Patents Examined by Mary K Zeman
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Patent number: 10580518Abstract: A system and method for performing similarity searching is disclosed wherein programmable logic devices such as field programmable gate arrays (FPGAs) can be used to implement Bloom filters for identifying possible matches between a query and data. The Bloom filters can be implemented in a parallel architecture where the different parallel Bloom filters share access to the same memory units. Further, a hash table may be generated to map a set of strings to keys. In other examples, the hash table may be used to map a set of substrings to a position in a larger string.Type: GrantFiled: January 11, 2017Date of Patent: March 3, 2020Assignee: WASHINGTON UNIVERSITYInventors: Jeremy Daniel Buhler, Roger Dean Chamberlain, Mark Allen Franklin, Kwame Gyang, Arpith Chacko Jacob, Praveen Krishnamurthy, Joseph Marion Lancaster
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Patent number: 10558930Abstract: An input sample SNP genotype is divided into a plurality of windows, each including a sequence of SNPs. For each window, a diploid hidden Markov Model (HMM) is built and from a haplotype Markov Model (MM). The diploid HMM for a window is used to determine the probability that the window corresponds to a pair of labels (e.g., ethnicity labels). An inter-window HMM, with a set of states for each window, is built based on the diploid HMMs for each window. Labels are assigned to the input sample genotype based on the inter-window HMM.Type: GrantFiled: July 13, 2016Date of Patent: February 11, 2020Assignee: Ancestry.com DNA, LLCInventors: Keith D. Noto, Yong Wang
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Patent number: 10529441Abstract: The present invention relates to genetic analysis and evaluation utilizing copy-number variants or polymorphisms. The methods utilize array comparative genomic hybridization and PCR assays to identify the significance of copy number variations in a subject or subject group.Type: GrantFiled: November 26, 2013Date of Patent: January 7, 2020Assignee: POPULATION BIO, INC.Inventors: James Chinitz, Eli Hatchwell
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Patent number: 10529444Abstract: System that generates the solvent-excluded surface (SES) of a molecule using a parallel algorithm that may execute on a GPU. Parallel execution allows a SES to be created in seconds even for a large protein, or to be recreated rapidly when exploring modifications to molecular structure. The algorithm calculates a spatial field that represents a signed distance between an atom-facing surface of a probe and each point in 3D grid. Spatial field calculations for different grid points may be performed in parallel. The SES is then obtained as the zero isosurface of the spatial field, using for example marching cubes. Atoms and probes may be placed into spatial buckets and indexed by bucket to improve efficiency by limiting calculations to atoms and probes in the proximity of a point.Type: GrantFiled: February 6, 2019Date of Patent: January 7, 2020Assignee: Nanome Inc.Inventors: Yang Zhou, Vincent Brunet, Kai Wang, Steven McCloskey
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Patent number: 10522240Abstract: The present invention relates to genetic analysis and evaluation utilizing copy-number variants or polymorphisms. The methods utilize array comparative genomic hybridization and PCR assays to identify the significance of copy number variations in a human, non-human animal, and plant subject or subject group.Type: GrantFiled: July 22, 2015Date of Patent: December 31, 2019Assignee: POPULATION BIO, INC.Inventors: James Chinitz, Eli Hatchwell
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Patent number: 10515447Abstract: Disclosed are methods and software for biological data analysis. Specifically, provided are methods, computer programs and systems for analyzing data in the form of various intensity measurements obtained from an oligonucleotides microarray experiment. Such data may be microarray data obtained from an experiment conducted to determine copy number of a human genetic sample. The data are corrected by application of one or more covariate adjusters which may be applied simultaneously and which may be selected by a user. Further, the present application provides methods of filtering image data and signal restoration of image data using log2 ratio data.Type: GrantFiled: November 29, 2012Date of Patent: December 24, 2019Assignee: Affymetrix, Inc.Inventors: Benjamin M. Bolstad, Harry Zuzan
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Patent number: 10504611Abstract: Described are computational methods to reconstruct the chromosomes (and genomes) of ancestors given genetic data, IBD information, and full or partial pedigree information of some number of their descendants.Type: GrantFiled: October 19, 2015Date of Patent: December 10, 2019Assignee: Ancestry.com DNA, LLCInventors: Julie M. Granka, Keith D. Noto
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Patent number: 10488402Abstract: A computer system is provided for determining the relative effectiveness of anti-cancer drugs. The interface has selectable options, including an option to manage drug testing parameters, and enables user selection of desired drug testing parameters in relation to a virtual well plate associated with a physical well plate of a spectrophotometer. The computer system causes the spectrophotometer to start a drug test, wherein the physical well plate includes at least one test well containing viable cancer cells; and at least one drug candidate in a predetermined concentration; and at least one control well containing the viable cancer cells alone. The system records the optical density of the well at a predetermined wavelength at selected time intervals for a selected duration of time, and stores the optical density and time measurements in the database.Type: GrantFiled: October 4, 2016Date of Patent: November 26, 2019Assignee: Pierian Biosciences, LLCInventors: Mathieu Perree, Allan E. Hallquist, Olivier Petit
