Patents Examined by Kaitlyn L Minchella
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Patent number: 11959856Abstract: Methods and algorithms for a multiplexed single detection channel amplification process and quantification of generated amplicons is presented. Various mathematical approaches for quantifying and verifying the amplicons in a reaction are presented. Usage of such methods and approaches allow upgrading of existing single and multiple channel instruments for further multiplexing capabilities.Type: GrantFiled: September 11, 2017Date of Patent: April 16, 2024Assignee: California Institute of TechnologyInventors: Imran R. Malik, Xiomara Linnette Madero, Erika F. Garcia, Sheel Mukesh Shah, Axel Scherer
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Patent number: 11926821Abstract: The quality of cell-free DNA for analysis is improved by techniques described herein. Cell-free DNA may include DNA with defects that do not allow for analysis of those DNA with techniques such as sequencing and targeted capture enrichment. These defects may be defects within the strands of the DNA and not present at the ends of the DNA. These intrastrand defects in cell-free DNA can be repaired. The repair of the defects in cell-free DNA may then allow for these repaired cell-free DNA to be analyzed by techniques, including sequencing and targeted capture enrichment.Type: GrantFiled: October 21, 2019Date of Patent: March 12, 2024Assignee: The Chinese University of Hong KongInventors: Yuk-Ming Dennis Lo, Cheuk Ho Tsang, Peiyong Jiang, Si Long Vong, Rossa Wai Kwun Chiu
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Patent number: 11929149Abstract: Provided herein are methods for aligning raw genetic sequence data generated by a sequencing device. Also provided herein are methods and systems for quantifying the probability that possible alignments for one or more read pairs are correct, for calling known variants, and for detecting novel structural variants.Type: GrantFiled: August 4, 2016Date of Patent: March 12, 2024Assignee: ARC BIO, LLCInventors: Alejandro Quiroz Zarate, Roberto Olivares-Amaya, Thomas James Watson, Jr., Helen Cecile Van Aggelen, Eduardo Coronado Sroka, Carlos Antonio Angulo Sermeno, Fernando Fimbres Jurado, Abraham Solis Garcia-Inda, Fernando Fontove Herrera, Pablo G. Coste
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Patent number: 11925462Abstract: A system for analyzing glucose monitoring data indicative of a glucose level in a bodily fluid. The system includes an input device, a data processing device, an output device, a display device, and machine readable instructions that are executed by the data processing device, wherein the machine readable instructions cause the data processing device to receive glucose monitoring data via the input device, the glucose monitoring data indicating a glucose level in a bodily fluid sampled for a person at a plurality of sample times over a measurement time period in a glucose level measurement, and comprising a plurality of glucose profiles, each of the glucose profiles comprising a plurality of glucose values assigned to one of the plurality of sample times. Furthermore, a method for analyzing glucose monitoring data indicative of a glucose level in a system is provided.Type: GrantFiled: January 24, 2017Date of Patent: March 12, 2024Assignee: Roche Diabetes Care, Inc.Inventors: Matthias Koehler, Timm Wiedemann
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Patent number: 11718869Abstract: A method and a kit for determining genome instability based on next generation sequencing (NGS) are disclosed. The new method is used to determine whether there is homologous recombination defect by calculating a comprehensive value of one or more of pathogenic germline and somatic mutations, such as SNV, indels, and CNVs, and Biallelic germline and somatic mutations, pathogenic mutational signature, copy number variation (CNV) in homologous recombination repair (HRR) gene, genomic structural variation and genome instability. The genomics DNA is interrupted and added with an A adapter; then corresponding polymerase chain reaction (PCR) is conducted, and Whole genome sequencing is performed; the hybrid capture is conducted with designed probes of HRR genes and SNPs, and a captured DNA library is subjected to amplification and library sequencing; and then professional bioinformatics software is used for evaluation to determine the homologous recombination deficiency (HRD) status.Type: GrantFiled: March 15, 2021Date of Patent: August 8, 2023Assignee: ZHENYUE BIOTECHNOLOGY JIANGSU CO., LTD.Inventors: Fang Lv, Huiting Yan, Yaxi Zhang, Shiqi Zheng, Yiqian Liu, Jianing Yu, Hong Lv, Weizhi Chen, Shan Zheng, Ji He, Bo Du
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Patent number: 11697605Abstract: A computer of a microbial community analysis system includes an input unit configured to input a plurality of data groups including information indicating a nucleotide sequence of a gene of each of a plurality of microorganisms included in activated sludge in which a water treatment is performed; a similarity calculating unit configured to calculate a similarity between data groups on the basis of the nucleotide sequences included in the input data groups, and a coordinates calculating unit configured to calculate coordinates in a multidimensional space of each of the data groups on the basis of the calculated similarity.Type: GrantFiled: March 30, 2016Date of Patent: July 11, 2023Assignee: Sumitomo Chemical Company, LimitedInventors: Hiroyuki Asako, Fumiyoshi Okazaki
