Abstract: The present inventors identified a subpopulation of genes induced by type I and type II IFNs in a human submandibular gland (HSG) epithelial cell line. Unexpectedly, it was found that the majority of genes that are highly up-regulated by IFN-? are also highly induced by IFN-?. In contrast, there was a substantial group of genes that are highly induced by IFN-? only. In target tissues, this identified subpopulation of genes and probes allow different IFN patterns to be discerned, enabling more precise molecular classification of patient subpopulations. The identified gene probes are useful for selecting and monitoring therapy, and for defining efficacy of novel agents in the autoimmune rheumatic diseases.
Type:
Grant
Filed:
May 8, 2018
Date of Patent:
June 21, 2022
Assignee:
The Johns Hopkins University
Inventors:
John Clayton Hall, Livia Casciola-Rosen, Antony Rosen
Abstract: A system and method for isolating and analyzing single cells, wherein the system includes: an array of wells defined at a substrate, each well including an open surface and a well cavity configured to capture cells in one of a single-cell format and single-cluster format, and a fluid delivery module including a fluid reservoir through which fluid flow is controlled along a fluid path; and wherein the method includes: capturing a population of particles into the array of wells in single-particle format; releasing, from the particles, a set of probes into the array of wells; capturing a population of cells into the array of wells in single-cell format; releasing biomolecules from each captured cell into the array of wells; and generating a set of genetic complexes comprising the biomolecules associated with a single captured cell and a subset of probes within individual wells of the array of wells.
Type:
Grant
Filed:
May 28, 2021
Date of Patent:
June 14, 2022
Assignee:
Bio-Rad Laboratories, Inc.
Inventors:
Kalyan Handique, Vishal Sharma, Priyadarshini Gogoi, William Chow, Austin Payne, Kyle Gleason, Brian Boniface, John Connolly, Sam Tuck
Abstract: The invention relates to adaptors for sequencing nucleic acids. The adaptors may be used to generate single stranded constructs of nucleic acid for sequencing purposes. Such constructs may contain both strands from a double stranded deoxyribonucleic acid (DNA) or ribonucleic acid (RNA) template. The invention also relates to the constructs generated using the adaptors, methods of making the adaptors and constructs, as well as methods of sequencing double stranded nucleic acids.
Abstract: The present application generally to the diagnosis and treatment of diseases resulting from the alteration of chromatin boundaries between topologically-associated domains. In particular, the present application relates to detection of mutations causing DNA hypermethylation phenotypes, CpG methylation within CTCF binding motifs, and aberrant gene expression caused by altered chromatin topology. Applicants show that IDH mutant gliomas exhibit hyper-methylation at CTCF binding sites, compromising binding of this methylation-sensitive insulator protein. Applicants also demonstrate that loss of CTCF at a domain boundary permits a constitutive enhancer to aberrantly interact with the receptor tyrosine kinase gene PDGFRA, a prominent glioma oncogene. Thus, Applicants have uncovered that IDH mutations may promote gliomagenesis by disrupting chromosomal topology and allowing aberrant regulatory interactions that induce oncogene expression.
Type:
Grant
Filed:
December 14, 2016
Date of Patent:
May 24, 2022
Assignee:
The General Hospital Corporation
Inventors:
Bradley Bernstein, Yotam Drier, William Flavahan, Daniel Tarjan
Abstract: The present invention relates to a fast and efficient method of isolating nucleic acids in high yield and in high concentration from biological samples, using an aqueous two phase system without the need for instrumentation. The isolated nucleic acids can be used to facilitate the screening, prognosis and monitoring of disease progression.
Abstract: A DNA sequencing device, and related method, which include an electrode and a plurality of spaced apart alignment structures. The electrode defines an electrode gap, the electrode being operable to detect a change in tunneling current as a DNA strand passes through the electrode gap. The plurality of spaced apart alignment structures are arranged to position nucleotides of the DNA strand in a predetermined orientation as the DNA strand passes through the electrode gap.
