamy Vijayan, Yir-Shyuan Wu, Bala Murali Venkatesan, James Tsay, John M. Beierle, Lorenzo Berti, Sang Ryul Park
  • Publication number: 20180363039
    Abstract: In some aspects, the present disclosure provides methods for forming ligation products comprising single-stranded polynucleotides. Ligation products formed by various aspects of the present disclosure can be useful for various applications, including but not limited to sequence analysis. In some embodiments, the ligation products comprise cell-free polynucleotides. In some aspects, the present disclosure provides reaction mixtures, kits and complexes consistent with the methods herein.
    Type: Application
    Filed: December 2, 2016
    Publication date: December 20, 2018
    Inventors: Li WENG, Shengrong LIN, Malek FAHAM
  • Patent number: 10155980
    Abstract: In some aspects, the present disclosure provides methods for identifying sequence variants in a nucleic acid sample. In some embodiments, a method comprises identifying sequence differences between sequencing reads and a reference sequence, and calling a sequence difference that occurs in at least two different circular polynucleotides, such as two circular polynucleotides having different junctions, or two different sheared polynucleotides as the sequence variant. In some aspects, the present disclosure provides compositions and systems useful in the described methods.
    Type: Grant
    Filed: November 1, 2017
    Date of Patent: December 18, 2018
    Assignee: ACCURAGEN HOLDINGS LIMITED
    Inventors: Li Weng, Zhaohui Sun, Shengrong Lin
  • Publication number: 20180298434
    Abstract: In some aspects, the present disclosure provides methods for enriching amplicons, or amplification products, comprising a concatemer of at least two or more copies of a target polynucleotide. In some embodiments, a method comprises sequencing the amplicons comprising at least two or more copies of a target polynucleotide. In some embodiments, the target polynucleotides comprise sequences resulting from chromosome rearrangement, including but not limited to point mutations, single nucleotide polymorphisms, insertions, deletions, and translocations including fusion genes. In some aspects, the present disclosure provides compositions and reaction mixtures useful in the described methods.
    Type: Application
    Filed: April 6, 2018
    Publication date: October 18, 2018
    Inventors: Li Weng, Shengrong Lin, Ling Fung Tang
  • Publication number: 20180291444
    Abstract: The present disclosure relates to the field of molecular biology and more specifically to methods for capturing, amplifying and sequencing target polynucleotides on a solid surface.
    Type: Application
    Filed: March 26, 2018
    Publication date: October 11, 2018
    Applicant: ILLUMINA, INC.
    Inventors: Hongxia Xu, Alex Aravanis, Shengrong Lin