Patents Examined by Joseph Woitach
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Patent number: 11965214Abstract: Disclosed herein are methods for improving detection and monitoring of human diseases. The methods can be used to provide spatial and/or developmental localization of the source of each differential mutation within the body. The methods can also be used to generate a mutation map of a subject. And the mutation map can be used to monitoring state(s) of health of one or more tissues of a subject.Type: GrantFiled: May 31, 2022Date of Patent: April 23, 2024Assignee: Personalis, Inc.Inventor: John West
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Patent number: 11965215Abstract: Processes and materials to detect cancer from a biopsy are described. In some cases, cell-free nucleic acids can be sequenced, and the sequencing result can be utilized to detect sequences derived from a neoplasm. Detection of somatic variants occurring in phase can indicate the presence of cancer in a diagnostic scan and a clinical intervention can be performed.Type: GrantFiled: February 10, 2023Date of Patent: April 23, 2024Assignee: The Board of Trustees of the Leland Stanford Junior UniversityInventors: David M. Kurtz, Maximilian Diehn, Arash Ash Alizadeh
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Patent number: 11959075Abstract: The present invention generally relates to systems and methods for imaging or determining nucleic acids, for instance, within cells. In some embodiments, the transcriptome of a cell may be determined. Certain embodiments are directed to determining nucleic acids, such as mRNA, within cells at relatively high resolutions. In some embodiments, a plurality of nucleic acid probes may be applied to a sample, and their binding within the sample determined, e.g., using fluorescence, to determine locations of the nucleic acid probes within the sample. In some embodiments, codewords may be based on the binding of the plurality of nucleic acid probes, and in some cases, the codewords may define an error-correcting code to reduce or prevent misidentification of the nucleic acids. In certain cases, a relatively large number of different targets may be identified using a relatively small number of labels, e.g., by using various combinatorial approaches.Type: GrantFiled: March 16, 2023Date of Patent: April 16, 2024Assignee: President and Fellows of Harvard CollegeInventors: Xiaowei Zhuang, Kok-Hao Chen, Alistair Boettiger, Jeffrey R. Moffitt, Siyuan Wang
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Patent number: 11959077Abstract: The invention relates to control compositions for sequencing and for chemical analyses, such as analytical chemistry analyses. More particularly, the invention relates to control compositions for sequencing and for chemical analyses having at least one barcode sequence fragment and at least one universal sequence fragment, and to methods of their use.Type: GrantFiled: May 21, 2019Date of Patent: April 16, 2024Assignee: BATTELLE MEMORIAL INSTITUTEInventors: Rachel R. Spurbeck, Richard Mon Che Chou, Anthony D. Duong
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Patent number: 11955241Abstract: The disclosure provides for pathogenic biomarkers and serum extracellular vesicular biomarkers that are associated with vascular anomalies and malformation of endothelial cells, and uses thereof, including for diagnosis, prognosis and therapy.Type: GrantFiled: June 3, 2019Date of Patent: April 9, 2024Assignee: The Regents of the University of CaliforniaInventors: Wenbin Tan, John Stuart Nelson, Dongbao Chen
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Patent number: 11915794Abstract: In one aspect, methods are described herein for enhancing one or more nucleic acid interactions. For example, in some embodiments, methods of enhancing one or more steps of polymerase chain reaction (PCR) are described herein. In some embodiments, the optimal temperature cycling protocol for one or more PCR cycles can be determined according to methods described herein.Type: GrantFiled: February 20, 2019Date of Patent: February 27, 2024Assignee: Chakrabarti Advanced Technology LLCInventor: Raj Chakrabarti
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Patent number: 11901042Abstract: Somatic mutations are associated with cancer progression and treatment using targeted therapies. Somatic mutations are not inherited and could be present at low concentrations in biopsy samples. Hence, there is a need for more sensitive assays to detect these changes in the presence of heterogeneous cell populations. The efficacy of such detection is determined by two factors; the ability to detect a minimum number of copies of the target mutation in the sample (Lower limit of detection), and the ratio of target mutation to that of wild-type in the sample (Tumor content). A new algorithm Detection Index (DI) is formulated to evaluate the efficacy of detection for a molecular testing method.Type: GrantFiled: May 11, 2018Date of Patent: February 13, 2024Inventor: Thuraiayah Vinayagamoorthy
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Patent number: 11898206Abstract: Methods for screening clonotypes are provided. Data representing a plurality of cells from a single subject is obtained. The data represents a plurality of clonotypes. The data includes a plurality of contigs for each respective clonotype in the plurality of clonotypes. Each respective contig in the plurality of contigs comprises (i) an indication of chain type for the respective contig and (ii) a contig sequence of an mRNA of the respective cell. There is determined, using the data, for each respective clonotype in the plurality of clonotypes, a number of the plurality of cells that represent the respective clonotype. In some instances, more than one cell in the plurality of cells have the same clonotype in the plurality of clonotypes. In some instances, the plurality of clonotypes comprises 25 clonotypes and where the plurality of cells includes at least one cell for each clonotype in the plurality of clonotypes.Type: GrantFiled: May 19, 2018Date of Patent: February 13, 2024Assignee: 10X GENOMICS, INC.Inventors: Alexander Y. Wong, Jeffrey Mellen, Kevin Wu, Paul Ryvkin
