Patents by Inventor John Stuelpnagel

John Stuelpnagel 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).

  • ANALYSIS OF NUCLEIC ACID SEQUENCES
    Publication number: 20240384348
    Abstract: The present disclosure relates to methods, compositions and systems for haplotype phasing and copy number variation assays. Included within this disclosure are methods and systems for combining the barcode comprising beads with samples in multiple separate partitions, as well as methods of processing, sequencing and analyzing barcoded samples.
    Type: Application
    Filed: July 26, 2024
    Publication date: November 21, 2024
    Inventors: Michael SCHNALL-LEVIN, Mirna Jarosz, Christopher Hindson, Kevin Ness, Serge Saxonov, Benjamin Hindson, Xinying Zheng, Patrick Marks, John Stuelpnagel
  • PROCESSES FOR CALCULATING PHASED FETAL GENOMIC SEQUENCES
    Publication number: 20230107747
    Abstract: The present invention provides processes for calculating phased genomic sequences of the fetal genome using fetal DNA obtained from a maternal sample. The processes and systems of the present invention utilize novel technological and computational approaches to detect fetal genomic sequences and determine the phased heritable genomic sequences. The invention could be used, e.g., to identify in utero deleterious mutations carried by the parents and inherited by a fetus within a particular heritable genomic region.
    Type: Application
    Filed: July 12, 2022
    Publication date: April 6, 2023
    Inventors: John Stuelpnagel, Craig Struble, Eric Wang
  • Processes for calculating phased fetal genomic sequences
    Patent number: 11404142
    Abstract: The present invention provides processes for calculating phased genomic sequences of the fetal genome using fetal DNA obtained from a maternal sample. The processes and systems of the present invention utilize novel technological and computational approaches to detect fetal genomic sequences and determine the phased heritable genomic sequences. The invention could be used, e.g., to identify in utero deleterious mutations carried by the parents and inherited by a fetus within a particular heritable genomic region.
    Type: Grant
    Filed: May 13, 2019
    Date of Patent: August 2, 2022
    Assignee: Roche Molecular Systems, Inc.
    Inventors: John Stuelpnagel, Craig Struble, Eric Wang
  • DETERMINATION OF COPY NUMBER VARIATIONS USING BINOMIAL PROBABILITY CALCULATIONS
    Publication number: 20220208298
    Abstract: This invention relates to a binomial calculation of copy number of data obtained from a mixed sample having a first source and a second source.
    Type: Application
    Filed: March 18, 2022
    Publication date: June 30, 2022
    Inventors: Craig Struble, John Stuelpnagel
  • Assay systems for genetic analysis
    Patent number: 11319578
    Abstract: The present invention provides assays systems and methods for detection of chromosomal abnormalities and status of single loci associated with monogenic or polygenic traits in a sample containing nucleic acids from a maternal and a fetal source.
    Type: Grant
    Filed: December 21, 2017
    Date of Patent: May 3, 2022
    Assignee: Roche Molecular Systems, Inc.
    Inventors: Andrew Sparks, Arnold Oliphant, Jacob Zahn, Ken Song, John Stuelpnagel
  • Determination of copy number variations using binomial probability calculations
    Patent number: 11289176
    Abstract: This invention relates to a binomial calculation of copy number of data obtained from a mixed sample having a first source and a second source.
    Type: Grant
    Filed: February 10, 2014
    Date of Patent: March 29, 2022
    Assignee: Ariosa Diagnostics, Inc.
    Inventors: Craig Struble, John Stuelpnagel
  • ASSAY SYSTEMS FOR DETERMINATION OF FETAL COPY NUMBER VARIATION
    Publication number: 20210343361
    Abstract: The present invention provides processes for determining accurate risk probabilities for chromosome dosage abnormalities. Specifically, the invention provides non-invasive evaluation of genomic variations through chromosome-selective sequencing and non-host fraction data analysis of maternal samples.
