Abstract: Disclosed herein is a system and method for increasing the fidelity of measured genetic data, for making allele calls, and for determining the state of aneuploidy, in one or a small set of cells, or from fragmentary DNA, where a limited quantity of genetic data is available. Poorly or incorrectly measured base pairs, missing alleles and missing regions are reconstructed using expected similarities between the target genome and the genome of genetically related individuals. In accordance with one embodiment, incomplete genetic data from an embryonic cell are reconstructed at a plurality of loci using the more complete genetic data from a larger sample of diploid cells from one or both parents, with or without haploid genetic data from one or both parents. In another embodiment, the chromosome copy number can be determined from the measured genetic data, with or without genetic information from one or both parents.
Type:
Grant
Filed:
January 26, 2018
Date of Patent:
April 23, 2019
Assignee:
Natera, Inc.
Inventors:
Matthew Rabinowitz, Milena Banjevic, Zachary Demko, David Johnson, Dusan Kijacic, Dimitri Petrov, Joshua Sweetkind-Singer, Jing Xu
Abstract: Disclosed herein is a system and method for increasing the fidelity of measured genetic data, for making allele calls, and for determining the state of aneuploidy, in one or a small set of cells, or from fragmentary DNA, where a limited quantity of genetic data is available. Poorly or incorrectly measured base pairs, missing alleles and missing regions are reconstructed using expected similarities between the target genome and the genome of genetically related individuals. In accordance with one embodiment, incomplete genetic data from an embryonic cell are reconstructed at a plurality of loci using the more complete genetic data from a larger sample of diploid cells from one or both parents, with or without haploid genetic data from one or both parents. In another embodiment, the chromosome copy number can be determined from the measured genetic data, with or without genetic information from one or both parents.
Type:
Grant
Filed:
March 1, 2017
Date of Patent:
April 16, 2019
Assignee:
Natera, Inc.
Inventors:
Matthew Rabinowitz, Milena Banjevic, Zachary Demko, David Johnson, Dusan Kijacic, Dimitri Petrov, Joshua Sweetkind-Singer, Jing Xu
Abstract: LAMP primer sets for detecting eight mastitis pathogens are disclosed. Methods and kits of using the primer sets to simultaneously detect at least two of the eight mastitis pathogens are also described.
Abstract: The invention relates to methods for the detection of a specific sequence of RNA in a cell or tissue sample. The invention also relates to methods to enzymatically manipulate the RNA in a crude cell lysate in a number of applications.
Abstract: The invention provides a rapid, accurate, sensitive, and low-cost detection method for screening a biological sample for one or more desired bacterial species. The inventive method employs a two-step multiplex real-time PCR assay that comprises an internal amplification control and specific primer sets to detect and discriminate bacterial species based the unique melting temperatures of specific DNA sequences of each strain.
Type:
Grant
Filed:
July 27, 2015
Date of Patent:
January 29, 2019
Assignee:
The Curators of the University of Missouri
Abstract: Methods for the rapid detection of the presence or absence of mecC-containing Staphylococcus aureus (mecC-MRSA) in a biological or non-biological sample are described. The methods can include performing an amplifying step, a hybridizing step, and a detecting step. Furthermore, primers, probes targeting the genes for mecC-MRSA, along with kits are provided that are designed for the detection of mecC-MRSA.
Abstract: The present invention provides methods, compositions and kits for using a transposase and a transposon end for generating extensive fragmentation and 5?-tagging of double-stranded target DNA in vitro, then using a DNA polymerase for generating 5?- and 3?-tagged single-stranded DNA fragments without performing a PCR amplification reaction, wherein the first tag on the 5?-ends exhibits the sequence of the transferred transposon end and optionally, an additional arbitrary sequence, and the second tag on the 3?-ends exhibits a different sequence from the sequence exhibited by the first tag. The method is useful for generating 5?- and 3?-tagged DNA fragments for use in a variety of processes, including processes for metagenomic analysis of DNA in environmental samples, copy number variation (CNV) analysis of DNA, and comparative genomic sequencing (CGS), including massively parallel DNA sequencing (so-called “next generation sequencing).