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Patent number: 11875877Abstract: Systems and methods for prediction of the treatment outcome for immune therapy are presented in which omics data of a patient tumor sample are used. Most typically, the omics data are processed to identify mutational signatures (especially APOBEC/POLE signatures), immune checkpoint expression, and MSI status as leading indicators to predict the treatment outcome for immune therapy. Such prediction advantageously integrates various parameters that would otherwise, when individually considered, skew prediction outcome.Type: GrantFiled: August 25, 2017Date of Patent: January 16, 2024Assignee: NantOmics, LLCInventors: Andrew Nguyen, John Zachary Sanborn, Shahrooz Rabizadeh
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Patent number: 11866772Abstract: Techniques are provided for determining settings of a dPCR experiment for the detection of a chromosomal aneuploidy in a plasma sample from a female pregnant with a fetus. Data about the sample, the dPCR process, and a desired accuracy can be used to determine the settings. Such settings can include a minimal input number of control chromosome molecules for the dPCR experiment, a minimal number of control chromosome molecules for a pre-amplification procedure, and a number of PCR cycles in the pre-amplification procedure. These settings can be used to satisfy the accuracy specified by the accuracy data. Thus, the dPCR experiment can be designed to achieve the desired accuracy while reducing cost, e.g., by not using more of a sample than needed and not performing more pre-amplification than needed or performing more manipulations than needed.Type: GrantFiled: February 13, 2020Date of Patent: January 9, 2024Assignee: Roche Molecular Systems, Inc.Inventors: Yu Chuan Tai, Nancy Schoenbrunner
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Patent number: 11862297Abstract: A method includes accessing genomic data from a first cohort and a second cohort of patients that are encrypted to comprise a probabilistic and irreversible hash of each patient's genomic sequence data; based on the probabilistic and irreversible hashes, determining one or more variants residing in a particular locale indicating where the one or more variants reside; comparing a first number of variants determined to reside in the particular locale for the first cohort of patients with a second number of variants determined to reside in the particular locale for the second cohort of patients; and in response to determining that the first number of variants determined to reside in the particular locale for the first cohort of patients and the second number of variants determined to reside in the particular locale for the second cohort of patients differ by more than a threshold value, identifying the particular locale.Type: GrantFiled: November 7, 2017Date of Patent: January 2, 2024Assignee: IQVIA Inc.Inventors: Ronald A. Miller, Kenneth Park
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Patent number: 11862299Abstract: The invention provides methods of determining a consensus sequence from multiple raw sequencing reads of a nucleic acid target. The nucleic acid target includes an anchor segment of known sequence and an adjacent segment of unknown sequence. The anchor segment provides a means to assess the quality of a raw target sequencing read. Raw target sequencing reads meeting or exceeding a threshold are assigned to an accepted class. The consensus sequence of the adjacent segment can be determined from raw target sequencing reads in the accepted class. Successive polling steps determine successive consensus nucleobases in a nascent sequence of the adjacent segment. Raw target sequencing reads can be removed or reintroduced from the accepted class depending on their correspondence to the most recently determined consensus nucleobase and/or the nascent sequence.Type: GrantFiled: October 30, 2018Date of Patent: January 2, 2024Assignee: GEN-PROBE INCORPORATEDInventors: Tongjia Yin, Steven T. Brentano, Jennifer Bungo, Xianqun Wang, Michael Hadjisavas
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Patent number: 11851716Abstract: Processes and materials to detect cancer from a biopsy are described. In some cases, cell-free nucleic acids can be sequenced, and the sequencing result can be utilized to detect sequences derived from a neoplasm. Detection of somatic variants occurring in phase can indicate the presence of cancer in a diagnostic scan and a clinical intervention can be performed.Type: GrantFiled: November 17, 2022Date of Patent: December 26, 2023Assignee: The Board of Trustees of the Leland Stanford Junior UniversityInventors: David M. Kurtz, Maximilian Diehn, Arash Ash Alizadeh
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Patent number: 11854666Abstract: Fetal maternal samples taken from pregnant women include both maternal cell-free DNA and fetal cell-free DNA. Described herein are methods for determining a chromosomal abnormality of a test chromosome or a portion thereof in a fetus by analyzing a test maternal sample of a woman carrying said fetus, wherein the test maternal sample comprises fetal cell-free DNA and maternal cell-free DNA. The chromosomal abnormality can be, for example, aneuploidy or the presence of a microdeletion. In some embodiments, the chromosomal abnormality is determined by measuring a dosage of the test chromosome or portion thereof in the test maternal sample, measuring a fetal fraction of cell-free DNA in the test maternal sample, and determining an initial value of likelihood that the test chromosome or the portion thereof in the fetal cell-free DNA is abnormal based on the measured dosage, an expected dosage of the test chromosome or portion thereof, and the measured fetal fraction.Type: GrantFiled: September 29, 2017Date of Patent: December 26, 2023Assignee: Myriad Women's Health, Inc.Inventors: Dale Muzzey, Carlo G. Artieri, Eric Andrew Evans, Imran Saeedul Haque
