Patents by Inventor Kenneth Kinzler

Kenneth Kinzler 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).

  • Patent number: 12359250
    Abstract: Bottleneck Sequencing System (BotSeqS) is a next-generation sequencing method that simultaneously quantifies rare somatic point mutations across the mitochondrial and nuclear genomes. BotSeqS combines molecular barcoding with a simple dilution step immediately prior to library amplification. BotSeqS can be used to show age and tissue-dependent accumulations of rare mutations and demonstrate that somatic mutational burden in normal tissues can vary by several orders of magnitude, depending on biologic and environmental factors. BotSeqS has been used to show major differences between the mutational patterns of the mitochondrial and nuclear genomes in normal tissues. Lastly, BotSeqS has shown that the mutation spectra of normal tissues were different from each other, but similar to those of the cancers that arose in them.
    Type: Grant
    Filed: January 27, 2017
    Date of Patent: July 15, 2025
    Assignee: The Johns Hopkins University
    Inventors: Bert Vogelstein, Kenneth Kinzler, Margaret Hoang, Nickolas Papadopoulos
  • Publication number: 20240068033
    Abstract: A method of detecting Barrett's esophagus with low grade dysplasia, or Barrett's esophagus with high grade dysplasia, or adenocarcinoma of the esophagus, applying a Repetitive Element Aneuploidy Sequencing System (RealSeqS) methodology to a biological sample from the esophagus of the subject to detect Barrett's esophagus with low grade dysplasia, or Barrett's esophagus with high grade dysplasia, or adenocarcinoma of the esophagus.
    Type: Application
    Filed: January 14, 2022
    Publication date: February 29, 2024
    Inventors: Sanford Markowitz, Amitabh Chak, Helen Moinova, Joseph Willis, Bert Vogelstein, Kenneth Kinzler, Nickolas Papadopoulos, Chetan Bettewgowda, Christopher Douville
  • Patent number: 10704105
    Abstract: Phosphatidylinositol 3-kinases (PI3Ks) are known to be important regulators of signaling pathways. To determine whether PI3Ks are genetically altered in cancers, we analyzed the sequences of the PI3K gene family and discovered that one family member, PIK3CA, is frequently mutated in cancers of the colon and other organs. The majority of mutations clustered near two positions within the PI3K helical or kinase domains. PIK3CA represents one of the most highly mutated oncogenes yet identified in human cancers and is useful as a diagnostic and therapeutic target.
    Type: Grant
    Filed: December 8, 2017
    Date of Patent: July 7, 2020
    Assignee: The Johns Hopkins University
    Inventors: Yardena Samuels, Victor Velculescu, Kenneth Kinzler, Bert Vogelstein
  • Publication number: 20190300946
    Abstract: Bottleneck Sequencing System (BotSeqS) is a next-generation sequencing method that simultaneously quantifies rare somatic point mutations across the mitochondrial and nuclear genomes. BotSeqS combines molecular barcoding with a simple dilution step immediately prior to library amplification. BotSeqS can be used to show age and tissue-dependent accumulations of rare mutations and demonstrate that somatic mutational burden in normal tissues can vary by several orders of magnitude, depending on biologic and environmental factors. BotSeqS has been used to show major differences between the mutational patterns of the mitochondrial and nuclear genomes in normal tissues. Lastly, BotSeqS has shown that the mutation spectra of normal tissues were different from each other, but similar to those of the cancers that arose in them.
    Type: Application
    Filed: January 27, 2017
    Publication date: October 3, 2019
    Inventors: Bert Vogelstein, Kenneth Kinzler, Margaret Hoang, Nickolas Papadopoulos
  • Publication number: 20180119231
    Abstract: Phosphatidylinositol 3-kinases (PI3Ks) are known to be important regulators of signaling pathways. To determine whether PI3Ks are genetically altered in cancers, we analyzed the sequences of the PI3K gene family and discovered that one family member, PIK3CA, is frequently mutated in cancers of the colon and other organs. The majority of mutations clustered near two positions within the PI3K helical or kinase domains. PIK3CA represents one of the most highly mutated oncogenes yet identified in human cancers and is useful as a diagnostic and therapeutic target.