Type:
Grant
Filed:
July 21, 2015
Date of Patent:
January 22, 2019
Assignee:
Epicentre Technologies Corporation
Inventors:
Haiying Li Grunenwald, Nicholas Caruccio, Jerome Jendrisak, Gary Dahl
Abstract: A method of estimating the amount of a methylated locus is provided. In certain embodiments the method comprises: digesting a nucleic acid sample that contains both unmethylated and methylated copies of a genomic locus with an MspJI family member to produce a population of fragments that are in the range of 20-40 nucleotides in length, ligating adaptor sequence A and adaptor sequence B to the respective ends of a target fragment of sequence X, and quantifying the amount of ligation products of formula A-X-B. A kit for performing the method is also provided.
Type:
Grant
Filed:
July 30, 2015
Date of Patent:
January 8, 2019
Assignee:
Vanadis Diagnostics
Inventors:
Carl Oscar Fredrik Dahl, Olof John Ericsson, Johan Banér
Abstract: The present invention relates to methods and apparatuses for amplifying, detecting, and optionally quantifying, nucleic acids. In one aspect the method comprises (a) providing a reaction volume comprising (i) a first electrode comprising an electrochemically-active conducting polymer, a first single-stranded nucleic acid molecule capable of hybridizing to a target nucleic acid, wherein the first nucleic acid molecule is covalently attached to the electrochemically-active conducting polymer, and (ii) a second electrode, (b) providing a reaction mixture to the reaction volume, the reaction mixture comprising a target nucleic acid, a nucleic acid polymerase, a redox couple, and nucleic acid amplification reagents, (c) amplifying the nucleic acid, and (d) measuring the impedance of the first electrode at least once during the nucleic acid amplification reaction.
Type:
Grant
Filed:
June 12, 2015
Date of Patent:
January 1, 2019
Assignee:
AUCKLAND UNISERVICES LIMITED
Inventors:
Nihan Aydemir, Jadranka Travas-Sejdic, Clive William Evans, David Edward Williams
Abstract: Methods and compositions for enriching a population of particles containing an analyte are disclosed. In one embodiment, enrichment beads are used that are larger in size than the beads used for amplification. A separation device is employed that can retain larger beads with bound amplified beads. The technique finds many uses, including enriching for beads with clonally amplified template, which can be used in a variety of assays, including nucleic acid sequencing.
Type:
Grant
Filed:
April 29, 2014
Date of Patent:
December 25, 2018
Assignee:
QIAGEN WALTHAM, INC.
Inventors:
Jerzy Olejnik, Steven Gordon, Martina Werner
Abstract: Provided is a gene amplifying and detecting device. The gene amplifying and detecting device includes: a gene amplifying chip including a chamber formed therein; a reaction solution filled in the chamber and including a fluorescent material; a light source located at one side of the gene amplifying chip; a light detector located at the other side of the gene amplifying chip; and a graphene heater formed on an inner surface or outer surface of the gene amplifying chip so as to heat the reaction solution.
Type:
Grant
Filed:
November 26, 2014
Date of Patent:
November 27, 2018
Assignee:
ELECTRONICS AND TELECOMMUNICATIONS RESEARCH INSTITUTE
Inventors:
Kwang Hyo Chung, Jin Tae Kim, Yo Han Choi, Choon Gi Choi, Hong Kyw Choi, Young Jun Yu, Doo Hyeb Youn, Jin Sik Choi
Abstract: Parallel isolation of a double-stranded nucleic acid and a single-stranded nucleic acid is possible from a sample that contains these acids, without separating the acids, by mixing the sample with a lysis buffer having high salt concentration or low salt concentration, or having a proteolytic enzyme. The sample that contains nucleic acid before its lysis, or the sample that has already been lysed or homogenized, is adjusted with a binding buffer in such a manner that the total nucleic acid is adsorbed onto a solid carrier. The binding buffer contains at least one non-ionic detergent in a high concentration. With the exception of the detergent, the sample contains no other non-acidic organic component miscible in water. The carrier with the adsorbed total nucleic acid is removed. The adsorbed total nucleic acid is washed and eluted.
Abstract: The present invention relates to compositions, methods, and kits for determining the presence or absence of HIV in a sample, in particular for determining HIV-1 group M, HIV-1 group O, and/or HIV-2, in particular for simultaneous determining of HIV-1 group M, HIV-1 group O, and HIV-2.
