Patents by Inventor Aly Khan
Aly Khan 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).
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Publication number: 20230245788Abstract: A method for data intake and consumption includes the steps of: storing a plurality of micro-service programs, operational user application programs, and analytical user application programs in at least one computer system, storing system data received from a plurality of different sources in a database, the system data includes clinical records data in original forms, the clinical records data including cancer state information, treatment types, and treatment efficacy information, consuming, by each of the micro-service programs, defined subsets of the system data to generate a new data product, storing the new data product in a second database, and consuming the new data product by others of the micro-service programs or the operational or analytical user application programs.Type: ApplicationFiled: April 11, 2023Publication date: August 3, 2023Inventors: Shane Colley, Isaiah Simpson, Brian Reuter, Robert Tell, Hailey Lefkofsky, Hunter Lane, Kevin White, Nike Beaubier, Stephen Bush, Aly Khan, Denise Lau, Kaanan Shah, Eric Lefkofsky
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Patent number: 11705226Abstract: A method and system for storing user application programs and micro-service programs, for each of multiple patients that have cancerous cells and receive treatment, includes obtaining clinical records data in original forms, storing it in a semi-structured first database, generating sequencing data for the patient's cancerous and normal cells using a next generation genomic sequencer, storing the sequencing data in the first database, shaping at least some of the first database data to generate system structured data optimized for searching and including clinical record data, storing the structured data in a second database, for each user application program, selecting an application-specific subset of data from the second database and storing it in a structure optimized for application program interfacing in a third database, wherein an orchestration manager operatively connected to one or more micro-service programs receives status messages and initiates a respective micro-service program when program prereType: GrantFiled: October 18, 2019Date of Patent: July 18, 2023Assignee: Tempus Labs, Inc.Inventors: Shane Colley, Isaiah Simpson, Brian Reuter, Robert Tell, Hailey Lefkofsky, Hunter Lane, Kevin White, Nike Beaubier, Stephen Bush, Aly Khan, Denise Lau, Kaanan Shah, Eric Lefkofsky
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Publication number: 20230223121Abstract: A method and system comprising storing a set of user application programs each requiring an application specific subset of data to perform application processes and generate a respective genomic variant characterization for each of a plurality of patients with cancerous cells and receiving cancer treatment. The method including, obtaining clinical records data including cancer related information, generating genomic sequencing data for the patient's cancerous cells and normal cells, shaping at least a subset of the genomic sequencing data to generate system structured data. Storing the system structured data in a first database, selecting the application specific data from the first database, storing the application specific data in a second database for application program interfacing, receiving the respective genomic variant characterization from the user application program, and storing the genomic variant characterization from the user application program in a third database.Type: ApplicationFiled: March 22, 2023Publication date: July 13, 2023Inventors: Shane Colley, Isaiah Simpson, Brian Reuter, Robert Tell, Hailey Lefkofsky, Hunter Lane, Kevin White, Nike Beaubier, Stephen Bush, Aly Khan, Denise Lau, Kaanan Shah, Eric Lefkofsky
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Publication number: 20230197269Abstract: Methods, systems, and software are provided for determining whether a subject is afflicted with an oncogenic pathogen. Nucleic acids from a biological sample of the subject are hybridized to a probe set that includes probes for human genomic loci and for genomic loci of oncogenic pathogens. Sequence reads of the hybridized nucleic acid are obtained and it’s determined whether each sequence read aligns to a human reference genome. For each sequence read that fails to align to the human reference genome, it’s determined whether the sequence read aligns to a reference genome of an oncogenic pathogen. Sequence reads that both (i) fail to align to the human reference genome and (ii) align to a reference genome of an oncogenic pathogen are tracked, thereby obtaining a sequence read count for the oncogenic pathogen. The sequence read count is used to ascertain whether the subject is afflicted with the oncogenic pathogen.Type: ApplicationFiled: February 18, 2021Publication date: June 22, 2023Inventors: Robert Tell, Jerod Parsons, Stephen J. Bush, Aly A. Khan, Ariane Lozac'hmeur, Denise Lau
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Publication number: 20230145084Abstract: The disclosure provides a method of generating an artificial immunohistochemistry (IHC) image of cells. The method includes receiving a hematoxylin and eosin (H&E) stained whole slide image (WSI) generated by a brightfield microscopy imaging modality of at least a portion of cells included in a specimen, applying, to the H&E brightfield image, at least one trained model, the trained model being trained to generate the artificial IHC image based on the H&E brightfield image, receiving the artificial IHC image from the trained model.Type: ApplicationFiled: January 4, 2023Publication date: May 11, 2023Inventors: Madhavi Kannan, Brian Larsen, Aly Khan, Ameen Salahudeen