Type:
Grant
Filed:
July 28, 2020
Date of Patent:
May 3, 2022
Assignee:
SEAGATE TECHNOLOGY LLC
Inventors:
Thomas Young Chang, David S. Kuo, Kim Yang Lee, Koichi Wago
Abstract: The present invention provides assays systems and methods for detection of chromosomal abnormalities and status of single loci associated with monogenic or polygenic traits in a sample containing nucleic acids from a maternal and a fetal source.
Type:
Grant
Filed:
December 21, 2017
Date of Patent:
May 3, 2022
Assignee:
Roche Molecular Systems, Inc.
Inventors:
Andrew Sparks, Arnold Oliphant, Jacob Zahn, Ken Song, John Stuelpnagel
Abstract: Devices and methods generate an ordered restriction map of genomic DNA extracted from whole cells, nuclei, whole chromosomes, or other sources of long DNA molecules. The devices have a fluidic microchannel that merges into a reaction nanochannel that merges into a detection nanochannel at an interface where the nanochannel diameter decreases in size by between 50% to 99%. Intact molecules of DNA are transported to the reaction nanochannel and then fragmented in the reaction nanochannel using restriction endonuclease enzymes. The reaction nanochannel is sized and configured so that the fragments stay in an original order until they are injected into the detection nanochannel. Signal at one or more locations along the detection nanochannel is detected to map fragments in the order they occur along a long DNA molecule.
Type:
Grant
Filed:
January 17, 2020
Date of Patent:
April 19, 2022
Assignee:
The University of North Carolina at Chapel Hill
Abstract: The present invention provides assay systems and methods for detection of copy number variation at one or more loci and polymorphism detection at one or more loci in a mixed sample from an individual.
Type:
Grant
Filed:
May 23, 2019
Date of Patent:
April 12, 2022
Assignee:
Ariosa Diagnostics, Inc.
Inventors:
Andrew Sparks, Craig Struble, Eric Wang, Arnold Oliphant
Abstract: Methods for predicting the response of prostate cancer to androgen deprivation therapy (ADT) using a gene signature of five genes (CSPG5, FKBP6, FOSB, STMN1, and TTC27) is provided. Also provided are sets containing specific binding molecules for each of CSPG5, FKBP6, FOSB, STMN1, and TTC27 and kits containing such sets.
Type:
Grant
Filed:
July 5, 2019
Date of Patent:
April 12, 2022
Assignee:
Rutgers, The State University of New Jersey
Abstract: The inventions provided herein relate to detection reagents, compositions, methods, and kits comprising the detection reagents for use in detection, identification, and/or quantification of analytes in a sample. Such detection reagents and methods described herein allow multiplexing of many more labeled species in the same procedure than conventional methods, in which multiplexing is limited by the number of available and practically usable colors.
Type:
Grant
Filed:
April 24, 2019
Date of Patent:
April 5, 2022
Assignee:
President and Fellows of Harvard College
Inventors:
Daniel Levner, Je-hyuk Lee, George M. Church, Michael Super
Abstract: Methods of quantifying N2-carboxyethyl-2?-deoxyguanosine (CEdG) levels in biological samples and comparing those levels to known normal levels can diagnose a number of disorders, including diabetes and cancer. Methods can also determine whether therapies for disorders are effective by measuring CEdG levels before and after treatment. Measurement of CEdG levels occurs using liquid chromatography electrospray ionization tandem mass spectrometry.
Type:
Grant
Filed:
December 29, 2017
Date of Patent:
March 8, 2022
Assignee:
CITY OF HOPE
Inventors:
Samuel Rahbar, Timothy W. Synold, John Termini, Daniel Tamae, Gerald Wuenschell
Abstract: The present invention provides methods of treating cancer based on the methylation status of the ERBB2 gene. One aspect of the invention provides a method of administering an EGFR inhibitor therapy based on the methylation status of the ERBB2 gene.
