AU2011265205A1 - Nucleic acids for multiplex organism detection and methods of use and making the same - Google Patents

Nucleic acids for multiplex organism detection and methods of use and making the same Download PDF

Info

Publication number
AU2011265205A1
AU2011265205A1 AU2011265205A AU2011265205A AU2011265205A1 AU 2011265205 A1 AU2011265205 A1 AU 2011265205A1 AU 2011265205 A AU2011265205 A AU 2011265205A AU 2011265205 A AU2011265205 A AU 2011265205A AU 2011265205 A1 AU2011265205 A1 AU 2011265205A1
Authority
AU
Australia
Prior art keywords
probe
mixture
sequence
probes
target
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Abandoned
Application number
AU2011265205A
Other languages
English (en)
Inventor
Lisa Diamond
Jochen Kumm
Philip Alexander Rolfe
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
PATHOGENICA Inc
Original Assignee
PATHOGENICA Inc
PATHOGENICA Inc
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by PATHOGENICA Inc, PATHOGENICA Inc filed Critical PATHOGENICA Inc
Publication of AU2011265205A1 publication Critical patent/AU2011265205A1/en
Abandoned legal-status Critical Current

Links

Classifications

    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6844Nucleic acid amplification reactions
    • C12Q1/6853Nucleic acid amplification reactions using modified primers or templates
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/70Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving virus or bacteriophage
    • C12Q1/701Specific hybridization probes
    • C12Q1/708Specific hybridization probes for papilloma
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12NMICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09Recombinant DNA-technology
    • C12N15/10Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1034Isolating an individual clone by screening libraries
    • C12N15/1089Design, preparation, screening or analysis of libraries using computer algorithms
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6869Methods for sequencing
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6888Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms
    • C12Q1/689Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms for bacteria
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/70Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving virus or bacteriophage
    • C12Q1/701Specific hybridization probes

Landscapes

  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Organic Chemistry (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • General Engineering & Computer Science (AREA)
  • Analytical Chemistry (AREA)
  • Genetics & Genomics (AREA)
  • Immunology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biotechnology (AREA)
  • Biophysics (AREA)
  • Physics & Mathematics (AREA)
  • Biochemistry (AREA)
  • Molecular Biology (AREA)
  • General Health & Medical Sciences (AREA)
  • Microbiology (AREA)
  • Virology (AREA)
  • Biomedical Technology (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Plant Pathology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
AU2011265205A 2010-06-11 2011-06-10 Nucleic acids for multiplex organism detection and methods of use and making the same Abandoned AU2011265205A1 (en)

Applications Claiming Priority (7)

Application Number Priority Date Filing Date Title
US35401110P 2010-06-11 2010-06-11
US61/354,011 2010-06-11
US37404110P 2010-08-16 2010-08-16
US61/374,041 2010-08-16
US201161439167P 2011-02-03 2011-02-03
US61/439,167 2011-02-03
PCT/US2011/040106 WO2011156795A2 (en) 2010-06-11 2011-06-10 Nucleic acids for multiplex organism detection and methods of use and making the same

Publications (1)

Publication Number Publication Date
AU2011265205A1 true AU2011265205A1 (en) 2013-01-31

Family

ID=45098726

Family Applications (1)

Application Number Title Priority Date Filing Date
AU2011265205A Abandoned AU2011265205A1 (en) 2010-06-11 2011-06-10 Nucleic acids for multiplex organism detection and methods of use and making the same

Country Status (6)

Country Link
US (1) US20130261196A1 (enExample)
EP (1) EP2580354A4 (enExample)
JP (1) JP2013531983A (enExample)
AU (1) AU2011265205A1 (enExample)
SG (1) SG186987A1 (enExample)
WO (1) WO2011156795A2 (enExample)

