Title:
METHODS OF ENRICHING AND DETERMINING TARGET NUCLEOTIDE SEQUENCES
Document Type and Number:
WIPO Patent Application WO/2019/023924
Kind Code:
A1
Abstract:
The present invention provides methods, compositions and kits for enriching and determining nucleotide sequences of a plurality of target loci from a sample comprising nucleic acids. The methods comprise one or more cycles of primer extension followedby PCR amplification of target sequences using nested target-specific primers.
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Inventors:
ZHENG ZONGLI (CN)
Application Number:
PCT/CN2017/095404
Publication Date:
February 07, 2019
Filing Date:
August 01, 2017
Export Citation:
Assignee:
HELITEC LTD (CN)
International Classes:
C12Q1/68
Domestic Patent References:
| WO2015112948A2 | 2015-07-30 | |||
| WO1991006678A1 | 1991-05-16 | |||
| WO2007123744A2 | 2007-11-01 | |||
| WO2005065814A1 | 2005-07-21 | |||
| WO2006064199A1 | 2006-06-22 | |||
| WO2007010251A2 | 2007-01-25 |
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Other References:
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S. GOODWIN ET AL., NAT. REV. GENETICS, vol. 17, 2016, pages 333
L. MAMANOVA ET AL., NAT. METHODS, vol. 7, no. 2, 2010, pages 111
"PCR Protocols: A Guide to Methods and Applications", 1990
SAMBROOK ET AL.: "Molecular Cloning: A Laboratory Manual", 2001, COLD SPRING HARBOR LABORATORY PRESS
DAVIS ET AL.: "Basic Methods in Molecular Biology", 1995, ELSEVIER SCIENCE PUBLISHING, INC.
FRIEIR ET AL., PNAS, vol. 83, 1986, pages 9373 - 9377
MARGULIES, M. ET AL.: "Genome Sequencing in Microfabricated. High-Density Picoliter Reactors", NATURE, vol. 437, 2005, pages 376 - 80
MIKKELSEN, T. ET AL.: "Genome-Wide Maps of Chromatin State in Pluripotent and Lineage-Committed. Cells", NATURE, vol. 448, pages 553 - 60, XP008156077, DOI: doi:10.1038/nature06008
MCLAUGHLIN, S. ET AL.: "Whole-Genome Resequencing With Short Reads; Accurate Mutation Discovery With Mate Pairs and Quality Values", ASHG ANNUAL MEETING, 2007
SHENDURE I. ET AL.: "Accurate Multiplex Polony Sequencing of an Evolved Bacterial Genome", SCIENCE, vol. 309, 2005, pages 1728 - 32, XP002427180, DOI: doi:10.1126/science.1117389
HARRIS, T. ET AL.: "Single-Molecule DNA Sequencing of a Viral Genome", SCIENCE, vol. 320, 2008, pages 106 - 9, XP055412280, DOI: doi:10.1126/science.1150427
SIMEN, B. ET AL.: "Prevalence of LOW Abundance Drug Resistant Variants by Ultra Deep Sequencing in Chronically HIV-infected Antiretroviral (ARV) Naive Patients and the impact on Virologic Outcomes", 16TH INTERNATIONAL HIV DRUG RESISTANCE WORKSHOP, BARBADOS, 2007
THOMAS, R. ET AL.: "Sensitive Mutation Detection in Heterogeneous Cancer Specimens by Massively Parallel Picoliter Reactor Sequencing", NATURE MED., vol. 12, 2006, pages 852 - 855, XP002634143, DOI: doi:10.1038/NM1437
MITSUYA, Y ET AL.: "Minority Human Immunodeficiency Virus Type I Variants in Antiretroviral-Naive Persons With Reverse Transcriptase Codon 215 Revertant Mutations", I. VIR., vol. 82, 2008, pages 10747 - 10755
