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 (cg-RX-API-DMAC7.html)
EP (1) EP2580354A4 (cg-RX-API-DMAC7.html)
JP (1) JP2013531983A (cg-RX-API-DMAC7.html)
AU (1) AU2011265205A1 (cg-RX-API-DMAC7.html)
SG (1) SG186987A1 (cg-RX-API-DMAC7.html)
WO (1) WO2011156795A2 (cg-RX-API-DMAC7.html)

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
EP2315629B1 (en) 2008-07-18 2021-12-15 Bio-Rad Laboratories, Inc. Droplet libraries
US12038438B2 (en) 2008-07-18 2024-07-16 Bio-Rad Laboratories, Inc. Enzyme quantification
US10351905B2 (en) * 2010-02-12 2019-07-16 Bio-Rad Laboratories, Inc. Digital analyte analysis
CA2789425C (en) 2010-02-12 2020-04-28 Raindance Technologies, Inc. Digital analyte analysis with polymerase error correction
EP3736281A1 (en) 2011-02-18 2020-11-11 Bio-Rad Laboratories, Inc. Compositions and methods for molecular labeling
WO2013173774A2 (en) * 2012-05-18 2013-11-21 Pathogenica, Inc. Molecular inversion probes
WO2013173795A1 (en) * 2012-05-18 2013-11-21 Pathogenica, Inc. Realtime sequence based biosurveillance system
WO2014113204A1 (en) 2013-01-17 2014-07-24 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
CA2907484C (en) 2013-03-13 2021-06-29 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
GB2534067B (en) 2013-08-30 2021-07-21 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
CA2944896A1 (en) * 2014-04-11 2015-10-15 The Trustees Of The University Of Pennsylvania Compositions and methods for metagenome biomarker detection
EP3074539B1 (en) 2014-06-13 2018-01-10 Q-Linea AB Method for detecting and characterising a microorganism
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
WO2017070096A1 (en) * 2015-10-18 2017-04-27 Affymetrix, Inc. Multiallelic genotyping of single nucleotide polymorphisms and indels
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
EA201990860A1 (ru) 2016-09-30 2019-10-31 Рнк-направляемые модифицирующие нуклеиновые кислоты ферменты и способы их применения
KR20230170126A (ko) 2016-09-30 2023-12-18 더 리젠츠 오브 더 유니버시티 오브 캘리포니아 Rna-가이드된 핵산 변형 효소 및 이의 사용 방법
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
US11459603B2 (en) * 2017-05-23 2022-10-04 Rutgers, The State University Of New Jersey Target mediated in situ signal amplification with dual interacting hairpin probes
US11646100B2 (en) 2017-08-04 2023-05-09 Billiontoone, Inc. Target-associated molecules for characterization associated with biological targets
US11519024B2 (en) 2017-08-04 2022-12-06 Billiontoone, Inc. Homologous genomic regions 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
MX2020004578A (es) 2017-11-01 2020-12-03 Univ California Composiciones de casz y metodos de uso.
US12227753B2 (en) 2017-11-01 2025-02-18 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
WO2019135790A1 (en) 2018-01-05 2019-07-11 Billiontoone, Inc. Quality control templates for ensuring validity of sequencing-based assays
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
WO2019226648A1 (en) * 2018-05-21 2019-11-28 Battelle Memorial Institute Methods and control compositions for sequencing and chemical analyses
US10801064B2 (en) * 2018-05-31 2020-10-13 Personalis, Inc. Compositions, methods and systems for processing or analyzing multi-species nucleic acid samples
EP3830301B1 (en) 2018-08-01 2024-05-22 Mammoth Biosciences, Inc. Programmable nuclease compositions and methods of use thereof
CA3108755C (en) 2018-08-06 2021-09-14 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
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
US11920183B2 (en) 2019-03-11 2024-03-05 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
CN120158497A (zh) 2021-02-23 2025-06-17 10X基因组学有限公司 基于探针的核酸和蛋白质分析
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
WO2023183812A2 (en) 2022-03-21 2023-09-28 Billion Toone, Inc. Molecule counting of methylated cell-free dna 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
JP4287652B2 (ja) * 2000-10-24 2009-07-01 ザ・ボード・オブ・トラスティーズ・オブ・ザ・レランド・スタンフォード・ジュニア・ユニバーシティ ゲノムdnaの直接多重処理による性状分析
EP1522853A4 (en) * 2002-06-24 2005-10-19 Canon Kk DNA MICROARRAY WITH STANDARD PROBE AND KIT CONTAINING THE MICROARRAY
WO2005113804A1 (en) * 2004-05-20 2005-12-01 Trillion Genomics Limited Use of mass labelled probes to detect target nucleic acids using mass spectrometry
WO2007106407A2 (en) * 2006-03-10 2007-09-20 Wyeth 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
JP5908397B2 (ja) * 2009-06-09 2016-04-26 デフィルス、インコーポレイテッドDefyrus, Inc. 病原体感染を予防又は治療するためのインターフェロン投与

Also Published As

Publication number Publication date
WO2011156795A2 (en) 2011-12-15
EP2580354A4 (en) 2013-10-30
US20130261196A1 (en) 2013-10-03
EP2580354A2 (en) 2013-04-17
JP2013531983A (ja) 2013-08-15
WO2011156795A3 (en) 2012-04-05
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
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
CN112752852A (zh) 用于检测供体来源的细胞游离dna的方法
US20150344973A1 (en) Method and System for Detection of an Organism
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
CN115916996A (zh) 用于分析样品的系统和方法
JP2023520590A (ja) 病原体診断検査
WO2013173795A1 (en) Realtime sequence based biosurveillance system
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
CN121079433A (zh) 用于减轻dna测序中索引跳跃的方法和组合物