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Patent number: 10468141Abstract: Disclosed herein are methods and systems for calculating genetic risk scores (GRS) representing the likelihood that an individual will develop a specific trait based on the ancestry of the individual. Also provided are methods and systems for providing a recommendation to the individual to modify a behavior related to a specific trait, based on the individual's GRS for that trait.Type: GrantFiled: December 11, 2018Date of Patent: November 5, 2019Assignee: ASIA GENOMICS PTE. LTD.Inventors: Robert Keams Valenzuela, Vishweshwaran Sridhar, Chun Meng Ong, Jia Yi Har, Pauline C. Ng, Mun Yew Wong
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Patent number: 10458984Abstract: A method for evaluation of an interaction between an analyte in a fluid sample and a ligand immobilized on a sensor surface of a biosensor, which comprises the steps of: providing a reference binding curve, representing a reference interaction for a predetermined acquisition cycle, acquiring, using the biosensor, a sample binding curve for the analyte ligand interaction for the predetermined acquisition cycle, registering the deviation of the sample binding curve from the reference binding curve, and classifying the analyte ligand interaction as equivalent to the reference interaction when the registered deviation is less than a predetermined deviation criteria. There is further provided a biosensor system and a computer program.Type: GrantFiled: January 29, 2015Date of Patent: October 29, 2019Assignee: GE Healthcare Bio-Sciences ABInventor: Robert Karlsson
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Patent number: 10457990Abstract: Embodiments of the present invention provide methods, systems, and apparatus for deducing the fetal DNA fraction in maternal plasma without using paternal or fetal genotypes. Maternal genotype information may be obtained from a maternal-only DNA sample or may be assumed from shallow-depth sequencing of a biological sample having both maternal and fetal DNA molecules. Because sequencing may be at shallow depths, a locus may have only few reads and may fail to exhibit a non-maternal allele even if a non-maternal allele is present. However, normalized parameters that characterize non-maternal alleles sequenced can be used to provide an accurate estimate of the fetal DNA fraction, even if the amount of non-maternal alleles is in error. Methods described herein may not need high-depth sequencing or enrichment of specific regions. As a result, these methods can be integrated into widely used non-invasive prenatal testing and other diagnostics.Type: GrantFiled: September 22, 2016Date of Patent: October 29, 2019Assignee: The Chinese University of Hong KongInventors: Yuk-Ming Dennis Lo, Peiyong Jiang, Kwan Chee Chan, Rossa Wai Kwun Chiu
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Patent number: 10451536Abstract: In one aspect, the present invention relates to a method 200 for identifying one or more phenotypes from a multi-parameter data set. The method 200 comprises measuring 202 correlation between pairs of parameters within the multi-parameter data set, modifying 204 correlated parameter values within a predetermined multi-parameter data analysis set to form an analysis parameter set, and analyzing 206 the multi-parameter data set using the analysis parameter set to identify one or more phenotypes from the multi-parameter data set. Various embodiments of the present invention may, for example, be used in an automated high-content screening (HCS) apparatus 100 for biological cellular analysis.Type: GrantFiled: April 23, 2010Date of Patent: October 22, 2019Assignee: GE HEALTHCARE UK LIMITEDInventor: Nicholas Thomas
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Patent number: 10453555Abstract: Regulated changes in gene expression underlie many biological processes, but globally profiling cell-to-cell variations in transcriptional regulation is problematic when measuring single cells. Transcriptome-wide identification of regulatory heterogeneities can be robustly achieved by randomly collecting small numbers of cells followed by statistical analysis. However, this stochastic-profiling approach blurs out the expression states of the individual cells in each pooled sample. Various aspects of the disclosure show that the underlying distribution of single-cell regulatory states can be deconvolved from stochastic-profiling data through maximum-likelihood inference. Guided by the mechanisms of transcriptional regulation, the disclosure provides mixture models for cell-to-cell regulatory heterogeneity which result in likelihood functions to infer model parameters.Type: GrantFiled: January 19, 2016Date of Patent: October 22, 2019Assignee: University of Virginia Patent FoundationInventors: Kevin Janes, Sameer Bajikar, Fabian Theis, Christiane Fuchs
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Patent number: 10453558Abstract: The present invention relates to a method for constructing quadrants corresponding to different diseases in a frame of concentrations of multiple independent biomarkers, comprising: (a) transferring original distributed concentrations of every independent biomarker to modified distributed concentrations, comprising: calculating the mean value and the standard deviation of the original distributed concentrations for a given independent biomarker; individually subtracting all the original distributed concentrations by the mean value for the given independent biomarker; and individually dividing all the differences by the standard deviation to get the modified distributed concentrations for the given independent biomarker; (b) positing the modified distributed concentrations in a frame of multiple independent biomarkers; and (c) finding a boundary optimally separating neighboring quadrants corresponding to different diseases.Type: GrantFiled: April 21, 2016Date of Patent: October 22, 2019Assignee: MAGQU CO. LTD.Inventor: Shieh-Yueh Yang