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Patent number: 11664092Abstract: Disclosed herein are biomarkers associated with a disease state such as lung cancer, and methods of discovering or using biomarkers. Also disclosed herein are classifiers built on biomarkers and methods of detecting the disease state in samples from subjects. The method may include obtaining a data set that includes protein information from a biofluid sample, and may involve using a classifier to identify the sample as indicative of a healthy state, a disease state, or a comorbidity.Type: GrantFiled: January 26, 2022Date of Patent: May 30, 2023Assignee: PrognomIQ, Inc.Inventors: John E. Blume, William C. Manning, Gregory Troiano, Asim Siddiqui, Philip Ma, Omid C. Farokhzad
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Patent number: 11636951Abstract: A system for generating a genotypic causal model of a disease state includes a computing device that generates a causal graph containing genotypic causal nodes and connected symptomatic causal nodes, which contains causal paths from gene combinations to symptomatic datums. Genotypic causal nodes and/or connected symptomatic causal nodes may be generated by feature learning algorithms from training data.Type: GrantFiled: October 2, 2019Date of Patent: April 25, 2023Assignee: KPN INNOVATIONS, LLC.Inventor: Kenneth Neumann
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Patent number: 11538554Abstract: Nick-based methods, devices, and systems for nick-based data storage in a deoxyribonucleic acid (DNA) sequence are disclosed. Digital information is encoded in a register of at least one copy of a double-stranded DNA sequence having a plurality of nickable positions. The data is translated into a sequence of values from a nick alphabet that is subsequently mapped to the plurality of nickable positions, and the DNA sequence is nicked according to the mapped values. Because the digital information is encoded as a series of nicked and non-nicked positions of a double-stranded DNA sequence, the nucleotide sequence of the DNA can be non-synthetic, or “native” DNA.Type: GrantFiled: September 19, 2018Date of Patent: December 27, 2022Assignee: THE BOARD OF TRUSTEES OF THE UNIV OF ILLINOISInventors: Olgica Milenkovic, Alvaro Gonzalo Hernandez, Seyed Kasra Tabatabaei, Huimin Zhao
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Patent number: 11527323Abstract: Systems and methods are provided for identifying a diagnosis of a cancer condition for a somatic tumor specimen of a subject. The method receives sequencing information comprising analysis of a plurality of nucleic acids derived from the somatic tumor specimen. The method identifies a plurality of features from the sequencing information, including two or more of RNA, DNA, RNA splicing, viral, and copy number features. The method provides a first subset of features and a second subset of features from the identified plurality of features as inputs to a first classifier and a second classifier, respectively. The method generates, from two or more classifiers, two or more predictions of cancer condition based at least in part on the identified plurality of features. The method combines, at a final classifier, the two or more predictions to identify the diagnosis of the cancer condition for the somatic tumor specimen of the subject.Type: GrantFiled: May 12, 2020Date of Patent: December 13, 2022Assignee: Tempus Labs, Inc.Inventors: Jackson Michuda, Kyle Ashley Beauchamp, Joshuah Kapilivsky, Calvin McCarter, Nike Beaubier, Martin Christian Stumpe, Catherine Igartua, Joshua S K Bell, Timothy Taxter, Raphael Pelossof
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Patent number: 11512306Abstract: Temporal variations in one or more characteristics measured from a cell-free DNA sample are used to estimate a gestational age of a fetus. Example characteristics include the methylation level measured from the cell-free DNA sample, size of DNA fragments measured from the cell-free DNA sample (e.g., proportion of fetal-derived DNA fragments longer than a specified size), and ending patterns of the DNA fragments align to a reference genome.Type: GrantFiled: October 18, 2017Date of Patent: November 29, 2022Assignee: 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: 11482305Abstract: A system and method may be provided to receive sample RNA reads from patients and generate lists of genes and their associated RNA expression levels in each patient. Some of the RNA reads may be matched to an RNA transcript or gene or gene family in terms of their match likelihood and other RNA reads may be matched to an RNA transcript or gene or gene family through the use of one or more machine learning classifiers. A machine learning classifier may be trained based on the plurality of the lists and a plurality of corresponding patients' clinical status data to identify gene patterns that recur with a high degree of frequency in the plurality of the lists. Those gene patterns can be capable of modifying a disease or treatment response and can be targeted for drug/treatment development.Type: GrantFiled: August 19, 2019Date of Patent: October 25, 2022Assignee: Synkrino Biotherapeutics, Inc.Inventors: Jason Barbour, David Ott
