KR20230163434A - 라이브러리에서 dna 손상을 평가하고 앰플리콘 크기 바이어스를 정규화하기 위한 조성물 및 방법 - Google Patents

라이브러리에서 dna 손상을 평가하고 앰플리콘 크기 바이어스를 정규화하기 위한 조성물 및 방법 Download PDF

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KR20230163434A
KR20230163434A KR1020237034174A KR20237034174A KR20230163434A KR 20230163434 A KR20230163434 A KR 20230163434A KR 1020237034174 A KR1020237034174 A KR 1020237034174A KR 20237034174 A KR20237034174 A KR 20237034174A KR 20230163434 A KR20230163434 A KR 20230163434A
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dna
standards
sequence
nucleic acid
library
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앤드류 비. 케네디
레나 스톰스
페이 션
올리비아 베니스
에릭 머트펠트
케이틀린 퍼글리즈
마이클 하워드
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일루미나, 인코포레이티드
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    • C12Q2525/00—Reactions involving modified oligonucleotides, nucleic acids, or nucleotides
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    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/166—Oligonucleotides used as internal standards, controls or normalisation probes

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  • General Health & Medical Sciences (AREA)
  • Genetics & Genomics (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
KR1020237034174A 2021-03-29 2022-03-28 라이브러리에서 dna 손상을 평가하고 앰플리콘 크기 바이어스를 정규화하기 위한 조성물 및 방법 Pending KR20230163434A (ko)

Applications Claiming Priority (5)

Application Number Priority Date Filing Date Title
US202163167171P 2021-03-29 2021-03-29
US63/167,171 2021-03-29
US202163227550P 2021-07-30 2021-07-30
US63/227,550 2021-07-30
PCT/US2022/022184 WO2022212280A1 (en) 2021-03-29 2022-03-28 Compositions and methods for assessing dna damage in a library and normalizing amplicon size bias

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KR20230163434A true KR20230163434A (ko) 2023-11-30

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KR1020237034174A Pending KR20230163434A (ko) 2021-03-29 2022-03-28 라이브러리에서 dna 손상을 평가하고 앰플리콘 크기 바이어스를 정규화하기 위한 조성물 및 방법

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US (1) US20240026431A1 (https=)
EP (1) EP4314328A1 (https=)
JP (1) JP2024513187A (https=)
KR (1) KR20230163434A (https=)
AU (1) AU2022246569A1 (https=)
BR (1) BR112023019894A2 (https=)
CA (1) CA3214282A1 (https=)
IL (1) IL307177A (https=)
MX (1) MX2023011219A (https=)
WO (1) WO2022212280A1 (https=)

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WO2024124008A2 (en) 2022-12-07 2024-06-13 Element Biosciences, Inc. Cyanine derivatives and related uses

