Patents by Inventor Nathan Hunkapiller

Nathan Hunkapiller 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).

  • Publication number: 20240309461
    Abstract: Methods and systems for sample contamination detection are disclosed. In particular, sample barcodes are utilized, wherein each sample barcode is assigned to a sample and ligated to fragments from the sample. The sample barcodes are used in conjunction with indices from sequencing libraries to accurately assign sequence reads to samples during multiplex sequencing. Molecule identifiers may also be utilized to aid in de-duping of sequence reads to precisely identify original NA fragments from a sample. Accordingly, in one or more embodiments, a sequencing method includes isolating DNA fragments in a sample, ligating the DNA fragments with unique molecule identifiers (UMIs), performing an amplification process resulting in amplicons, ligating a sample barcode onto the amplicons, and performing amplicon sequencing. The analytics system looks to whether indices are matched and whether a sample barcode matches to the pair of indices when identifying single-index or double-index hopping events.
    Type: Application
    Filed: March 13, 2024
    Publication date: September 19, 2024
    Inventors: Seyedmedhi Shojaee, Nathan Hunkapiller, Byoungsok Jung, Farnaz Absalan, Chenlu Hou, Sahar Nohzadeh-Malakshah, Christopher Chang
  • Publication number: 20220348907
    Abstract: Methods for preparing sequencing libraries from a DNA-containing test sample, as well as methods for correcting sequencing-derived errors, are provided.
    Type: Application
    Filed: June 29, 2022
    Publication date: November 3, 2022
    Inventors: Lijuan Ji, Nathan Hunkapiller, Suchitra Ramani
  • Patent number: 11414656
    Abstract: Methods for preparing sequencing libraries from a DNA-containing test sample, as well as methods for correcting sequencing-derived errors, are provided.
    Type: Grant
    Filed: December 14, 2018
    Date of Patent: August 16, 2022
    Assignee: GRAIL, Inc.
    Inventors: Lijuan Ji, Nathan Hunkapiller, Suchitra Ramani
  • Publication number: 20190225962
    Abstract: Methods for preparing sequencing libraries from a DNA-containing test sample, as well as methods for correcting sequencing-derived errors, are provided.
    Type: Application
    Filed: December 14, 2018
    Publication date: July 25, 2019
    Inventors: Lijuan Ji, Nathan Hunkapiller, Suchitra Ramani
  • Publication number: 20190185930
    Abstract: Methods for preparing sequencing libraries from a DNA-containing test sample, as well as methods for correcting sequencing-derived errors in sequence reads, and methods for identifying rare variants in a test sample, are provided.
    Type: Application
    Filed: December 20, 2018
    Publication date: June 20, 2019
    Inventors: Lijuan Ji, Nathan Hunkapiller, Nicholas Eattock, Byoungsok Jung
  • Publication number: 20140051585
    Abstract: Embodiments include methods, compositions, and kits for creating genetic libraries useful for massively parallel genetic sequencing. Some embodiments are directed to methods of preventing the contamination of genetic libraries with material generated during the formation of other genetic libraries. In some embodiments, the methods employ adapters comprising universal priming sites. The methods can employ non-ligatable primers to generate non-ligatable amplification products so as to prevent unwanted ligation to adapters. In some embodiments, the non-ligatable primers contain uracil. Genetic material can be treated with uracil N glycosylase to prevent the unwanted ligation of uracil containing amplicons to adapters used for creating a second genetic library.
    Type: Application
    Filed: August 15, 2013
    Publication date: February 20, 2014
    Applicant: NATERA, INC.
    Inventors: Dennis Prosen, Johan Baner, Nathan Hunkapiller, Matthew Hill, Bernhard Zimmermann