Patents by Inventor Arnold Oliphant

Arnold Oliphant 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: 20190276879
    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: May 23, 2019
    Publication date: September 12, 2019
    Inventors: Andrew Sparks, Craig Struble, Eric Wang, Arnold Oliphant
  • Patent number: 10400272
    Abstract: Methods, compositions, kits and apparatuses that include a fluid, the fluid containing a ternary complex and Li+, wherein the ternary complex includes a primed template nucleic acid, a polymerase, and a nucleotide cognate for the next correct base for the primed template nucleic acid molecule. As an alternative or addition to Li+, the fluid can contain betaine or a metal ion that inhibits polymerase catalysis such as Ca2+. In addition to Li+, the fluid can contain polyethylenimine (PEI) with or without betaine.
    Type: Grant
    Filed: March 15, 2019
    Date of Patent: September 3, 2019
    Assignee: OMNIOME, INC.
    Inventors: Morassa Mohseni Middleton, Mark C. Wallen, Pinar Iyidogan, Michael James Schmidt, Brittany A. Rohrman, Ying Lin Liu, Fabian Block, Arnold Oliphant
  • Publication number: 20190241945
    Abstract: A method of characterizing a nucleic acid that includes steps of (a) contacting a primer-template nucleic acid hybrid with a polymerase and a mixture of nucleotides to produce an extended primer hybrid and to form a stabilized ternary complex including the extended primer hybrid, the polymerase and a nucleotide cognate of the next base in the template, wherein the mixture contains nucleotide cognates of four different base types, wherein the nucleotide cognate of the first base type has a reversible terminator, and wherein nucleotide cognates of the second, third and fourth base types are extendable; (b) detecting the stabilized ternary complex to distinguish the next base from other base types in the template; and (c) determining the presence of a base multiplet in the template nucleic acid, the base multiplet including the first base type followed by the next base.
    Type: Application
    Filed: February 1, 2019
    Publication date: August 8, 2019
    Inventors: Denis Malyshev, Arnold Oliphant
  • 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
  • Publication number: 20190169688
    Abstract: A method of determining a nucleic acid sequence that includes steps of: (a) contacting a primed template nucleic acid with a series of mixtures for forming ternary complexes, wherein each of the mixtures includes a polymerase and nucleotide cognates for at least two different base types suspected of being present at the next template position of the template nucleic acid; (b) monitoring the next template position for ternary complexes formed by the series of mixtures, wherein a signal state indicates presence or absence of ternary complex formed at the next template position by each individual mixture, thereby determining a series of signal states that encodes a base call for the next template position; and (c) decoding the series of signal states to distinguish a correct base call for the next template position from an error in the base call.
    Type: Application
    Filed: October 8, 2018
    Publication date: June 6, 2019
    Inventors: Sean STROMBERG, John VIECELI, Kandaswamy VIJAYAN, Arnold OLIPHANT
  • Patent number: 10308981
    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: August 8, 2011
    Date of Patent: June 4, 2019
    Assignee: Ariosa Diagnostics, Inc.
    Inventors: Andrew Sparks, Craig Struble, Eric Wang, Arnold Oliphant
  • 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
  • Patent number: 10233496
    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: October 9, 2015
    Date of Patent: March 19, 2019
    Assignee: Ariosa Diagnostics, Inc.
    Inventors: Arnold Oliphant, Andrew Sparks, John Stuelpnagel, Ken Song
  • Publication number: 20190055606
    Abstract: The present invention provides assay systems and methods for determining the percent fetal contribution of cell-free DNA in a maternal sample from a pregnant female with an egg donor pregnancy. Further provided, are assay systems and methods for determining a statistical likelihood of the presence or absence of a fetal aneuploidy in a maternal sample using a determined percent fetal cell-free DNA in the sample.
    Type: Application
    Filed: October 24, 2018
    Publication date: February 21, 2019
    Inventors: Arnold Oliphant, Eric Wang, Craig Struble
  • Publication number: 20190055598
    Abstract: An apparatus can include a vessel, a reference surface, a preload, a scan actuator, and a transmitter. The reference surface can form a structural loop with a detector. The preload can be configured to urge the vessel to contact an area on the reference surface. The scan actuator can be configured to slide the vessel along the reference surface in a scan dimension. The transmitter can be configured to direct signal from the vessel to a detector and/or direct energy from an energy source to the vessel, when the vessel is urged by the preload to contact the reference surface.
    Type: Application
    Filed: September 25, 2018
    Publication date: February 21, 2019
    Inventors: Dale Buermann, Michael John Erickstad, Rebecca McGinley, Alex Nemiroski, Harry Scott Rapoport, Arnold Oliphant
  • Publication number: 20190055596
    Abstract: An apparatus can include a vessel, a reference surface, a preload, a scan actuator, and a transmitter. The reference surface can form a structural loop with a detector. The preload can be configured to urge the vessel to contact an area on the reference surface. The scan actuator can be configured to slide the vessel along the reference surface in a scan dimension. The transmitter can be configured to direct signal from the vessel to a detector and/or direct energy from an energy source to the vessel, when the vessel is urged by the preload to contact the reference surface.
