Patents by Inventor Nickolas Papadopoulos
Nickolas Papadopoulos 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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Patent number: 11591393Abstract: Blockade of immune checkpoints such as cytotoxic T-lymphocyte antigen-4 (CTLA-4) and programmed death-1 (PD-1) shows promise in patients with cancer. Inhibitory antibodies directed at these receptors have been shown to break immune tolerance and promote anti-tumor immunity. These agents work particularly well in patients with a certain category of tumor. Such tumors may be particularly susceptible to treatment because of the multitude of neoantigens which they produce.Type: GrantFiled: September 2, 2021Date of Patent: February 28, 2023Assignee: The Johns Hopkins UniversityInventors: Luis Diaz, Bert Vogelstein, Kenneth W. Kinzler, Nickolas Papadopoulos, Dung Le, Drew M. Pardoll, Suzanne L. Topalian
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Publication number: 20230051847Abstract: This document provides methods and materials for assessing a mammal having or suspected of having cancer and/or for treating a mammal having cancer. For example, molecules including one or more antigen-binding domains (e.g., a single-chain variable fragment (scFv)) that can bind to a modified peptide (e.g., a tumor antigen), as well as method for using such molecules, are provided.Type: ApplicationFiled: December 17, 2020Publication date: February 16, 2023Inventors: Bert Vogelstein, Kenneth W. Kinzler, Emily Han-Chung Hsiue, Jacqueline Douglass, Michael S. Hwang, Alexander Pearlman, Nickolas Papadopoulos, Shibin Zhou, Brian Mog, Katharine M. Wright, Sandra B. Gabelli
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Publication number: 20230026716Abstract: Blockade of immune checkpoints such as cytotoxic T-lymphocyte antigen-4 (CTLA-4) and programmed death-1 (PD-1) shows promise in patients with cancer. Inhibitory antibodies directed at these receptors have been shown to break immune tolerance and promote anti-tumor immunity. These agents work particularly well in patients with a certain category of tumor. Such tumors may be particularly susceptible to treatment because of the multitude of neoantigens which they produce.Type: ApplicationFiled: September 26, 2022Publication date: January 26, 2023Inventors: Luis Diaz, Bert Vogelstein, Kenneth W. Kinzler, Nickolas Papadopoulos, Dung Le, Drew M. Pardoll, Suzanne L. Topalian
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Patent number: 11525163Abstract: The recently developed liquid-based Papanicolaou (Pap) smear allows not only cytologic evaluation but also collection of DNA for detection of HPV, the causative agent of cervical cancer. We tested these samples to detect somatic mutations present in rare tumor cells that might accumulate in the cervix once shed from endometrial and ovarian cancers. A panel of commonly mutated genes in endometrial and ovarian cancers was assembled and used to identify mutations in all 46 endometrial or cervical cancer tissue samples. We were able also able to identify the same mutations in the DNA from liquid Pap smears in 100% of endometrial cancers (24 of 24) and in 41% of ovarian cancers (9 of 22). We developed a sequence-based method to query mutations in 12 genes in a single liquid Pap smear without prior knowledge of the tumor's genotype.Type: GrantFiled: October 17, 2013Date of Patent: December 13, 2022Assignee: The Johns Hopkins UniversityInventors: Isaac Kinde, Kenneth W. Kinzler, Bert Vogelstein, Nickolas Papadopoulos, Luis Diaz, Chetan Bettegowda, Yuxuan Wang
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Publication number: 20220316005Abstract: The identification of mutations that are present in a small fraction of DNA templates is essential for progress in several areas of biomedical research. Though massively parallel sequencing instruments are in principle well-suited to this task, the error rates in such instruments are generally too high to allow confident identification of rare variants. We here describe an approach that can substantially increase the sensitivity of massively parallel sequencing instruments for this purpose. One example of this approach, called “Safe-SeqS” for (Safe-Sequencing System) includes (i) assignment of a unique identifier (UID) to each template molecule; (ii) amplification of each uniquely tagged template molecule to create UID-families; and (iii) redundant sequencing of the amplification products. PCR fragments with the same UID are truly mutant (“super-mutants”) if ?95% of them contain the identical mutation.Type: ApplicationFiled: June 10, 2022Publication date: October 6, 2022Inventors: Bert Vogelstein, Kenneth W. Kinzler, Nickolas Papadopoulos, Isaac A. Kinde