BINLADEN, J. ET AL.: "The Use of Coded PCR Primers Enables High-Throughput Sequencing of Multiple HomologAmplification Products by 454 Parallel Sequencing", PLOS ONE, vol. 2, 2007, pages el97
HOFFMANN, C. ET AL.: "DNA Bar Coding and Pyrosequencing to Identify Rare HIV Drug Resistance Mutations", NUC. ACIDS RES., vol. 35, 2007, pages e91, XP055059023, DOI: doi:10.1093/nar/gkm435
DIAGNOSTICS Z. ET AL.: "The elimination of primer-dimer accumulation in PCR", NUC. ACIDS RES., vol. 25, no. 16, 1997, pages 3235 - 3241
SHENDURE ET AL.: "Next-generation DNA sequencing", NATURE, vol. 26, no. 10, 2008, pages 1 135 - 1 145, XP002572506, DOI: doi:10.1038/nbt1486
MARDIS: "The impact of next-generation sequencing technology on genetics", TRENDS IN GENETICS, vol. 24, no. 3, 2007, pages 133 - 141, XP022498431
SU ET AL.: "Next-generation sequencing and its applications in molecular diagnostics", EXPERT REV MOL DIAGN, vol. 1 1, no. 3, 2011, pages 333 - 43, XP009505883, DOI: doi:10.1586/erm.11.3
ZHANG ET AL.: "The impact of next-generation sequencing on genomics", J GENET GENOMICS, vol. 38, no. 3, 2011, pages 95 - 109, XP028188028, DOI: doi:10.1016/j.jgg.2011.02.003
NYREN, P. ET AL., ANAL BIOCHEM, vol. 208, 1993, pages 17175
BENTLEY, D. R., CURR OPIN GENET DEV, vol. 16, 2006, pages 545 - 52
STRAUSBERG, R. L. ET AL., DRUG DISC TODAY, vol. 13, 2008, pages 569 - 77
RONAGHI, M.; KARAMOHAMED, S.; PETTERSSON, B.; UHLEN, M.; NYREN, P.: "Real-time DNA sequencing using detection of pyrophosphate release", ANALYTICAL BIOCHEMISTRY, vol. 242, no. 1, 1996, pages 84 - 9, XP002388725, DOI: doi:10.1006/abio.1996.0432
RONAGHI, M.: "Pyrosequencing sheds light on DNA sequencing", GENOME RES, vol. 11, no. 1, 2001, pages 3 - 11, XP000980886, DOI: doi:10.1101/gr.11.1.3
RONAGHI, M.; UHLEN, M.; NYREN, P.: "A sequencing method based on real-time pyrophosphate", SCIENCE, vol. 281, no. 5375, 1998, pages 363, XP002135869, DOI: doi:10.1126/science.281.5375.363
DEAMER, D. W.; AKESON, M.: "Nanopores and nucleic acids: prospects for ultrarapid sequencing", TRENDS BIOTECHNOL, vol. 18, 2000, pages 147 - 151, XP004194002, DOI: doi:10.1016/S0167-7799(00)01426-8
DEAMER, D.; D. BRANTON: "Characterization of nucleic acids by nanopore analysis", ACC. CHEM. RES., vol. 35, 2002, pages 817 - 825, XP002226144, DOI: doi:10.1021/ar000138m
LI, J.; M. GERSHOW; D. STEIN; E. BRANDIN; J. A. GOLOVCHENKO: "DNA molecules and configurations in a solid-state nanopore microscope", NAT. MATER., vol. 2, 2003, pages 611 - 615, XP009039572, DOI: doi:10.1038/nmat965
SONI, G. V.; MELLER: "A. Progress toward ultrafast DNA sequencing using solid-state nanopores", CLIN. CHEM., vol. 53, 2007, pages 1996 - 2001, XP055076185, DOI: doi:10.1373/clinchem.2007.091231
HEALY, K.: "Nanopore-based single-molecule DNA analysis", NANOMED, vol. 2, 2007, pages 459 - 481, XP009111262, DOI: doi:10.2217/17435889.2.4.459
COCKROFT, S. L.; CHU, J.; AMORIN, M.; GHADIRI, M. R.: "A single-molecule nanopore device detects DNA polymerase activity with single-nucleotide resolution", J. AM. CHEM. SOC., vol. 130, 2008, pages 818 - 820, XP055097434, DOI: doi:10.1021/ja077082c