    Type: Application
    Filed: December 8, 2017
    Publication date: May 3, 2018
    Inventors: Yardena Samuels, Victor Velculescu, Kenneth Kinzler, Bert Vogelstein
  • Patent number: 9695479
    Abstract: Medulloblastoma (MB) is the most common malignant brain tumor of children. To identify the genetic alterations in this tumor type, we searched for copy number alterations using high density microarrays and sequenced all known protein-coding genes and miRNA genes using Sanger sequencing. We found that, on average, each tumor had 11 gene alterations, markedly fewer than in common adult cancers. In addition to alterations in the Hedgehog and Wnt pathways, our analysis led to the discovery of genes not previously known to be altered in MBs. Most notably, inactivating mutations of the histone H3K4 trimethylase genes MLL2 or MLL3 were identified in 16% of MB patients. These results demonstrate key differences between the genetic landscapes of adult and childhood cancers, highlight dysregulation of developmental pathways as an important mechanism underlying MBs, and identify a role for a specific type of histone methylation in human tumorigenesis.
    Type: Grant
    Filed: November 8, 2011
    Date of Patent: July 4, 2017
    Assignees: The Johns Hopkins University, Duke University
    Inventors: Bert Vogelstein, Kenneth Kinzler, Nickolas Papadopoulos, Donald Williams Parsons, Rebecca J. Leary, Meng Li, Xiaosong Zhang, Sian Jones, Gregory J. Riggins, Victor Velculescu, Darell Bigner, Hai Yan
  • Publication number: 20170020931
    Abstract: The presently disclosed subject matter provides methods and kits for treating solid tumors in a subject by using a combination of anti-CTLA-4 and/or anti-PD-1 antibodies with at least one member of the group consisting of a bacterium, bacterial product, and an immunoregulatory entity. In particular embodiments, the bacteria are toxin-depleted, anaerobic bacteria, such as Clostridium novyi-NT.
    Type: Application
    Filed: March 31, 2015
    Publication date: January 26, 2017
    Applicant: THE JOHNS HOPKINS UNIVERSITY
    Inventors: SHIBIN ZHOU, BERT VOGELSTEIN, KENNETH KINZLER, KIBEM KIM, SAURABH SAHA
  • Patent number: 8691186
    Abstract: The instant invention provides a method for diagnosing an infection in a subject by administering to the subject a compound suitable for imaging which binds to a thymidine kinase present in the infecting organism, and obtaining an image of the subject to determine the presence and location of the compound, wherein a localization of the compound is indicative that the subject has an infection.
    Type: Grant
    Filed: August 28, 2012
    Date of Patent: April 8, 2014
    Assignee: The Johns Hopkins University
    Inventors: Martin G. Pomper, Chetan Bettegowda, Catherine Foss, Shibin Zhou, Kenneth Kinzler, Bert Vogelstein
  • Publication number: 20130323167
    Abstract: Several agents capable of inducing vascular responses akin to those observed in inflammatory processes enhance the accumulation of nanoparticles in tumors. Exemplary vascular-active agents include a bacterium, a pro-inflammatory cytokine, and microtubule-destabilizing drugs. Such agents can increase the tumor to blood ratio of radioactivity by more than 20-fold compared to nanoparticles alone. Moreover, vascular-active agents dramatically improved the therapeutic effect of nanoparticles containing radioactive isotopes or chemotherapeutic agents.
    Type: Application
    Filed: October 20, 2011
    Publication date: December 5, 2013
    Applicant: THE JOHNS HOPKINS UNIVERSITY
    Inventors: Bert Vogelstein, Yuan Qiao, Xin Huang, Kenneth Kinzler, Shibin Zhou, Luis Diaz
  • Publication number: 20130296408
    Abstract: Medulloblastoma (MB) is the most common malignant brain tumor of children. To identify the genetic alterations in this tumor type, we searched for copy number alterations using high density microarrays and sequenced all known protein-coding genes and miRNA genes using Sanger sequencing. We found that, on average, each tumor had 11 gene alterations, markedly fewer than in common adult cancers. In addition to alterations in the Hedgehog and Wnt pathways, our analysis led to the discovery of genes not previously known to be altered in MBs. Most notably, inactivating mutations of the histone H3K4 trimethylase genes MLL2 or MLL3 were identified in 16% of MB patients. These results demonstrate key differences between the genetic landscapes of adult and childhood cancers, highlight dysregulation of developmental pathways as an important mechanism underlying MBs, and identify a role for a specific type of histone methylation in human tumorigenesis.