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Patent number: 11459611Abstract: The identification of mutations that are present in a small fraction of DNA templates is essential for progress in several areas of biomedical research. Though massively parallel sequencing instruments are in principle well-suited to this task, the error rates in such instruments are generally too high to allow confident identification of rare variants. We here describe an approach that can substantially increase the sensitivity of massively parallel sequencing instruments for this purpose. One example of this approach, called “Safe-SeqS” for (Safe-Sequencing System) includes (i) assignment of a unique identifier (UID) to each template molecule; (ii) amplification of each uniquely tagged template molecule to create UID-families; and (iii) redundant sequencing of the amplification products. PCR fragments with the same UID are truly mutant (“super-mutants”) if ?95% of them contain the identical mutation.Type: GrantFiled: May 21, 2019Date of Patent: October 4, 2022Assignee: The Johns Hopkins UniversityInventors: Bert Vogelstein, Kenneth W. Kinzler, Nickolas Papadopoulos, Isaac A. Kinde
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Patent number: 11453913Abstract: The identification of mutations that are present in a small fraction of DNA templates is essential for progress in several areas of biomedical research. Though massively parallel sequencing instruments are in principle well-suited to this task, the error rates in such instruments are generally too high to allow confident identification of rare variants. We here describe an approach that can substantially increase the sensitivity of massively parallel sequencing instruments for this purpose. One example of this approach, called “Safe-SeqS” for (Safe-Sequencing System) includes (i) assignment of a unique identifier (UID) to each template molecule; (ii) amplification of each uniquely tagged template molecule to create UID-families; and (iii) redundant sequencing of the amplification products. PCR fragments with the same UID are truly mutant (“super-mutants”) if ?95% of them contain the identical mutation.Type: GrantFiled: May 19, 2021Date of Patent: September 27, 2022Assignee: The Johns Hopkins UniversityInventors: Bert Vogelstein, Kenneth W. Kinzler, Nickolas Papadopoulos, Isaac A. Kinde
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Publication number: 20220275086Abstract: Blockade of immune checkpoints such as cytotoxic T-lymphocyte antigen-4 (CTLA-4) and programmed death-1 (PD-1) shows promise in patients with cancer. Inhibitory antibodies directed at these receptors have been shown to break immune tolerance and promote anti-tumor immunity. These agents work particularly well in patients with a certain category of tumor. Such tumors may be particularly susceptible to treatment because of the multitude of neoantigens which they produce.Type: ApplicationFiled: May 9, 2022Publication date: September 1, 2022Inventors: Luis Diaz, Bert Vogelstein, Kenneth W. Kinzler, Nickolas Papadopoulos, Dung Le, Drew M. Pardoll, Suzanne L. Topalian
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Publication number: 20220259668Abstract: This document provides methods and materials for identifying chromosomal anomalies that can be used to identify a mammal as having a disease (e.g., cancer or congenital abnormality). For example, this document provides methods and materials for evaluating sequencing data to identify a mammal as having a disease associated with one or more chromosomal anomalies (e.g., cancer or congenital abnormalities). For example, this document provides methods and materials for evaluating sequencing data that can be used in cancer diagnostics, non-invasive prenatal testing (NIPT), preimplantation genetic diagnosis and evaluation of congenital abnormalities.Type: ApplicationFiled: May 15, 2020Publication date: August 18, 2022Inventors: Bert Vogelstein, Kenneth W. Kinzler, Christopher Douville, Nickolas Papadopoulos, Cristian Tomasetti
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Publication number: 20220259312Abstract: Blockade of immune checkpoints such as cytotoxic T-lymphocyte antigen-4 (CTLA-4) and programmed death-1 (PD-1) shows promise in patients with cancer. Inhibitory antibodies directed at these receptors have been shown to break immune tolerance and promote anti-tumor immunity. These agents work particularly well in patients with a certain category of tumor. Such tumors may be particularly susceptible to treatment because of the multitude of neoantigens which they produce.Type: ApplicationFiled: May 9, 2022Publication date: August 18, 2022Inventors: Luis Diaz, Bert Vogelstein, Kenneth W. Kinzler, Nickolas Papadopoulos, Dung Le, Drew M. Pardoll, Suzanne L. Topalian