LEVENE, M. J. ET AL.: "Zero-mode waveguides for single-molecule analysis at high concentrations", SCIENCE, vol. 299, 2003, pages 682 - 686, XP002341055, DOI: doi:10.1126/science.1079700
LUNDQUIST, P. M. ET AL.: "Parallel confocal detection of single molecules in real time", OPT. LETT., vol. 33, 2008, pages 1026 - 1028, XP001522593, DOI: doi:10.1364/OL.33.001026
KORLACH, J. ET AL.: "Selective aluminum passivation for targeted immobilization of single DNA polymerase molecules in zero-mode waveguide nanostructures", PROC. NATL. ACAD. SCI. USA, vol. 105, 2008, pages 1176 - 1181, XP002632441, DOI: doi:10.1073/PNAS.0710982105
KORLACH J. ET AL.: "Long, processive enzymatic DNA synthesis using 100% dye-labeled terminal phosphate-linked nucleotides", NUCLEOSIDES, NUCLEOTIDES AND NUCLEIC ACIDS, vol. 27, 2008, pages 1072 - 1083
HARRIS T. D. ET AL.: "Single Molecule DNA Sequencing of a viral Genome", SCIENCE, vol. 320, 2008, pages 106 - 109, XP055412280, DOI: doi:10.1126/science.1150427
SODA ET AL., NATURE, 2007, pages 448561 - 6
RIKOVA ET AL., CELL, vol. 131, 2007, pages 1190 - 1203
KOHNO ET AL., NATURE MEDICINE, vol. 18, 2012, pages 375 - 7
TAKOUCHI ET AL., NATURE MEDICINE, vol. 18, 2012, pages 378 - 81
ZHENG Z. ET AL., NATURE MEDICINE, vol. 20, 2014, pages 1479 - 1484
See also references of EP 3545106A4
S. GOODWIN ET AL., NAT. REV. GENETICS, vol. 17, 2016, pages 333
L. MAMANOVA ET AL., NAT. METHODS, vol. 7, no. 2, 2010, pages 111
"PCR Protocols: A Guide to Methods and Applications", 1990
SAMBROOK ET AL.: "Molecular Cloning: A Laboratory Manual", 2001, COLD SPRING HARBOR LABORATORY PRESS
DAVIS ET AL.: "Basic Methods in Molecular Biology", 1995, ELSEVIER SCIENCE PUBLISHING, INC.
FRIEIR ET AL., PNAS, vol. 83, 1986, pages 9373 - 9377
MARGULIES, M. ET AL.: "Genome Sequencing in Microfabricated. High-Density Picoliter Reactors", NATURE, vol. 437, 2005, pages 376 - 80
MIKKELSEN, T. ET AL.: "Genome-Wide Maps of Chromatin State in Pluripotent and Lineage-Committed. Cells", NATURE, vol. 448, pages 553 - 60, XP008156077, DOI: doi:10.1038/nature06008
MCLAUGHLIN, S. ET AL.: "Whole-Genome Resequencing With Short Reads; Accurate Mutation Discovery With Mate Pairs and Quality Values", ASHG ANNUAL MEETING, 2007
SHENDURE I. ET AL.: "Accurate Multiplex Polony Sequencing of an Evolved Bacterial Genome", SCIENCE, vol. 309, 2005, pages 1728 - 32, XP002427180, DOI: doi:10.1126/science.1117389
HARRIS, T. ET AL.: "Single-Molecule DNA Sequencing of a Viral Genome", SCIENCE, vol. 320, 2008, pages 106 - 9, XP055412280, DOI: doi:10.1126/science.1150427
SIMEN, B. ET AL.: "Prevalence of LOW Abundance Drug Resistant Variants by Ultra Deep Sequencing in Chronically HIV-infected Antiretroviral (ARV) Naive Patients and the impact on Virologic Outcomes", 16TH INTERNATIONAL HIV DRUG RESISTANCE WORKSHOP, BARBADOS, 2007
THOMAS, R. ET AL.: "Sensitive Mutation Detection in Heterogeneous Cancer Specimens by Massively Parallel Picoliter Reactor Sequencing", NATURE MED., vol. 12, 2006, pages 852 - 855, XP002634143, DOI: doi:10.1038/NM1437