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Patent number: 11640859Abstract: A method and system for conducting genomic sequencing, the method comprising storing a set of user application programs wherein each of the programs requires an application specific subset of data, for each of a plurality of patients that have cancerous cells and that receive cancer treatment, obtaining clinical records data in original forms including cancer state information, treatment types and treatment efficacy information, storing the clinical records data in a semi-structured first database, for each patient, using a genomic sequencer to generate genomic sequencing data for the patient's cancerous cells and normal cells, storing the sequencing data in the first database, shaping at least a subset of the first database data to generate system structured data including clinical record data and sequencing data wherein the system structured data is optimized for searching, storing the system structured data in a second database, for each user application program, selecting the application specific subset oType: GrantFiled: October 17, 2019Date of Patent: May 2, 2023Assignee: Tempus Labs, Inc.Inventors: Shane Colley, Isaiah Simpson, Brian Reuter, Robert Tell, Hailey Lefkofsky, Hunter Lane, Kevin White, Nike Beaubier, Stephen Bush, Aly Khan, Denise Lau, Kaanan Shah, Eric Lefkofsky
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Publication number: 20230121729Abstract: This present disclosure relates to systems, methods, and compositions useful for profiling T cell receptor (TCR) and B cell receptor (BCR) repertoire using next-generation sequencing (NGS) methods. The present disclosure also relates to systems and methods for diagnosing, treating, or predicting infection, disease, medical conditions, therapeutic outcome, or therapeutic efficacy based on the TCR/BCR profile data from a subject in need thereof.Type: ApplicationFiled: August 12, 2022Publication date: April 20, 2023Inventors: Jason Perera, Taylor Harding, Brittany Mineo, Aly A. Khan, Richard Blidner, Jenna L. Malinauskas
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Patent number: 11561178Abstract: The disclosure provides a method of generating an artificial fluorescent image of cells is provided.Type: GrantFiled: April 20, 2021Date of Patent: January 24, 2023Assignee: Tempus Labs, Inc.Inventors: Madhavi Kannan, Brian Larsen, Aly A. Khan, Ameen Salahudeen
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Publication number: 20220392640Abstract: Methods, systems, and software are provided for using organoid cultures, e.g., patient-derived tumor organoid cultures, to improve treatment predictions and outcomes.Type: ApplicationFiled: October 22, 2020Publication date: December 8, 2022Inventors: Ameen Salahudeen, Brian M. Larsen, Michelle M. Stein, Luka A. Karginov, Madhavi Kannan, Aly A. Khan, Verónica Sánchez Freire, Yilin Zhang
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Publication number: 20220341914Abstract: Methods, systems, and software are provided for using organoid cultures, e.g., patient-derived tumor organoid cultures, to improve treatment predictions and outcomes.Type: ApplicationFiled: July 5, 2022Publication date: October 27, 2022Inventors: Brian M. Larsen, Michelle M. Stein, Luka A. Karginov, Ameen Salahudeen, Madhavi Kannan, Aly A. Khan, Verónica Sánchez Freire, Yilin Zhang
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Patent number: 11415571Abstract: Methods, systems, and software are provided for using organoid cultures, e.g., patient-derived tumor organoid cultures, to improve treatment predictions and outcomes.Type: GrantFiled: December 7, 2020Date of Patent: August 16, 2022Assignee: Tempus Labs, Inc.Inventors: Brian M. Larsen, Michelle M. Stein, Luka A. Karginov, Ameen Salahudeen, Madhavi Kannan, Aly A. Khan, Verónica Sánchez Freire, Yilin Zhang
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Patent number: 11414700Abstract: Disclosed herein are systems, methods, and compositions useful for profiling T cell receptor (TCR) and B cell receptor (BCR) repertoire using next-generation sequencing (NGS) methods. In certain embodiments, the methods include enriching a sample for TCR/BCR RNA sequences, and determining the TCR/BCR profile of a subject using five different oligonucleotide pools. Also disclosed herein are systems and methods for diagnosing, treating, or predicting infection, disease, medical conditions, therapeutic outcome, or therapeutic efficacy based on the TCR/BCR profile data from a subject in need thereof.Type: GrantFiled: April 21, 2021Date of Patent: August 16, 2022Assignee: Tempus Labs, Inc.Inventors: Jason Perera, Taylor Harding, Brittany Mineo, Aly A. Khan, Richard Blidner, Jenna L. Malinauskas
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Publication number: 20220154284Abstract: Disclosed herein are systems, methods, and compositions for treating a subject diagnosed with, or suffering from cancer. In some embodiments, the method comprises determining whether a tumor sample from the subject includes a cytotoxic gene signature, and treating the subject based on the determination. In some embodiments, the subject has or is suspected of having a loss of heterozygosity in human leukocyte antigen (HLA) class I genes. In some embodiments, the therapy comprises one or more checkpoint inhibitors. In some embodiments, the cancer is colorectal, uterine, stomach, lung, skin, head or neck, or non-small cell lung carcinoma.Type: ApplicationFiled: November 19, 2021Publication date: May 19, 2022Inventors: Denise Lau, Aly A. Khan, Yinjie Gao, Michelle Marie Stein, Ameen Salahudeen, Timothy Rand, Sonal Khare