Type:
Grant
Filed:
March 21, 2014
Date of Patent:
October 30, 2018
Assignee:
Grifols Therapeutics Inc.
Inventors:
Danuta Wronska, Terri W Journigan, James D Mellott
Abstract: The present invention relates to a method and a kit of parts for detecting the presence or absence of one or more target nucleic acid sequences in a sample, the method comprising a sequence of steps for pre-amplifying the sample by means of a polymerase chain reaction, followed by a sequence of steps comprising an isothermal amplification of the pre-amplified sample, wherein the isothermal amplification comprises a pair of primers comprising a forward primer having a 3? part that is substantially complementary to a first part of the target sequence, the presence or absence of which is to be detected, and a 5? part that is substantially homolog to a second part of the target sequence, and a reverse primer comprising a 3? part that is substantially homolog to a fourth part of the target sequence and a 5? part that is substantially complementary to a third part of the target sequence.
Abstract: The invention provides materials and methods to identify and analyze in a genome-wide manner the structural determinants of this organization. Next generation sequencing methods, combined with a novel assay and integrated data analysis, are used to map the long-range interactions in chromatin that are involved in the regulation of transcription.
Type:
Grant
Filed:
April 26, 2016
Date of Patent:
October 16, 2018
Assignee:
Board of Regents, The University of Texas System
Abstract: Disclosed herein is a system and method for increasing the fidelity of measured genetic data, for making allele calls, and for determining the state of aneuploidy, in one or a small set of cells, or from fragmentary DNA, where a limited quantity of genetic data is available. Poorly or incorrectly measured base pairs, missing alleles and missing regions are reconstructed using expected similarities between the target genome and the genome of genetically related individuals. In accordance with one embodiment, incomplete genetic data from an embryonic cell are reconstructed at a plurality of loci using the more complete genetic data from a larger sample of diploid cells from one or both parents, with or without haploid genetic data from one or both parents. In another embodiment, the chromosome copy number can be determined from the measured genetic data, with or without genetic information from one or both parents.
Type:
Grant
Filed:
July 23, 2013
Date of Patent:
September 25, 2018
Assignee:
Natera, Inc.
Inventors:
Matthew Rabinowitz, Milena Banjevic, Zachary Demko, David Johnson, Dusan Kijacic, Dimitri Petrov, Joshua Sweetkind-Singer, Jing Xu
Abstract: Disclosed herein is a system and method for increasing the fidelity of measured genetic data, for making allele calls, and for determining the state of aneuploidy, in one or a small set of cells, or from fragmentary DNA, where a limited quantity of genetic data is available. Poorly or incorrectly measured base pairs, missing alleles and missing regions are reconstructed using expected similarities between the target genome and the genome of genetically related individuals. In accordance with one embodiment, incomplete genetic data from an embryonic cell are reconstructed at a plurality of loci using the more complete genetic data from a larger sample of diploid cells from one or both parents, with or without haploid genetic data from one or both parents. In another embodiment, the chromosome copy number can be determined from the measured genetic data, with or without genetic information from one or both parents.
Type:
Grant
Filed:
January 23, 2017
Date of Patent:
September 25, 2018
Assignee:
Natera, Inc
Inventors:
Matthew Rabinowitz, Milena Banjevic, Zachary Demko, David Johnson, Dusan Kijacic, Dimitri Petrov, Joshua Sweetkind-Singer, Jing Xu
Abstract: The invention provides an oligonucleotide comprising a nucleotide sequence consisting of SEQ ID NO: 1. The invention also provides method for detecting target DNA in a sample with the oligonucleotide.
Abstract: The present invention provides methods, compositions and kits for targeted nucleic acid sequence enrichment in a nucleic acid sample and for high efficiency nucleic acid library generation for next generation sequencing (NGS). Specifically, the methods, compositions and kits provided herein are useful for the production and capture of amplification-ready, target-specific and strand-specific regions of interest from nucleic acid samples containing complex DNA.
Type:
Grant
Filed:
March 28, 2017
Date of Patent:
July 31, 2018
Assignee:
NUGEN TECHNOLOGIES, INC.
Inventors:
Doug Amorese, Chris Armour, Nurith Kurn