SG186987A1 - 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
SG186987A1
SG186987A1 SG2013001573A SG2013001573A SG186987A1 SG 186987 A1 SG186987 A1 SG 186987A1 SG 2013001573 A SG2013001573 A SG 2013001573A SG 2013001573 A SG2013001573 A SG 2013001573A SG 186987 A1 SG186987 A1 SG 186987A1
Authority
SG
Singapore
Prior art keywords
probe
mixture
sequence
probes
target
Prior art date
Application number
SG2013001573A
Other languages
English (en)
Inventor
Lisa Diamond
Jochen Kumm
Philip Alexander Rolfe
Original Assignee
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 filed Critical Pathogenica Inc
Publication of SG186987A1 publication Critical patent/SG186987A1/en

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
    • C12Q1/70Measuring 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
    • 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
    • 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)
SG2013001573A 2010-06-11 2011-06-10 Nucleic acids for multiplex organism detection and methods of use and making the same SG186987A1 (en)

Applications Claiming Priority (4)

Application Number Priority Date Filing Date Title
US35401110P 2010-06-11 2010-06-11
US37404110P 2010-08-16 2010-08-16
US201161439167P 2011-02-03 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
SG186987A1 true SG186987A1 (en) 2013-02-28

Family

ID=45098726

Family Applications (1)

Application Number Title Priority Date Filing Date
SG2013001573A SG186987A1 (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 (56)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
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
EP4047367A1 (en) 2008-07-18 2022-08-24 Bio-Rad Laboratories, Inc. Method for detecting target analytes with droplet libraries
EP3392349A1 (en) 2010-02-12 2018-10-24 Raindance Technologies, Inc. Digital analyte analysis
US10351905B2 (en) * 2010-02-12 2019-07-16 Bio-Rad Laboratories, Inc. Digital analyte analysis
EP3736281A1 (en) 2011-02-18 2020-11-11 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
EP4414990A3 (en) 2013-01-17 2024-11-06 Personalis, Inc. Methods and systems for genetic analysis
ES2900102T3 (es) * 2013-02-20 2022-03-15 Univ Emory Composiciones para la secuenciación de ácidos nucleicos en mezclas
EP2971069B1 (en) 2013-03-13 2018-10-17 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)
JP2016528913A (ja) * 2013-08-26 2016-09-23 ザ・トランスレーショナル・ジェノミクス・リサーチ・インスティチュート 病原体試料におけるマイナー変異体突然変異検出のための単一分子重複読み取り分析
EP4567682A3 (en) 2013-08-30 2025-09-03 Personalis, Inc. Methods 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
CN106661606B (zh) 2014-06-13 2021-12-21 Q-莱纳公司 用于检测和表征微生物的方法
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
EP3212808B1 (en) 2014-10-30 2022-03-02 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
KR20180071299A (ko) * 2015-10-18 2018-06-27 아피메트릭스, 인코포레이티드 단일 뉴클레오타이드 다형 및 인델의 다대립유전자 유전자형분석
CN109312400A (zh) 2016-03-25 2019-02-05 凯锐思公司 合成核酸掺入物
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
WO2018064371A1 (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
CA3038982A1 (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
US10550429B2 (en) 2016-12-22 2020-02-04 10X Genomics, Inc. Methods and systems for processing polynucleotides
US10815525B2 (en) 2016-12-22 2020-10-27 10X Genomics, Inc. Methods and systems for processing polynucleotides
AU2018272848B2 (en) * 2017-05-23 2022-03-31 Rutgers, The State University Of New Jersey Target mediated
KR102372572B1 (ko) 2017-08-04 2022-03-08 빌리언투원, 인크. 생물학적 표적과 연관된 정량화에서 표적 연관 분자를 이용한 서열분석 출력값 측정 및 분석
EP3662480A4 (en) 2017-08-04 2021-05-19 BillionToOne, Inc. MOLECULES ASSOCIATED WITH A TARGET FOR A CHARACTERIZATION ASSOCIATED WITH BIOLOGICAL TARGETS
US11519024B2 (en) 2017-08-04 2022-12-06 Billiontoone, Inc. Homologous genomic regions for characterization associated with biological targets
WO2019089808A1 (en) 2017-11-01 2019-05-09 The Regents Of The University Of California Class 2 crispr/cas compositions and methods of use
EP3704239A4 (en) 2017-11-01 2021-08-18 The Regents of The University of California CASZ COMPOSITIONS AND METHODS OF USE
US12227753B2 (en) 2017-11-01 2025-02-18 The Regents Of The University Of California CasY compositions and methods of use
JP7164125B2 (ja) 2018-01-05 2022-11-01 ビリオントゥーワン,インコーポレイテッド シーケンシングベースのアッセイの妥当性を確保するための品質管理鋳型
WO2019157529A1 (en) 2018-02-12 2019-08-15 10X Genomics, Inc. Methods characterizing multiple analytes from individual cells or cell populations
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
US11702653B2 (en) 2018-05-21 2023-07-18 Battelle Memorial Institute Control compositions and methods 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
US12071651B2 (en) 2018-08-06 2024-08-27 Billiontoone, Inc. Dilution tagging for quantification of biological targets
EP3884065B1 (en) 2018-11-21 2024-08-14 Karius, Inc. Direct-to-library methods, systems, and compositions
US11441176B2 (en) 2018-12-13 2022-09-13 Battelle Memorial Institute Methods and control compositions for a quantitative polymerase chain reaction
EP3931313A2 (en) 2019-01-04 2022-01-05 Mammoth Biosciences, Inc. Programmable nuclease improvements and compositions and methods for nucleic acid amplification and detection
EP3938537A1 (en) 2019-03-11 2022-01-19 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
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
US12297508B2 (en) 2021-10-05 2025-05-13 Personalis, Inc. Customized assays 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
WO2002057491A2 (en) * 2000-10-24 2002-07-25 The Board Of Trustees Of The Leland Stanford Junior University Direct multiplex characterization of genomic dna
CN1668923A (zh) * 2002-06-24 2005-09-14 佳能株式会社 带有标准探针的dna微阵列以及包含该阵列的试剂盒
EP1756307A1 (en) * 2004-05-20 2007-02-28 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
CA2764759A1 (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
EP2580354A2 (en) 2013-04-17
JP2013531983A (ja) 2013-08-15
EP2580354A4 (en) 2013-10-30
WO2011156795A3 (en) 2012-04-05
US20130261196A1 (en) 2013-10-03
WO2011156795A2 (en) 2011-12-15
AU2011265205A1 (en) 2013-01-31