    Type: Application
    Filed: May 20, 2021
    Publication date: November 4, 2021
    Inventors: John Stuelpnagel, Ken Song, Arnold Oliphant, Craig Struble
  • Assay systems for genetic analysis
    Patent number: 11091807
    Abstract: The present invention provides assay systems and methods for detection of copy number variation at one or more loci and polymorphism detection at one or more loci in a mixed sample from an individual.
    Type: Grant
    Filed: October 12, 2018
    Date of Patent: August 17, 2021
    Assignee: Ariosa Diagnostics, Inc.
    Inventors: Andrew Sparks, Arnold Oliphant, Jacob Zahn, Ken Song, John Stuelpnagel
  • ASSAY SYSTEMS FOR DETERMINATION OF FETAL COPY NUMBER VARIATION
    Publication number: 20210202030
    Abstract: The present invention provides processes for determining accurate risk probabilities for chromosome dosage abnormalities. Specifically, the invention provides non-invasive evaluation of genomic variations through chromosome-selective sequencing and non-host fraction data analysis of maternal samples.
    Type: Application
    Filed: March 21, 2012
    Publication date: July 1, 2021
    Inventors: John Stuelpnagel, Ken Song, Arnold Oliphant, Craig Struble
  • Assay systems for determination of fetal copy number variation
    Patent number: 11031095
    Abstract: The present invention provides processes for determining accurate risk probabilities for chromosome dosage abnormalities. Specifically, the invention provides non-invasive evaluation of genomic variations through chromosome-selective sequencing and non-host fraction data analysis of maternal samples.
    Type: Grant
    Filed: March 21, 2012
    Date of Patent: June 8, 2021
    Assignee: Ariosa Diagnostics, Inc.
    Inventors: John Stuelpnagel, Ken Song, Arnold Oliphant, Craig Struble
  • ANALYSIS OF NUCLEIC ACID SEQUENCES
    Publication number: 20210123103
    Abstract: The present disclosure relates to methods, compositions and systems for haplotype phasing and copy number variation assays. Included within this disclosure are methods and systems for combining the barcode comprising beads with samples in multiple separate partitions, as well as methods of processing, sequencing and analyzing barcoded samples.
    Type: Application
    Filed: June 11, 2020
    Publication date: April 29, 2021
    Inventors: Michael Schnall-Levin, Mirna Jarosz, Christopher Hindson, Kevin Ness, Serge Saxonov, Benjamin Hindson, Xinying Zheng, Patrick Marks, John Stuelpnagel
  • Ligation-based detection of genetic variants
    Patent number: 10954566
    Abstract: The present invention provides assays systems and methods for detection of genetic variants in a sample, including copy number variation and single nucleotide polymorphisms. The invention preferably employs the technique of tandem ligation—, e.g., the ligation of two or more fixed sequence oligonucleotides and one or more bridging oligonucleotides complementary to a region between the fixed sequence oligonucleotides—combined with detection of levels of particular genomic regions using array hybridization.
    Type: Grant
    Filed: January 23, 2019
    Date of Patent: March 23, 2021
    Assignee: Ariosa Diagnostics, Inc.
    Inventors: Arnold Oliphant, Andrew Sparks, John Stuelpnagel, Ken Song
  • Assay systems for genetic analysis
    Patent number: 10907198
    Abstract: The present invention provides assays systems and methods for detection of chromosomal abnormalities and status of single loci associated with monogenic or polygenic traits in a sample containing nucleic acids from a maternal and a fetal source.
    Type: Grant
    Filed: October 12, 2018
    Date of Patent: February 2, 2021
    Assignee: Ariosa Diagnostics, Inc.
    Inventors: Andrew Sparks, Arnold Oliphant, Jacob Zahn, Ken Song, John Stuelpnagel
  • Methods and Compositions for Sample Analysis
    Publication number: 20200399631
    Abstract: The present disclosure relates to methods and systems for sample processing and analyzing when the total quantity of input sample is low or when a target of interest is present as a relatively minor or rare population within the overall sample. The disclosure particularly relates to analyzing nucleic acid samples, including samples where a target nucleic acid of interest is present as a relatively low proportion of the overall nucleic acids.