Family Cites Families (57)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CA1323293C (en) 1987-12-11 1993-10-19 Keith C. Backman Assay using template-dependent nucleic acid probe reorganization
CA1341584C (en) 1988-04-06 2008-11-18 Bruce Wallace Method of amplifying and detecting nucleic acid sequences
AU3539089A (en) 1988-04-08 1989-11-03 Salk Institute For Biological Studies, The Ligase-based amplification method
ATE144556T1 (de) 1988-06-24 1996-11-15 Amgen Inc Verfahren und mittel zum nachweis von nukleinsäuresequenzen
US5130238A (en) 1988-06-24 1992-07-14 Cangene Corporation Enhanced nucleic acid amplification process
ATE138106T1 (de) 1988-07-20 1996-06-15 David Segev Verfahren zur amplifizierung und zum nachweis von nukleinsäuresequenzen
US5185243A (en) 1988-08-25 1993-02-09 Syntex (U.S.A.) Inc. Method for detection of specific nucleic acid sequences
WO1991006678A1 (en) 1989-10-26 1991-05-16 Sri International Dna sequencing
US5573907A (en) 1990-01-26 1996-11-12 Abbott Laboratories Detecting and amplifying target nucleic acids using exonucleolytic activity
CA2035010C (en) 1990-01-26 1996-12-10 Keith C. Backman Method of amplifying target nucleic acids applicable to both polymerase and ligase chain reactions
US5455166A (en) 1991-01-31 1995-10-03 Becton, Dickinson And Company Strand displacement amplification
WO1995021271A1 (en) 1994-02-07 1995-08-10 Molecular Tool, Inc. Ligase/polymerase-mediated genetic bit analysistm of single nucleotide polymorphisms and its use in genetic analysis
WO1995025180A1 (en) 1994-03-16 1995-09-21 Gen-Probe Incorporated Isothermal strand displacement nucleic acid amplification
GB9620209D0 (en) 1996-09-27 1996-11-13 Cemu Bioteknik Ab Method of sequencing DNA
GB9626815D0 (en) 1996-12-23 1997-02-12 Cemu Bioteknik Ab Method of sequencing DNA
JP2002503954A (ja) 1997-04-01 2002-02-05 グラクソ、グループ、リミテッド 核酸増幅法
AR021833A1 (es) 1998-09-30 2002-08-07 Applied Research Systems Metodos de amplificacion y secuenciacion de acido nucleico
US20050244870A1 (en) 1999-04-20 2005-11-03 Illumina, Inc. Nucleic acid sequencing using microsphere arrays
US6355431B1 (en) 1999-04-20 2002-03-12 Illumina, Inc. Detection of nucleic acid amplification reactions using bead arrays
US20060275782A1 (en) 1999-04-20 2006-12-07 Illumina, Inc. Detection of nucleic acid reactions on bead arrays
US6274320B1 (en) 1999-09-16 2001-08-14 Curagen Corporation Method of sequencing a nucleic acid
US7244559B2 (en) 1999-09-16 2007-07-17 454 Life Sciences Corporation Method of sequencing a nucleic acid
US7582420B2 (en) 2001-07-12 2009-09-01 Illumina, Inc. Multiplex nucleic acid reactions
US7955794B2 (en) 2000-09-21 2011-06-07 Illumina, Inc. Multiplex nucleic acid reactions
DK1259643T3 (da) 2000-02-07 2009-02-23 Illumina Inc Fremgangsmåde til detektion af nukleinsyre ved anvendelse af universel priming
US7611869B2 (en) 2000-02-07 2009-11-03 Illumina, Inc. Multiplexed methylation detection methods
US6913884B2 (en) 2001-08-16 2005-07-05 Illumina, Inc. Compositions and methods for repetitive use of genomic DNA
US7001792B2 (en) 2000-04-24 2006-02-21 Eagle Research & Development, Llc Ultra-fast nucleic acid sequencing device and a method for making and using the same
ATE377093T1 (de) 2000-07-07 2007-11-15 Visigen Biotechnologies Inc Sequenzbestimmung in echtzeit
AU2002227156A1 (en) 2000-12-01 2002-06-11 Visigen Biotechnologies, Inc. Enzymatic nucleic acid synthesis: compositions and methods for altering monomer incorporation fidelity
US7057026B2 (en) 2001-12-04 2006-06-06 Solexa Limited Labelled nucleotides
WO2004018497A2 (en) 2002-08-23 2004-03-04 Solexa Limited Modified nucleotides for polynucleotide sequencing
US7595883B1 (en) 2002-09-16 2009-09-29 The Board Of Trustees Of The Leland Stanford Junior University Biological analysis arrangement and approach therefor
WO2005003304A2 (en) 2003-06-20 2005-01-13 Illumina, Inc. Methods and compositions for whole genome amplification and genotyping
CA2579150C (en) 2004-09-17 2014-11-25 Pacific Biosciences Of California, Inc. Apparatus and method for analysis of molecules
US7405281B2 (en) 2005-09-29 2008-07-29 Pacific Biosciences Of California, Inc. Fluorescent nucleotide analogs and uses therefor
CA2648149A1 (en) 2006-03-31 2007-11-01 Solexa, Inc. Systems and devices for sequence by synthesis analysis
US8343746B2 (en) 2006-10-23 2013-01-01 Pacific Biosciences Of California, Inc. Polymerase enzymes and reagents for enhanced nucleic acid sequencing
GB2457851B (en) 2006-12-14 2011-01-05 Ion Torrent Systems Inc Methods and apparatus for measuring analytes using large scale fet arrays
US8349167B2 (en) 2006-12-14 2013-01-08 Life Technologies Corporation Methods and apparatus for detecting molecular interactions using FET arrays
US8262900B2 (en) 2006-12-14 2012-09-11 Life Technologies Corporation Methods and apparatus for measuring analytes using large scale FET arrays
US20090042205A1 (en) 2007-07-09 2009-02-12 Baylor College Of Medicine Fluorescence detection of dna breaks using molecular oscillators
US8580516B2 (en) 2008-09-05 2013-11-12 University Of Chicago Methods and compositions for direct detection of DNA damage
US20100137143A1 (en) 2008-10-22 2010-06-03 Ion Torrent Systems Incorporated Methods and apparatus for measuring analytes
SG10201508373UA (en) 2010-10-20 2015-11-27 Bionano Genomics Inc Systems and methods for assessing biomolecule characteristics
EP2632593B1 (en) 2010-10-27 2021-09-29 Illumina, Inc. Flow cells for biological or chemical analysis
US8951781B2 (en) 2011-01-10 2015-02-10 Illumina, Inc. Systems, methods, and apparatuses to image a sample for biological or chemical analysis
US10844428B2 (en) 2015-04-28 2020-11-24 Illumina, Inc. Error suppression in sequenced DNA fragments using redundant reads with unique molecular indices (UMIS)
EP3978627A1 (en) * 2016-03-25 2022-04-06 Karius, Inc. Methods using synthetic nucleic acid spike-ins
AU2018259206B2 (en) 2017-04-23 2024-07-11 Illumina Cambridge Limited Compositions and methods for improving sample identification in indexed nucleic acid libraries
EP3913053A1 (en) 2017-04-23 2021-11-24 Illumina Cambridge Limited Compositions and methods for improving sample identification in indexed nucleic acid libraries
AU2018260627B2 (en) 2017-04-23 2024-08-22 Illumina Cambridge Limited Compositions and methods for improving sample identification in indexed nucleic acid libraries
AU2018261332B2 (en) 2017-05-01 2024-12-05 Illumina, Inc. Optimal index sequences for multiplex massively parallel sequencing
GB2578038B (en) * 2017-06-16 2022-11-23 Life Technologies Corp Control nucleic acids, and compositions, kits, and uses thereof
ES2898644T3 (es) * 2017-06-27 2022-03-08 Hoffmann La Roche Adaptadores de ácido nucleico modulares
EP3861135B1 (en) * 2018-10-04 2023-08-02 Arc Bio, LLC Normalization controls for managing low sample inputs in next generation sequencing
US20200232010A1 (en) * 2018-12-20 2020-07-23 Guardant Health, Inc. Methods, compositions, and systems for improving recovery of nucleic acid molecules

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BR112023019894A2 (pt) 2023-11-14
EP4314328A1 (en) 2024-02-07
IL307177A (en) 2023-11-01
CA3214282A1 (en) 2022-10-06
MX2023011219A (es) 2023-10-02
AU2022246569A1 (en) 2023-09-14
JP2024513187A (ja) 2024-03-22
US20240026431A1 (en) 2024-01-25
WO2022212280A1 (en) 2022-10-06

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