Abstract: The present invention relates to the selection of patients with enhanced antipsychotic treatment efficacy with iloperidone based on a patient's genotype at one or more single nucleotide polymorphism (SNP) loci and to treatment of such patients based upon the identification of their genetic information.
Type:
Grant
Filed:
August 16, 2019
Date of Patent:
January 4, 2022
Assignee:
VANDA PHARMACEUTICALS INC.
Inventors:
Mihael H. Polymeropoulos, Sandra Smieszek
Abstract: The methods disclosed herein can be used to determine sample integrity, such as sample identity, by using kinship coefficients. Kinship coefficients between two samples can be determined by measuring genetic relatedness in order to determine whether the samples are related or not related.
Type:
Grant
Filed:
June 25, 2018
Date of Patent:
January 4, 2022
Assignee:
Veracyte, Inc.
Inventors:
Yoonha Choi, Joshua Babiarz, Giulia C. Kennedy, Jing Huang
Abstract: The present invention is directed to methods for identifying the presence of one or more target nucleotide sequences in a sample that involve a ligation and/or polymerase reaction. In some embodiments, the ligation products formed in the ligation process of the present invention are subsequently amplified using a polymerase chain reaction. The ligated product sequences or extension products thereof are detected, and the presence of one or more target nucleotide sequences in the sample is identified based on the detection.
Type:
Grant
Filed:
May 24, 2019
Date of Patent:
December 28, 2021
Assignee:
CORNELL UNIVERSITY
Inventors:
Francis Barany, Eugene Spier, Alain Mir
Abstract: The present invention provides synthetic DNA strands that find use as process controls in DNA processing and nucleic acid testing methods. In particular, provided herein are synthetic methylated DNA strands of known composition for use as control molecules in DNA testing, e.g., of mutations and/or methylation of DNA isolated from non-fish samples, such as human samples.
Type:
Grant
Filed:
July 19, 2017
Date of Patent:
December 28, 2021
Assignee:
Exact Sciences Development Company, LLC
Inventors:
Hatim T. Allawi, Graham P. Lidgard, Brian Aizenstein, Melissa M. Gray
Abstract: The present invention provides detection systems and methods for detection of loci and genomic regions in a sample, including mixed samples, using hybridization to an array.
Type:
Grant
Filed:
January 13, 2020
Date of Patent:
December 21, 2021
Assignee:
Ariosa Diagnostics, Inc.
Inventors:
Arnold Oliphant, Jacob Zahn, Kara Jeneau, Patrick Bogard, Stephanie Huang
Abstract: Methods, compositions, and kits for stabilizing both human and microbial deoxyribonucleic acid (DNA) present in complex biological samples, such as feces, are disclosed. In particular, aqueous compositions for stabilizing DNA contained in biological samples at ambient temperature are disclosed, together with associated methods and kits using same. In one aspect, the compositions comprise a chelating agent present at a concentration of at least about 150 mM, and the composition has a pH of at least about 9.5.
Type:
Grant
Filed:
October 7, 2019
Date of Patent:
December 14, 2021
Assignee:
DNA Genotek Inc.
Inventors:
Hyman Chaim Birnboim, Lindsay Pozza, Carlos Alberto Merino Hernandez, Evgueni Vladimirovitch Doukhanine
Abstract: Methods of quantifying a N2-(1-carboxyethyl)-2?-deoxyguanosine (CEdG) levels in biological samples and comparing those levels to known normal levels can diagnose a number of metabolic disorders or complications associated therewith, including diabetes, its associated complications, and cancer. Methods can also determine whether therapies for disorders are effective by measuring CEdG levels before and after treatment. Measurement of CEdG levels is achieved by using liquid chromatography electrospray ionization tandem mass spectrometry.
Type:
Grant
Filed:
February 2, 2018
Date of Patent:
November 23, 2021
Assignee:
CITY OF HOPE
Inventors:
Samuel Rahbar, Timothy W. Synold, John Termini, Gerald Wuenschell, Daniel Tamae