    Type: Application
    Filed: November 8, 2011
    Publication date: November 7, 2013
    Inventors: Bert Vogelstein, Kenneth Kinzler, Nickolas Papadopoulos, Donald Williams Parsons, Rebecca J. Leary, Meng Li, Xiaosong Zhang, Sian Jones, Gregory J. Riggins, Victor Velculescu
  • Publication number: 20130064767
    Abstract: The instant invention provides a method for diagnosing an infection in a subject by administering to the subject a compound suitable for imaging which binds to a thymidine kinase present in the infecting organism, and obtaining an image of the subject to determine the presence and location of the compound, wherein a localization of the compound is indicative that the subject has an infection.
    Type: Application
    Filed: August 28, 2012
    Publication date: March 14, 2013
    Applicant: The Johns Hopkins University
    Inventors: Martin G. Pomper, Chetan Bettegowda, Catherine Foss, Shibin Zhou, Kenneth Kinzler, Bert Vogelstein
  • Patent number: 8273326
    Abstract: The instant invention provides a method for diagnosing an infection in a subject by administering to the subject a compound suitable for imaging which binds to a thymidine kinase present in the infecting organism, and obtaining an image of the subject to determine the presence and location of the compound, wherein a localization of the compound is indicative that the subject has an infection.
    Type: Grant
    Filed: June 20, 2005
    Date of Patent: September 25, 2012
    Assignee: The Johns Hopkins University
    Inventors: Martin G. Pomper, Chetan Bettegowda, Catherine Foss, Shibin Zhou, Kenneth Kinzler, Bert Vogelstein
  • Patent number: 7829338
    Abstract: Dominant negative alleles of human mismatch repair genes can be used to generate hypermutable cells and organisms. By introducing these genes into cells and transgenic animals, new cell lines and animal varieties with novel and useful properties can be prepared more efficiently than by relying on the natural rate of mutation.
    Type: Grant
    Filed: October 11, 2007
    Date of Patent: November 9, 2010
    Assignee: The Johns Hopkins University
    Inventors: Nicholas Nicolaides, Bert Vogelstein, Kenneth Kinzler
  • Patent number: 7704687
    Abstract: Alterations in the genetic content of a cell underlie many human diseases, including cancers. A method called Digital Karyotyping provides quantitative analysis of DNA copy number at high resolution. This approach involves the isolation and enumeration of short sequence tags from specific genomic loci. Analysis of human cancer cells using this method identified gross chromosomal changes as well as amplifications and deletions, including regions not previously known to be altered. Foreign DNA sequences not present in the normal human genome could also be readily identified. Digital Karyotyping provides a broadly applicable means for systematic detection of DNA copy number changes on a genomic scale.
    Type: Grant
    Filed: November 13, 2003
    Date of Patent: April 27, 2010
    Assignee: The Johns Hopkins University
    Inventors: Tian-Li Wang, Victor Velculescu, Kenneth Kinzler, Bert Vogelstein
  • Publication number: 20090286687
    Abstract: Many areas of biomedical research depend on the analysis of uncommon variations in individual genes or transcripts. Here we describe a method that can quantify such variation at a scale and ease heretofore unattainable. Each DNA molecule in a collection of such molecules is converted into a single particle to which thousands of copies of DNA identical in sequence to the original are bound. This population of beads then corresponds to a one-to-one representation of the starting DNA molecules. Variation within the original population of DNA molecules can then be simply assessed by counting fluorescently-labeled particles via flow cytometry. Millions of individual DNA molecules can be assessed in this fashion with standard laboratory equipment. Moreover, specific variants can be isolated by flow sorting and employed for further experimentation.