    Type: Application
    Filed: December 23, 2019
    Publication date: December 24, 2020
    Inventors: Mirna Jarosz, Christopher Hindson, Michael Schnall-Levin, Kevin Dean Ness, Serge Saxonov, Benjamin Hindson, John Stuelpnagel
  • Determination of copy number variations using binomial probability calculations
    Patent number: 10847250
    Abstract: This invention relates to a binomial calculation of copy number of data obtained from a mixed sample having a first source and a second source.
    Type: Grant
    Filed: February 10, 2014
    Date of Patent: November 24, 2020
    Assignee: Ariosa Diagnostics, Inc.
    Inventors: Craig Struble, John Stuelpnagel
  • LIGATION-BASED DETECTION OF GENETIC VARIANTS
    Publication number: 20200109450
    Abstract: The present invention provides assays systems and methods for detection of genetic variants in a sample, including copy number variation and single nucleotide polymorphisms. The invention preferably employs the technique of tandem ligation—, e.g., the ligation of two or more fixed sequence oligonucleotides and one or more bridging oligonucleotides complementary to a region between the fixed sequence oligonucleotides—combined with detection of levels of particular genomic regions using array hybridization.
    Type: Application
    Filed: January 23, 2019
    Publication date: April 9, 2020
    Inventors: Arnold Oliphant, Andrew Sparks, John Stuelpnagel, Ken Song
  • PROCESSES FOR CALCULATING PHASED FETAL GENOMIC SEQUENCES
    Publication number: 20190378593
    Abstract: The present invention provides processes for calculating phased genomic sequences of the fetal genome using fetal DNA obtained from a maternal sample. The processes and systems of the present invention utilize novel technological and computational approaches to detect fetal genomic sequences and determine the phased heritable genomic sequences. The invention could be used, e.g., to identify in utero deleterious mutations carried by the parents and inherited by a fetus within a particular heritable genomic region.
    Type: Application
    Filed: May 13, 2019
    Publication date: December 12, 2019
    Inventors: John Stuelpnagel, Craig Struble, Eric Wang
  • ASSAY SYSTEMS FOR GENETIC ANALYSIS
    Publication number: 20190169681
    Abstract: The present invention provides assays systems and methods for detection of chromosomal abnormalities and status of single loci associated with monogenic or polygenic traits in a sample containing nucleic acids from a maternal and a fetal source.
    Type: Application
    Filed: October 12, 2018
    Publication date: June 6, 2019
    Inventors: Andrew Sparks, Arnold Oliphant,, Jacob Zahn, Ken Song, John Stuelpnagel
  • Processes for calculating phased fetal genomic sequences
    Patent number: 10289800
    Abstract: The present invention provides processes for calculating phased genomic sequences of the fetal genome using fetal DNA obtained from a maternal sample. The processes and systems of the present invention utilize novel technological and computational approaches to detect fetal genomic sequences and determine the phased heritable genomic sequences. The invention could be used, e.g., to identify in utero deleterious mutations carried by the parents and inherited by a fetus within a particular heritable genomic region.
    Type: Grant
    Filed: May 20, 2013
    Date of Patent: May 14, 2019
    Inventors: John Stuelpnagel, Craig Struble, Eric Wang
  • ASSAY SYSTEMS FOR GENETIC ANALYSIS
    Publication number: 20190119752
    Abstract: The present invention provides assay systems and methods for detection of copy number variation at one or more loci and polymorphism detection at one or more loci in a mixed sample from an individual.
    Type: Application
    Filed: October 12, 2018
    Publication date: April 25, 2019
    Inventors: Andrew Sparks, Arnold Oliphant, Jacob Zahn, Ken Song, John Stuelpnagel