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Database and data processing system for use with a network-based personal genetics services platform
Patent number: 10437858Abstract: Databases and data processing systems for use with a network-based personal genetics services platform may include member information pertaining to a plurality of members of the network-based personal genetics services platform. The member information may include genetic information, family history information, environmental information, and phenotype information of the plurality of members. A data processing system may determine, based at least in part on the member information, a model for predicting a phenotype from genetic information, family history information, and environmental information, wherein determining the model includes training the model using the member information pertaining to a set of the plurality of members.Type: GrantFiled: May 10, 2016Date of Patent: October 8, 2019Assignee: 23andMe, Inc.Inventors: Brian Thomas Naughton, Chuong Do, John Michael Macpherson -
Patent number: 10418128Abstract: Disclosed are systems and methods for polynucleotide sequencing where detection and correction of base calling errors can be achieved without reliance on a reference sequence. In certain embodiments, redundant information can be introduced during measurement so as to allow such detection of errors. Such redundant information and measurements can be facilitated by encoding of nucleotide sequence being measured. Various examples of such encoding, redundancy introduction, and decoding are provided.Type: GrantFiled: November 25, 2015Date of Patent: September 17, 2019Assignee: Life Technologies CorporationInventors: Marcin Sikora, Alan Blanchard
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Patent number: 10407735Abstract: The present invention relates to compositions and methods for cancer diagnosis, research and therapy, including but not limited to, cancer markers. In particular, the present invention relates to ncRNAs as diagnostic markers and clinical targets for prostate, lung, breast and pancreatic cancer.Type: GrantFiled: May 17, 2016Date of Patent: September 10, 2019Assignee: THE REGENTS OF THE UNIVERSITY OF MICHIGANInventors: Arul Chinnaiyan, John Prensner, Matthew Iyer
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Patent number: 10385385Abstract: A method for performing digital polymerase chain reaction (dPCR) is provided. The method includes partitioning a biological sample volume including a plurality of target nucleic acids into a plurality of partitions, where at least one partition includes at least one target nucleic acid. The method further includes determining a model for volume variation of the plurality of partitions and determining a number of partitions including at least one target nucleic acid. The method includes generating a concentration of target nucleic acids in the biological sample based on the model for volume variation and the fraction of partitions including at least one target nucleic acid.Type: GrantFiled: April 22, 2016Date of Patent: August 20, 2019Assignee: Life Technologies CorporationInventors: Nivedita Sumi Majumdar, Swapnonil Banerjee
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Patent number: 10364467Abstract: Analysis of tumor-derived circulating cell-free DNA opens up new possibilities for performing liquid biopsies for solid tumor assessment or cancer screening. However, many aspects of the biological characteristics of tumor-derived cell-free DNA remain unclear. Regarding the size profile of plasma DNA molecules, some studies reported increased integrity of tumor-derived plasma DNA while others reported shorter tumor-derived plasma DNA molecules. We performed an analysis of the size profiles of plasma DNA in patients with cancer using massively parallel sequencing at single base resolution and in a genomewide manner. Tumor-derived plasma DNA molecules were further identified using chromosome arm-level z-score analysis (CAZA). We showed that populations of aberrantly short and long DNA molecules co-existed in the plasma of patients with cancer. The short ones preferentially carried the tumor-associated copy number aberrations. These results show the ability to use plasma DNA as a molecular diagnostic tool.Type: GrantFiled: January 12, 2016Date of Patent: July 30, 2019Assignee: The Chinese University of Hong KongInventors: Yuk-Ming Dennis Lo, Rossa Wai Kwun Chiu, Kwan Chee Chan, Peiyong Jiang
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Patent number: 10353869Abstract: A method, computer product, and computer system of minimizing surprisal data comprising: at a source, reading and identifying characteristics of a genetic sequence of an organism; receiving an input of rank of at least two identified characteristics of the genetic sequence of the organism; generating a hierarchy of ranked, identified characteristics based on the rank of the at least two identified characteristics of the genetic sequence of the organism; comparing the hierarchy of ranked, identified characteristics to a repository of reference genomes; and if at least one reference genome from the repository matches the hierarchy of ranked, identified characteristics, breaking the matched reference genomes into pieces, combining pieces associated with the identified characteristics from at least one matched reference genome to form a filter pattern to be compared to the nucleotides of the genetic sequence of the organism, to obtain differences and create surprisal data.Type: GrantFiled: June 8, 2012Date of Patent: July 16, 2019Assignee: International Business Machines CorporationInventors: Robert R. Friedlander, James R. Kraemer