    Type: Application
    Filed: January 29, 2009
    Publication date: November 19, 2009
    Applicant: The Johns Hopkins University
    Inventors: Devin DRESSMAN, Hai Yan, Kenneth Kinzler, Bert Volgelstein
  • Publication number: 20090233270
    Abstract: To gain a better understanding of tumor angiogenesis, new techniques for isolating endothelial cells (ECs) and evaluating gene expression patterns were developed. When transcripts from ECs derived from normal and malignant colorectal tissues were compared with transcripts from non-endothelial cells, over 170 genes predominantly expressed in the endothelium were identified. Comparison between normal- and tumor-derived endothelium revealed many differentially expressed genes, including a large nujber of genes that were specifically elevated in tumor-associated endothelium. Experiments with representative genes from this group demonstrated that most were similarly expressed in the endothelium of primary lung, breast, brain, and pancreatic cancers as well as in metastatic lesions fo the liver. Theses results demonstrate that neoplastic and normal endothelium in humans are distinct at the molecular level, and have significant implications for the development of anti-angiogenic.
    Type: Application
    Filed: July 2, 2003
    Publication date: September 17, 2009
    Inventors: Brad St. Croix, Kenneth Kinzler, Bert Vogelstein
  • Publication number: 20090208505
    Abstract: Phosphatidylinositol 3-kinases (PI3Ks) are known to be important regulators of signaling pathways. To determine whether PI3Ks are genetically altered in cancers, we analyzed the sequences of the P13K gene family and discovered that one family member, PIK3CA, is frequently mutated in cancers of the colon and other organs. The majority of mutations clustered near two positions within the P13K helical or kinase domains. PIK3CA represents one of the most highly mutated oncogenes yet identified in human cancers and is useful as a diagnostic and therapeutic target.
    Type: Application
    Filed: February 18, 2005
    Publication date: August 20, 2009
    Applicant: The Johns Hopkins University
    Inventors: Yardena Samuels, Victor Velculescu, Kenneth Kinzler, Bert Vogelstein
  • Patent number: 7504493
    Abstract: Yeast genes which are differentially expressed during the cell cycle are described. They can be used to study, affect, and monitor the cell cycle of a eukaryotic cell. They can be used to obtain human homologs involved in cell cycle regulation. They can be used to identify antifungal agents and other classes of drugs. They can be formed into arrays on solid supports for interrogation of a cell's transcriptome under various conditions.
    Type: Grant
    Filed: August 11, 2004
    Date of Patent: March 17, 2009
    Assignee: The John Hopkins University
    Inventors: Victor E. Velculescu, Bert Vogelstein, Kenneth Kinzler
  • Publication number: 20090010844
    Abstract: The instant invention provides a method for diagnosing an infection in a subject by administering to the subject a compound suitable for imaging which binds to a thymidine kinase present in the infecting organism, and obtaining an image of the subject to determine the presence and location of the compound, wherein a localization of the compound is indicative that the subject has an infection.
    Type: Application
    Filed: June 20, 2005
    Publication date: January 8, 2009
    Applicant: The John Hopkins University
    Inventors: Martin G. Pomper, Chetan Bettegowda, Catherine Foss, Shibin Zhou, Kenneth Kinzler, Bert Vogelstein
  • Publication number: 20070065823
    Abstract: Many areas of biomedical research depend on the analysis of uncommon variations in individual genes or transcripts. Here we describe a method that can quantify such variation at a scale and ease heretofore unattainable. Each DNA molecule in a collection of such molecules is converted into a single particle to which thousands of copies of DNA identical in sequence to the original are bound. This population of beads then corresponds to a one-to-one representation of the starting DNA molecules. Variation within the original population of DNA molecules can then be simply assessed by counting fluorescently-labeled particles via flow cytometry. Millions of individual DNA molecules can be assessed in this fashion with standard laboratory equipment. Moreover, specific variants can be isolated by flow sorting and employed for further experimentation.
    Type: Application
    Filed: June 9, 2004
    Publication date: March 22, 2007
    Inventors: Devin Dressman, Hai Yan, Kenneth Kinzler, Bert Vogelstein