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Publication number: 20210355533Abstract: This present disclosure relates to systems, methods, and compositions useful for profiling T cell receptor (TCR) and B cell receptor (BCR) repertoire using next-generation sequencing (NGS) methods. The present disclosure also relates to systems and methods for diagnosing, treating, or predicting infection, disease, medical conditions, therapeutic outcome, or therapeutic efficacy based on the TCR/BCR profile data from a subject in need thereof.Type: ApplicationFiled: April 21, 2021Publication date: November 18, 2021Inventors: Jason Perera, Taylor Harding, Brittany Mineo, Aly A. Khan, Richard Blidner, Jenna L. Malinauskas
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Publication number: 20210325308Abstract: The disclosure provides a method of generating an artificial fluorescent image of cells is provided.Type: ApplicationFiled: April 20, 2021Publication date: October 21, 2021Inventors: Madhavi Kannan, Brian Larsen, Aly A. Khan, Ameen Salahudeen
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Publication number: 20210272695Abstract: Systems and methods are provided for training a classifier to discriminate between a first cancer condition associated with an oncogenic pathogenic infection a second cancer condition that is not associated with an oncogenic pathogenic infection. Systems and methods are provided for distinguishing cancers associated with oncogenic pathogenic infections that contribute to the cancer pathology and cancers that are not associated with oncogenic pathogenic infections. Systems and methods are provided for treating cancer based on whether the cancer is associated with an oncogenic pathogenic infection.Type: ApplicationFiled: May 18, 2021Publication date: September 2, 2021Inventors: Ariane Lozac'hmeur, Denise Lau, Aly A. Khan
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Publication number: 20210233664Abstract: A method and system for conducting genomic sequencing, the method comprising storing a set of user application programs wherein each of the programs requires an application specific subset of data, for each of a plurality of patients that have cancerous cells and that receive cancer treatment, obtaining clinical records data in original forms including cancer state information, treatment types and treatment efficacy information, storing the clinical records data in a semi-structured first database, for each patient, using a genomic sequencer to generate genomic sequencing data for the patient's cancerous cells and normal cells, storing the sequencing data in the first database, shaping at least a subset of the first database data to generate system structured data including clinical record data and sequencing data wherein the system structured data is optimized for searching, storing the system structured data in a second database, for each user application program, selecting the application specific subset oType: ApplicationFiled: October 17, 2019Publication date: July 29, 2021Inventors: Shane Colley, Isaiah Simpson, Brian Reuter, Bob Tell, Hailey Lefkofsky, Hunter Lane, Kevin White, Nike Beaubier, Stephen Bush, Aly Khan, Denise Lau, Kaanan Shah, Eric Lefkofsky
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Patent number: 11043304Abstract: Systems and methods are provided for training a classifier to discriminate between a first cancer condition associated with an oncogenic pathogenic infection a second cancer condition that is not associated with an oncogenic pathogenic infection. Systems and methods are provided for distinguishing cancers associated with oncogenic pathogenic infections that contribute to the cancer pathology and cancers that are not associated with oncogenic pathogenic infections. Systems and methods are provided for treating cancer based on whether the cancer is associated with an oncogenic pathogenic infection.Type: GrantFiled: February 26, 2020Date of Patent: June 22, 2021Assignee: Tempus Labs, Inc.Inventors: Ariane Lozac'hmeur, Denise Lau, Aly A. Khan
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Publication number: 20210172931Abstract: Methods, systems, and software are provided for using organoid cultures, e.g., patient-derived tumor organoid cultures, to improve treatment predictions and outcomes.Type: ApplicationFiled: December 7, 2020Publication date: June 10, 2021Inventors: Brian M. Larsen, Michelle M. Stein, Luka A. Karginov, Ameen Salahudeen, Madhavi Kannan, Aly A. Khan, Verónica Sánchez Freire, Yilin Zhang
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Publication number: 20210098078Abstract: Methods, systems, and software are provided for determining a microsatellite instability (MSI) status of a subject. Nucleotide sequences are obtained for cell-free DNA molecules from a liquid biopsy sample of the subject. The nucleotide sequences are used to determine, for each respective microsatellite locus in a plurality of predetermined microsatellite loci, one or more independent corresponding metrics, where each metric in the one or more metrics is determined at least in part by the distribution of the number of repeat units at the respective microsatellite locus. The one or more metrics are input into a classifier trained to distinguish between stable and unstable microsatellite loci, in order to classify the MSI status of the subject. In certain aspects, microsatellite stability metrics are compared against metrics from solid tumor samples and/or normal tissues. In certain aspects, the microsatellite stability metrics are determined relative to a subject-specific standard for microsatellite stability.Type: ApplicationFiled: July 31, 2020Publication date: April 1, 2021Inventors: Ariane Lozac'hmeur, Aly A. Khan, Jason Perera, Denise Lau, Ashraf Hafez