Similar Documents

Publication Publication Date Title
SG186987A1 (en) Nucleic acids for multiplex organism detection and methods of use and making the same
US12264357B2 (en) Universal Sanger sequencing from next-gen sequencing amplicons
US20240412820A1 (en) Methods for generating sequencer-specific nucleic acid barcodes that reduce demultiplexing errors
CN108368542B (zh) 用于基因组组装、单元型定相以及独立于靶标的核酸检测的方法
Pestana et al. Early, rapid and sensitive veterinary molecular diagnostics-real time PCR applications
US20150344973A1 (en) Method and System for Detection of an Organism
AU2015296029A1 (en) Tagging nucleic acids for sequence assembly
US20220251669A1 (en) Compositions and methods for assessing microbial populations
WO2013173774A2 (en) Molecular inversion probes
EP2788506A2 (en) Method and system for detection of an organism
JP2016520326A (ja) マルチプレックス配列決定のための分子バーコード化
BRPI0517131B1 (pt) Métodos para simplificar ácidos nucléicos microbiais por modificação química de citosinas
JP2023519919A (ja) 病原体を検出するためのアッセイ
CN114269944A (zh) 使用探针、探针分子以及包含探针的阵列组合检测基因组序列用于对生物体特异性检测
US11866765B2 (en) Composition for improving molecular barcoding efficiency and use thereof
JP2023520590A (ja) 病原体診断検査
WO2013173795A1 (en) Realtime sequence based biosurveillance system
Bajaj et al. MICROBIAL GENOMICS
Commichaux et al. Optimizing source tracking of Listeria monocytogenes with quasimetagenomics and integrated long and short read sequencing
WO2019046783A1 (en) METHODS OF MAKING AND USING TANDEM MOLECULES WITH DOUBLE BAR CODES
EP4562181A1 (en) Methods and compositions for nucleic acid analysis
TWI403587B (zh) 特定群核酸序列組合之最小群多用引子及特異群雙重探針及其鑑別檢測應用方法
US20220411861A1 (en) A Multiplex Method of Preparing a Sequencing Library
HK40091651A (zh) 用於分析样品的系统和方法
TW202246525A (zh) 基因體序列之改善之偵測及用於其之探針分子