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Publication number: 20220220563Abstract: We queried DNA from saliva or plasma of 93 HNSCC patients, searching for somatic mutations or human papillomavirus genes, collectively referred to as tumor DNA. When both plasma and saliva were tested, tumor DNA was detected in 96% (95% CI, 84% to 99%) of 47 patients. The fractions of patients with detectable tumor DNA in early- and late-stage disease were 100% (n=10) and 95% (n=37), respectively. Saliva is preferentially enriched for tumor DNA from the oral cavity, whereas plasma is preferentially enriched for tumor DNA from the other sites. Tumor DNA in the saliva and plasma is a valuable biomarker for detection of HNSCC.Type: ApplicationFiled: January 27, 2022Publication date: July 14, 2022Inventors: Bert Vogelstein, Kenneth W. Kinzler, Luis Diaz, Nickolas Papadopoulos, Nishant Agrawal, Yuxuan Wang, Simeon Springer
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Publication number: 20220205048Abstract: A diagnostic test for ovarian cysts is based on the detection of mutations characteristic of the most common neoplasms giving rise to these lesions. With this test, tumor-specific mutations were detected in the cyst fluids of 19 of 24 (79%) borderline tumors and 28 of 31 (90%) malignant ovarian cancers. In contrast, we detected no mutations in the cyst fluids from 10 non-neoplastic cysts and 12 benign tumors. When categorized by the need for exploratory surgery (i.e., presence of a borderline tumor or malignant cancer), the sensitivity of this test was 85% and the specificity was 100%. These tests could inform the diagnosis of ovarian cysts and improve the clinical management of the large number of women with these lesions.Type: ApplicationFiled: January 14, 2022Publication date: June 30, 2022Inventors: Yuxuan Wang, Bert Vogelstein, Kenneth W. Kinzler, Luis Diaz, Nickolas Papadopoulos, Karin Sundfeldt, Bjorg Kristjansdottir
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Patent number: 11339219Abstract: Blockade of immune checkpoints such as cytotoxic T-lymphocyte antigen-4 (CTLA-4) and programmed death-1 (PD-1) shows promise in patients with cancer. Inhibitory antibodies directed at these receptors have been shown to break immune tolerance and promote anti-tumor immunity. These agents work particularly well in patients with a certain category of tumor. Such tumors may be particularly susceptible to treatment because of the multitude of neoantigens which they produce.Type: GrantFiled: December 22, 2020Date of Patent: May 24, 2022Assignee: The Johns Hopkins UniversityInventors: Luis Diaz, Bert Vogelstein, Kenneth W. Kinzler, Nickolas Papadopoulos, Dung Le, Drew M. Pardoll, Suzanne L. Topalian
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Patent number: 11325975Abstract: Blockade of immune checkpoints such as cytotoxic T-lymphocyte antigen-4 (CTLA-4) and programmed death-1 (PD-1) shows promise in patients with cancer. Inhibitory antibodies directed at these receptors have been shown to break immune tolerance and promote anti-tumor immunity. These agents work particularly well in patients with a certain category of tumor. Such tumors may be particularly susceptible to treatment because of the multitude of neoantigens which they produce.Type: GrantFiled: December 22, 2020Date of Patent: May 10, 2022Assignee: The Johns Hopkins UniversityInventors: Luis Diaz, Bert Vogelstein, Kenneth W. Kinzler, Nickolas Papadopoulos, Dung Le, Drew M. Pardoll, Suzanne L. Topalian
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Patent number: 11325974Abstract: Blockade of immune checkpoints such as cytotoxic T-lymphocyte antigen-4 (CTLA-4) and programmed death-1 (PD-1) shows promise in patients with cancer. Inhibitory antibodies directed at these receptors have been shown to break immune tolerance and promote anti-tumor immunity. These agents work particularly well in patients with a certain category of tumor. Such tumors may be particularly susceptible to treatment because of the multitude of neoantigens which they produce.Type: GrantFiled: December 22, 2020Date of Patent: May 10, 2022Assignee: The Johns Hopkins UniversityInventors: Luis Diaz, Bert Vogelstein, Kenneth W. Kinzler, Nickolas Papadopoulos, Dung Le, Drew M. Pardoll, Suzanne L. Topalian