Families Citing this family (58)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20100022414A1 (en) 2008-07-18 2010-01-28 Raindance Technologies, Inc. Droplet Libraries
US9562837B2 (en) 2006-05-11 2017-02-07 Raindance Technologies, Inc. Systems for handling microfludic droplets
US12038438B2 (en) 2008-07-18 2024-07-16 Bio-Rad Laboratories, Inc. Enzyme quantification
US9399797B2 (en) 2010-02-12 2016-07-26 Raindance Technologies, Inc. Digital analyte analysis
US10351905B2 (en) * 2010-02-12 2019-07-16 Bio-Rad Laboratories, Inc. Digital analyte analysis
EP4435111A1 (en) 2010-02-12 2024-09-25 Bio-Rad Laboratories, Inc. Digital analyte analysis
EP2675819B1 (en) 2011-02-18 2020-04-08 Bio-Rad Laboratories, Inc. Compositions and methods for molecular labeling
WO2013173795A1 (en) * 2012-05-18 2013-11-21 Pathogenica, Inc. Realtime sequence based biosurveillance system
WO2013173774A2 (en) * 2012-05-18 2013-11-21 Pathogenica, Inc. Molecular inversion probes
WO2014113204A1 (en) 2013-01-17 2014-07-24 Personalis, Inc. Methods and systems for genetic analysis
EP3988671A1 (en) * 2013-02-20 2022-04-27 Emory University Compositions for sequencing nucleic acids in mixtures
US20160110498A1 (en) 2013-03-13 2016-04-21 Illumina, Inc. Methods and systems for aligning repetitive dna elements
CA2905410A1 (en) * 2013-03-15 2014-09-25 Abbott Molecular Inc. Systems and methods for detection of genomic copy number changes
US20150141257A1 (en) * 2013-08-02 2015-05-21 Roche Nimblegen, Inc. Sequence capture method using specialized capture probes (heatseq)
EP3038649B1 (en) * 2013-08-26 2019-09-25 The Translational Genomics Research Institute Single molecule-overlapping read analysis for minor variant mutation detection in pathogen samples
WO2015031689A1 (en) 2013-08-30 2015-03-05 Personalis, Inc. Methods and systems for genomic analysis
WO2015071552A1 (en) * 2013-11-18 2015-05-21 Teknologian Tutkimuskeskus Vtt Multi-unit probes with high specificity and a method of designing the same
US10883145B2 (en) 2014-04-11 2021-01-05 The Trustees Of The University Of Pennsylvania Compositions and methods for metagenome biomarker detection
JP6976167B2 (ja) 2014-06-13 2021-12-08 キュー−リネア エービー 微生物の検出及び特徴付け方法
EP2960818A1 (en) * 2014-06-24 2015-12-30 Institut Pasteur Method, device, and computer program for assembling pieces of chromosomes from one or several organisms
WO2016070131A1 (en) 2014-10-30 2016-05-06 Personalis, Inc. Methods for using mosaicism in nucleic acids sampled distal to their origin
TWI577803B (zh) * 2015-01-15 2017-04-11 昕穎生醫技術股份有限公司 多重抗藥性結核病篩檢方法及套組
GB201507026D0 (en) 2015-04-24 2015-06-10 Linea Ab Q Medical sample transportation container
CN108138226B (zh) * 2015-10-18 2022-02-11 阿费梅特里克斯公司 单核苷酸多态性和插入缺失的多等位基因基因分型
EP3433382B1 (en) * 2016-03-25 2021-09-01 Karius, Inc. Synthetic nucleic acid spike-ins
GB2554767A (en) 2016-04-21 2018-04-11 Q Linea Ab Detecting and characterising a microorganism
US11299783B2 (en) 2016-05-27 2022-04-12 Personalis, Inc. Methods and systems for genetic analysis
US10337051B2 (en) 2016-06-16 2019-07-02 The Regents Of The University Of California Methods and compositions for detecting a target RNA
JP2019532644A (ja) 2016-09-30 2019-11-14 ザ リージェンツ オブ ザ ユニバーシティ オブ カリフォルニア Rna誘導型核酸修飾酵素及びその使用方法
WO2018064352A1 (en) 2016-09-30 2018-04-05 The Regents Of The University Of California Rna-guided nucleic acid modifying enzymes and methods of use thereof