    Type: Application
    Filed: August 15, 2018
    Publication date: February 21, 2019
    Inventors: Dale Buermann, Michael John Erickstad, Rebecca McGinley, Alex Nemiroski, Harry Scott Rapoport, Arnold Oliphant
  • Patent number: 10167508
    Abstract: The present invention provides assay systems and related methods for determining genetic abnormalities in mixed samples comprising cell free DNA from both normal and putative genetically atypical cells. Exemplary mixed samples for analysis using the assay systems of the invention include samples comprising both maternal and fetal cell free DNA and samples that contain DNA from normal cells and circulating cancerous cells.
    Type: Grant
    Filed: February 29, 2012
    Date of Patent: January 1, 2019
    Assignee: ARIOSA DIAGNOSTICS, INC.
    Inventors: Ken Song, Arnold Oliphant, John Stuelpnagel, Andrew Sparks
  • Patent number: 10161003
    Abstract: A method of determining a nucleic acid sequence that includes steps of: (a) contacting a primed template nucleic acid with a series of mixtures for forming ternary complexes, wherein each of the mixtures includes a polymerase and nucleotide cognates for at least two different base types suspected of being present at the next template position of the template nucleic acid; (b) monitoring the next template position for ternary complexes formed by the series of mixtures, wherein a signal state indicates presence or absence of ternary complex formed at the next template position by each individual mixture, thereby determining a series of signal states that encodes a base call for the next template position; and (c) decoding the series of signal states to distinguish a correct base call for the next template position from an error in the base call.
    Type: Grant
    Filed: March 15, 2018
    Date of Patent: December 25, 2018
    Assignee: Omniome, Inc.
    Inventors: Sean Stromberg, John Vieceli, Kandaswamy Vijayan, Arnold Oliphant
  • Publication number: 20180346986
    Abstract: The present invention provides processes for determining accurate risk probabilities for fetal aneuploidies. 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: August 8, 2018
    Publication date: December 6, 2018
    Inventors: Arnold Oliphant, Andrew Sparks, Eric Wang, Craig Struble
  • Publication number: 20180334719
    Abstract: The present invention provides methods for non-invasive determination of sex in a fetus or of Y chromosomal frequency abnormalities—indicative of aneuploidy or sex mosaicisms in a fetus—by detecting and determining the relative contribution genetic sequences from the Y chromosome in view of the percent fetal contribution in a maternal mixed sample.
    Type: Application
    Filed: May 18, 2018
    Publication date: November 22, 2018
    Inventors: Craig STRUBLE, Arnold OLIPHANT, Eric WANG
  • Patent number: 10131937
    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: November 10, 2011
    Date of Patent: November 20, 2018
    Assignee: ARIOSA DIAGNOSTICS, INC.
    Inventors: Andrew Sparks, Arnold Oliphant, Jacob Zahn, Ken Song, John Stuelpnagel
  • Patent number: 10131947
    Abstract: The present invention provides assay systems and methods for determining the percent fetal contribution of cell-free DNA in a maternal sample from a pregnant female with an egg donor pregnancy. Further provided, are assay systems and methods for determining a statistical likelihood of the presence or absence of a fetal aneuploidy in a maternal sample using a determined percent fetal cell-free DNA in the sample.
    Type: Grant
    Filed: December 19, 2012
    Date of Patent: November 20, 2018
    Assignee: ARIOSA DIAGNOSTICS, INC.
    Inventors: Arnold Oliphant, Eric Wang, Craig Struble
  • Patent number: 10131951
    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: July 8, 2016
    Date of Patent: November 20, 2018
    Assignee: ARIOSA DIAGNOSTICS, INC.
    Inventors: Andrew Sparks, Arnold Oliphant, Jacob Zahn, Ken Song, John Stuelpnagel
  • Publication number: 20180305749
    Abstract: A method of determining a nucleic acid sequence that includes steps of: (a) contacting a primed template nucleic acid with a series of mixtures for forming ternary complexes, wherein each of the mixtures includes a polymerase and nucleotide cognates for at least two different base types suspected of being present at the next template position of the template nucleic acid; (b) monitoring the next template position for ternary complexes formed by the series of mixtures, wherein a signal state indicates presence or absence of ternary complex formed at the next template position by each individual mixture, thereby determining a series of signal states that encodes a base call for the next template position; and (c) decoding the series of signal states to distinguish a correct base call for the next template position from an error in the base call.
    Type: Application
    Filed: March 15, 2018
    Publication date: October 25, 2018
    Inventors: Sean Stromberg, John VIECELI, Kandaswamy VIJAYAN, Arnold OLIPHANT
  • Patent number: 10017815
    Abstract: A scalable reaction and detection system for automated high throughput sequencing of nucleic acids involving a combination of chemical processes and observation processes independent of the chemistry processes. Discrete functional units may be configured in a manner that allows the system to interchangeably utilize different sequencing reaction components in conjunction with discrete apparatus components for optical image collection and/or analysis.
    Type: Grant
    Filed: August 28, 2015
    Date of Patent: July 10, 2018
    Assignee: Complete Genomics, Inc.
    Inventor: Arnold Oliphant