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Patent number: 11854667Abstract: In one aspect, methods are described herein for enhancing one or more nucleic acid interactions. For example, in some embodiments, methods of enhancing one or more steps of polymerase chain reaction (PCR) are described herein. In some embodiments, the optimal temperature cycling protocol for one or more PCR cycles can be determined according to methods described herein.Type: GrantFiled: February 20, 2019Date of Patent: December 26, 2023Assignee: Chakrabarti Advanced Technology LLCInventor: Raj Chakrabarti
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Patent number: 11817178Abstract: In one aspect, methods are described herein for enhancing one or more nucleic acid interactions. For example, in some embodiments, methods of enhancing one or more steps of polymerase chain reaction (PCR) are described herein. In some embodiments, the optimal temperature cycling protocol for one or more PCR cycles can be determined according to methods described herein.Type: GrantFiled: February 20, 2019Date of Patent: November 14, 2023Assignee: CHAKRABARTI ADVANCED TECHNOLOGY LLCInventor: Raj Chakrabarti
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Patent number: 11810647Abstract: In one aspect, methods are described herein for enhancing one or more nucleic acid interactions. For example, in some embodiments, methods of enhancing one or more steps of polymerase chain reaction (PCR) are described herein. In some embodiments, the optimal temperature cycling protocol for one or more PCR cycles can be determined according to methods described herein.Type: GrantFiled: February 20, 2019Date of Patent: November 7, 2023Assignee: Chakrabarti Advanced Technology LLCInventor: Raj Chakrabarti
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Patent number: 11810649Abstract: Embodiments disclosed herein provide methods for identifying new CRISPR loci and effectors, as well as different CRISPR loci combinations found in various organisms. Class-II CRISPR systems contain single-gene effectors that have been engineered for transformative biological discovery and biomedical applications. Discovery of additional single-gene or multi-component CRISPR effectors may enhance existing CRISPR applications, such as precision genome engineering. Comprehensive characterization of CRISPR-loci may identify novel functional roles of CRISPR loci enabling new tools for biomedicine and biological discovery. CRISPR loci have enormous feature complexity, but classification of CRISPR loci has been focused on a small fraction of highly abundant features. Increased genome sequencing has enhanced the sampling of this feature complexity.Type: GrantFiled: August 17, 2017Date of Patent: November 7, 2023Assignees: THE BROAD INSTITUTE, INC., MASSACHUSETTS INSTITUTE OF TECHNOLOGYInventors: Feng Zhang, David Arthur Scott
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Patent number: 11791017Abstract: The present invention provides a soybean anti-pod-shattering major QTLqPD05, and a mapping method and application thereof, and belongs to the field of QTL mapping. The soybean anti-pod-shattering major QTL is mapped on the chromosome 5 of soybean at a physical position between 40448596-40703417. For the method for mapping the soybean anti-pod-shattering major QTL, a SLAF marker is screened at the whole genome level of the soybean by utilizing a SLAF-seq sequencing technology, so as to explore the QTLs related to pod shattering from this population. By using a material of a RIL7 population which has pod-shattering soybean and anti-pod-shattering soybean as the parents, a high-density genetic linkage map covering the whole genome of soybean is constructed, and QTL mapping of the anti-pod-shattering trait is carried out on this population to obtain QTLs related to anti-pod-shattering.Type: GrantFiled: April 23, 2019Date of Patent: October 17, 2023Assignee: Institute of Crop Sciences, Chinese Academy of Agricultural SciencesInventors: Lijuan Qiu, Dezhi Han, Jianan Han, Hongrui Yan, Bohong Su
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Patent number: 11781189Abstract: The present invention is focused on a method, kit and system for determining the presence or absence of minimal residual disease in a subject who has been treated for a proliferative disease wherein said method, kit and system comprise: (A) amplifying and sequencing at least one nucleotide sequence comprised in genomic DNA from a biological sample obtained from said subject prior to treatment for said disease, to obtain a first list of characters reading from left to right; (B) amplifying and sequencing at least one nucleotide sequence comprised in genomic DNA from a biological sample obtained from said subject after treatment for said disease, to obtain a second list of characters reading from left to right, wherein when a nucleotide sequence is mutated it is a genetic marker for said proliferative disease; (C) determining, for each second list of characters obtained in step (B), the degree of similarity, DS, with each first list of characters obtained in step (A); (D) selecting, for each second list of cType: GrantFiled: August 27, 2020Date of Patent: October 10, 2023Inventors: Santiago Barrio García, Rosa María Ayala Díaz, María Inmaculada Rapado Martinez, Eva María Garrido Martín, Luis Paz-Ares Rodriguez, Maria Esther Onecha De La Fuente, Joaquín Martínez López