US10815525B2 (en) 2016-12-22 2020-10-27 10X Genomics, Inc. Methods and systems for processing polynucleotides
US10550429B2 (en) 2016-12-22 2020-02-04 10X Genomics, Inc. Methods and systems for processing polynucleotides
CN110730825B (zh) * 2017-05-23 2023-08-11 新泽西鲁特格斯州立大学 用双相互作用发夹探针进行的靶标介导的原位信号放大
WO2019028462A1 (en) 2017-08-04 2019-02-07 Billiontoone, Inc. TARGET-ASSOCIATED MOLECULES FOR CHARACTERIZATION ASSOCIATED WITH BIOLOGICAL TARGETS
KR102372572B1 (ko) 2017-08-04 2022-03-08 빌리언투원, 인크. 생물학적 표적과 연관된 정량화에서 표적 연관 분자를 이용한 서열분석 출력값 측정 및 분석
US11519024B2 (en) 2017-08-04 2022-12-06 Billiontoone, Inc. Homologous genomic regions for characterization associated with biological targets
CN117487776A (zh) 2017-11-01 2024-02-02 加利福尼亚大学董事会 Casz组合物和使用方法
WO2019089804A1 (en) 2017-11-01 2019-05-09 The Regents Of The University Of California Casy compositions and methods of use
US11970719B2 (en) 2017-11-01 2024-04-30 The Regents Of The University Of California Class 2 CRISPR/Cas compositions and methods of use
DK3735470T3 (da) 2018-01-05 2024-02-26 Billiontoone Inc Kvalitetskontroltemplates til sikring af validiteten af sekventeringsbaserede analyser
CN112005115A (zh) 2018-02-12 2020-11-27 10X基因组学有限公司 表征来自单个细胞或细胞群体的多种分析物的方法
US11639928B2 (en) 2018-02-22 2023-05-02 10X Genomics, Inc. Methods and systems for characterizing analytes from individual cells or cell populations
WO2019169028A1 (en) 2018-02-28 2019-09-06 10X Genomics, Inc. Transcriptome sequencing through random ligation
US11959077B2 (en) 2018-05-21 2024-04-16 Battelle Memorial Institute Methods and control compositions for sequencing
US10801064B2 (en) * 2018-05-31 2020-10-13 Personalis, Inc. Compositions, methods and systems for processing or analyzing multi-species nucleic acid samples
WO2020028729A1 (en) 2018-08-01 2020-02-06 Mammoth Biosciences, Inc. Programmable nuclease compositions and methods of use thereof
EP3833776A4 (en) 2018-08-06 2022-04-27 Billiontoone, Inc. DILUTION MARKER FOR QUANTIFICATION OF BIOLOGICAL TARGETS
DK4428234T3 (da) 2018-11-21 2026-01-26 Karius Inc Direkte-til-bibliotek-fremgangsmåder, systemer og sammensætninger
WO2020124003A1 (en) 2018-12-13 2020-06-18 Battelle Memorial Institute Methods and control compositions for a quantitative polymerase chain reaction
WO2020142754A2 (en) 2019-01-04 2020-07-09 Mammoth Biosciences, Inc. Programmable nuclease improvements and compositions and methods for nucleic acid amplification and detection
WO2020185791A1 (en) 2019-03-11 2020-09-17 10X Genomics, Inc. Systems and methods for processing optically tagged beads
CN111508561B (zh) * 2019-07-04 2024-02-06 北京希望组生物科技有限公司 同源序列和同源序列中串联重复序列的检测方法、计算机可读介质和应用
CN110592208B (zh) * 2019-10-08 2022-05-03 北京诺禾致源科技股份有限公司 地中海贫血症三类亚型的捕获探针组合物及其应用方法和应用装置
EP4055610A4 (en) 2019-11-05 2023-11-29 Personalis, Inc. ESTIMATION OF TUMOR PURITY FROM SINGLE SAMPLES
EP4298244A1 (en) 2021-02-23 2024-01-03 10X Genomics, Inc. Probe-based analysis of nucleic acids and proteins
EP4108783B1 (en) * 2021-06-24 2024-02-21 Miltenyi Biotec B.V. & Co. KG Spatial sequencing with mictag
EP4413580A4 (en) 2021-10-05 2025-08-13 Personalis Inc PERSONALIZED TESTS FOR PERSONALIZED CANCER MONITORING
CA3255101A1 (en) 2022-03-21 2023-09-28 Billion Toone, Inc. Counting of circulating methylated cell-free DNA molecules for treatment monitoring