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Patent number: 11306364Abstract: We surveyed 1,230 tumors of 60 different types and found that tumors could be divided into types with low (<15%) and high (?15%) frequencies of TERT promoter mutations. The nine TERT-high tumor types almost always originated in tissues with relatively low rates of self renewal, including melanomas, liposarcomas, hepatocellular carcinomas, urothelial carcinomas, squamous cell carcinomas of the tongue, medulloblastomas, and subtypes of gliomas (including 83% of primary glioblastoma, the most common brain tumor type). TERT and ATRX mutations were mutually exclusive, suggesting that these two genetic mechanisms confer equivalent selective growth advantages. In addition to their implications for understanding the relationship between telomeres and tumorigenesis, TERT mutations provide a biomarker for the early detection of urinary tract and liver tumors and aid in the classification and prognostication of brain tumors.Type: GrantFiled: July 14, 2020Date of Patent: April 19, 2022Assignees: Duke University, The Johns Hopkins UniversityInventors: Hai Yan, Bert Vogelstein, Nickolas Papadopoulos, Kenneth W. Kinzler, Yuchen Jiao, Chetan Bettegowda, Darell D. Bigner, Zachary J. Reitman, Patrick J. Killela
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Patent number: 11286531Abstract: A diagnostic test for ovarian cysts is based on the detection of mutations characteristic of the most common neoplasms giving rise to these lesions. With this test, tumor-specific mutations were detected in the cyst fluids of 19 of 24 (79%) borderline tumors and 28 of 31 (90%) malignant ovarian cancers. In contrast, we detected no mutations in the cyst fluids from 10 non-neoplastic cysts and 12 benign tumors. When categorized by the need for exploratory surgery (i.e., presence of a borderline tumor or malignant cancer), the sensitivity of this test was 85% and the specificity was 100%. These tests could inform the diagnosis of ovarian cysts and improve the clinical management of the large number of women with these lesions.Type: GrantFiled: August 11, 2016Date of Patent: March 29, 2022Assignee: The Johns Hopkins UniversityInventors: Yuxuan Wang, Bert Vogelstein, Kenneth W. Kinzler, Luis Diaz, Nickolas Papadopoulos, Karin Sundfeldt, Bjorg Kristjansdottir
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Publication number: 20220073977Abstract: Provided herein are systems, kits, compositions and methods for sequencing library preparation and sequencing workflow (e.g., for the identification of mutations). In certain embodiments, provides herein systems and methods to identically barcode both strands of templates, and PCR-based enrichment of each strand that does not require hybridization capture.Type: ApplicationFiled: February 12, 2021Publication date: March 10, 2022Inventors: Nickolas Papadopoulos, Kenneth W. Kinzler, Bert Vogelstein, Joshua David Cohen
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Patent number: 11268153Abstract: We queried DNA from saliva or plasma of 93 HNSCC patients, searching for somatic mutations or human papillomavirus genes, collectively referred to as tumor DNA. When both plasma and saliva were tested, tumor DNA was detected in 96% (95% CI, 84% to 99%) of 47 patients. The fractions of patients with detectable tumor DNA in early- and late-stage disease were 100% (n=10) and 95% (n=37), respectively. Saliva is preferentially enriched for tumor DNA from the oral cavity, whereas plasma is preferentially enriched for tumor DNA from the other sites. Tumor DNA in the saliva and plasma is a valuable biomarker for detection of HNSCC.Type: GrantFiled: June 16, 2016Date of Patent: March 8, 2022Assignee: The Johns Hopkins UniversityInventors: Bert Vogelstein, Kenneth W. Kinzler, Luis Diaz, Nickolas Papadopoulos, Nishant Agrawal, Yuxuan Wang, Simeon Springer
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Publication number: 20220056129Abstract: Blockade of immune checkpoints such as cytotoxic T-lymphocyte antigen-4 (CTLA-4) and programmed death-1 (PD-1) shows promise in patients with cancer. Inhibitory antibodies directed at these receptors have been shown to break immune tolerance and promote anti-tumor immunity. These agents work particularly well in patients with a certain category of tumor. Such tumors may be particularly susceptible to treatment because of the multitude of neoantigens which they produce.Type: ApplicationFiled: September 2, 2021Publication date: February 24, 2022Inventors: Luis Diaz, Bert Vogelstein, Kenneth W. Kinzler, Nickolas Papadopoulos, Dung Le, Drew M. Pardoll, Suzanne L. Topalian