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Patent number: 11401552Abstract: Methods are provided of identifying a male fertility condition in a subject. Methods of performing a fertility treatment and an in vitro fertilization procedure are also provided. The methods may comprise determining the DNA methylation pattern of DNA extracted from a semen sample of a subject.Type: GrantFiled: August 8, 2016Date of Patent: August 2, 2022Assignees: University of Utah Research Foundation, The University of Southern CaliforniaInventors: Douglas T. Carrell, Bradley Cairns, Kenneth I. Aston, Timothy Jenkins, Andrew David Smith, Philip James Uren, Alan Horsager
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Patent number: 11385215Abstract: In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.Type: GrantFiled: February 24, 2020Date of Patent: July 12, 2022Assignee: Trace Genomics, Inc.Inventors: Wyatt Hugh Hartman, David Curtis Stone, Ariel David Zajdband, Poornima Parameswaran, Di Wu, Deepak Chandran
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Patent number: 11377693Abstract: A gene expression platform, which is a combination of a set of genes that are correlated with response to a PD-1 antagonist in multiple tumor types and a normalization gene set, is disclosed. A method and system of using the gene expression platform to derive gene signature biomarkers of anti-tumor response to a PD-1 antagonist and to test patient samples for predictive gene signature biomarkers are also disclosed.Type: GrantFiled: December 8, 2015Date of Patent: July 5, 2022Assignee: Merck Sharp & Dohme LLCInventors: Mark D. Ayers, Andrey Loboda, Jared K. Lunceford, Terrill K. McClanahan, Erin E. Murphy, Michael Nebozhyn
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Patent number: 11363991Abstract: A computer-implemented method and a system for analyzing glucose monitoring data indicative of a glucose level, comprising: presenting by a data processing device provided a graphical window on a display device wherein the graphical window comprises a time abscissa axis that defines time units, and a glucose ordinate axis that defines glucose units; receiving a plurality of glucose monitoring values associated with a monitoring time period by the data processing device; segmenting the plurality of glucose monitoring values into a plurality of glucose monitoring traces indicative of the glucose level; defining a reference trace segment; determining the reference trace segment for each of the plurality of glucose monitoring traces; and plotting, for a time window comprising the reference trace segment, the plurality of glucose monitoring traces within the graphical window. Furthermore, a non-transitory computer readable medium is disclosed.Type: GrantFiled: February 28, 2017Date of Patent: June 21, 2022Assignee: Roche Diabetes Care, Inc.Inventors: Matthias Koehler, Bernd Steiger, Timm Wiedemann
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Patent number: 11326211Abstract: The present disclosure describes baseline and on treatment blood-based gene signature biomarkers that are predictive of tumor sensitivity to therapy with a PD-1 antagonist. The on-treatment biomarkers comprise a PD-L1 gene signature or an interferon gamma gene signature and the baseline gene signature biomarker comprises genes associated with the oxidative phosphorylation pathway. The disclosure also provides methods and kits for testing tumor samples for these biomarkers, as well as methods for treating subjects with a PD-1 antagonist based on the test results.Type: GrantFiled: April 12, 2016Date of Patent: May 10, 2022Assignee: Merck Sharp & Dohme Corp.Inventors: Mark Ayers, Jared Lunceford, Andrey Loboda, Michael Nebozhyn, Terrill K. McClanahan, Heather Hirsch
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Patent number: 11286516Abstract: Disclosed is a method of designing a valid primer pair satisfying a specificity condition. The method includes searching for an identifier of a base sequence from a genetic information index based on a query language associated with a gene, searching for a candidate primer from a provided candidate primer set index to satisfy the specificity condition based on the identifier of the base sequence, filtering the candidate primer based on primer-related filtering conditions, and providing information about a primer pair satisfying the query language and the filtering conditions based on a result of the filtering.Type: GrantFiled: April 26, 2017Date of Patent: March 29, 2022Assignee: Daegu Gyeongbuk Institute of Science and TechnologyInventors: Min Soo Kim, Hyerin Kim, Jaehyung Koo, Na Na Kang, KyuHyeon An
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Patent number: 11118212Abstract: The invention is directed to methods for identifying one or more introns of a gene that are rapidly processed from a nascent RNA molecule transcribed from the gene, which allows for the detection of allele-specific expression of a gene in a single cell.Type: GrantFiled: July 28, 2017Date of Patent: September 14, 2021Assignee: UNIVERSITY OF UTAH RESEARCH FOUNDATIONInventor: Christopher Gregg
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Patent number: 11031099Abstract: Systems, methods, and apparatuses are provided for detecting nucleic acid sequence variants. Other embodiments are directed to systems and computer readable media associated with methods described herein.Type: GrantFiled: November 8, 2017Date of Patent: June 8, 2021Assignee: Roche Molecular Systems, Inc.Inventor: Christina Bormann Chung