Family Cites Families (7)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20030134293A1 (en) * 1999-11-16 2003-07-17 Zhiping Liu Method for rapid and accurate identification of microorganisms
ATE380883T1 (de) * 2000-10-24 2007-12-15 Univ Leland Stanford Junior Direkte multiplex charakterisierung von genomischer dna
WO2004001412A1 (ja) * 2002-06-24 2003-12-31 Canon Kabushiki Kaisha 標準プローブを持つdnaマイクロアレイ及び該アレイを有するキット
US7618780B2 (en) * 2004-05-20 2009-11-17 Trillion Genomics Limited Use of mass labelled probes to detect target nucleic acids using mass spectrometry
US20110177960A1 (en) * 2006-03-10 2011-07-21 Ellen Murphy Microarray for monitoring gene expression in multiple strains of Streptococcus pneumoniae
US7897747B2 (en) * 2006-05-25 2011-03-01 The Board Of Trustees Of The Leland Stanford Junior University Method to produce single stranded DNA of defined length and sequence and DNA probes produced thereby
WO2010142017A1 (en) * 2009-06-09 2010-12-16 Defyrus, Inc . Administration of interferon for prophylaxis against or treatment of pathogenic infection

Also Published As

Publication number Publication date
WO2011156795A2 (en) 2011-12-15
WO2011156795A3 (en) 2012-04-05
EP2580354A4 (en) 2013-10-30
SG186987A1 (en) 2013-02-28
JP2013531983A (ja) 2013-08-15
US20130261196A1 (en) 2013-10-03
EP2580354A2 (en) 2013-04-17

Similar Documents

Publication Publication Date Title
US20130261196A1 (en) Nucleic Acids For Multiplex Organism Detection and Methods Of Use And Making The Same
EP4443436A2 (en) Universal short adapters for indexing of polynucleotide
AU2018331434A1 (en) Universal short adapters with variable length non-random unique molecular identifiers
US20150344973A1 (en) Method and System for Detection of an Organism
WO2013173774A2 (en) Molecular inversion probes
EP4041918B1 (en) Methods and systems for assessing microbial populations
EP2788506A2 (en) Method and system for detection of an organism
US20160115544A1 (en) Molecular barcoding for multiplex sequencing
BRPI0517131B1 (pt) Métodos para simplificar ácidos nucléicos microbiais por modificação química de citosinas
JP2023520590A (ja) 病原体診断検査
US20220267833A1 (en) Detection of genomic sequences using combinations of probes, probe molecules and arrays comprising the probes for the specific detection of organisms
US20260028669A1 (en) Methods and compositions for nucleic acid analysis
WO2013173795A1 (en) Realtime sequence based biosurveillance system
WO2013040060A2 (en) Nucleic acids for multiplex detection of hepatitis c virus
US20210017582A1 (en) Detection of genomic sequences and probe molecules therefor
CN114277183A (zh) 一种5种人肠病毒的mnp标记组合、引物对组合、试剂盒及其应用
Park et al. Detection strategies for foodborne salmonella and prospects for utilization of whole genome sequencing approaches
Yamana Species-specific primer design
US20240203528A1 (en) Improved detection of genomic sequences and probe molecules therefor
TW202246525A (zh) 基因體序列之改善之偵測及用於其之探針分子
KR20230025222A (ko) 박테로이데스 균주의 정량을 위한 프라이머 세트 및 이의 용도

Legal Events

Date Code Title Description
MK1 Application lapsed section 142(2)(a) - no request for examination in relevant period