MITSUYA, Y ET AL.: "Minority Human Immunodeficiency Virus Type I Variants in Antiretroviral-Naive Persons With Reverse Transcriptase Codon 215 Revertant Mutations", I. VIR., vol. 82, 2008, pages 10747 - 10755
BINLADEN, J. ET AL.: "The Use of Coded PCR Primers Enables High-Throughput Sequencing of Multiple HomologAmplification Products by 454 Parallel Sequencing", PLOS ONE, vol. 2, 2007, pages el97
HOFFMANN, C. ET AL.: "DNA Bar Coding and Pyrosequencing to Identify Rare HIV Drug Resistance Mutations", NUC. ACIDS RES., vol. 35, 2007, pages e91, XP055059023, DOI: doi:10.1093/nar/gkm435
DIAGNOSTICS Z. ET AL.: "The elimination of primer-dimer accumulation in PCR", NUC. ACIDS RES., vol. 25, no. 16, 1997, pages 3235 - 3241
SHENDURE ET AL.: "Next-generation DNA sequencing", NATURE, vol. 26, no. 10, 2008, pages 1 135 - 1 145, XP002572506, DOI: doi:10.1038/nbt1486
MARDIS: "The impact of next-generation sequencing technology on genetics", TRENDS IN GENETICS, vol. 24, no. 3, 2007, pages 133 - 141, XP022498431
SU ET AL.: "Next-generation sequencing and its applications in molecular diagnostics", EXPERT REV MOL DIAGN, vol. 1 1, no. 3, 2011, pages 333 - 43, XP009505883, DOI: doi:10.1586/erm.11.3
ZHANG ET AL.: "The impact of next-generation sequencing on genomics", J GENET GENOMICS, vol. 38, no. 3, 2011, pages 95 - 109, XP028188028, DOI: doi:10.1016/j.jgg.2011.02.003
NYREN, P. ET AL., ANAL BIOCHEM, vol. 208, 1993, pages 17175
BENTLEY, D. R., CURR OPIN GENET DEV, vol. 16, 2006, pages 545 - 52
STRAUSBERG, R. L. ET AL., DRUG DISC TODAY, vol. 13, 2008, pages 569 - 77
RONAGHI, M.; KARAMOHAMED, S.; PETTERSSON, B.; UHLEN, M.; NYREN, P.: "Real-time DNA sequencing using detection of pyrophosphate release", ANALYTICAL BIOCHEMISTRY, vol. 242, no. 1, 1996, pages 84 - 9, XP002388725, DOI: doi:10.1006/abio.1996.0432
RONAGHI, M.: "Pyrosequencing sheds light on DNA sequencing", GENOME RES, vol. 11, no. 1, 2001, pages 3 - 11, XP000980886, DOI: doi:10.1101/gr.11.1.3
RONAGHI, M.; UHLEN, M.; NYREN, P.: "A sequencing method based on real-time pyrophosphate", SCIENCE, vol. 281, no. 5375, 1998, pages 363, XP002135869, DOI: doi:10.1126/science.281.5375.363
DEAMER, D. W.; AKESON, M.: "Nanopores and nucleic acids: prospects for ultrarapid sequencing", TRENDS BIOTECHNOL, vol. 18, 2000, pages 147 - 151, XP004194002, DOI: doi:10.1016/S0167-7799(00)01426-8
DEAMER, D.; D. BRANTON: "Characterization of nucleic acids by nanopore analysis", ACC. CHEM. RES., vol. 35, 2002, pages 817 - 825, XP002226144, DOI: doi:10.1021/ar000138m
LI, J.; M. GERSHOW; D. STEIN; E. BRANDIN; J. A. GOLOVCHENKO: "DNA molecules and configurations in a solid-state nanopore microscope", NAT. MATER., vol. 2, 2003, pages 611 - 615, XP009039572, DOI: doi:10.1038/nmat965
SONI, G. V.; MELLER: "A. Progress toward ultrafast DNA sequencing using solid-state nanopores", CLIN. CHEM., vol. 53, 2007, pages 1996 - 2001, XP055076185, DOI: doi:10.1373/clinchem.2007.091231
HEALY, K.: "Nanopore-based single-molecule DNA analysis", NANOMED, vol. 2, 2007, pages 459 - 481, XP009111262, DOI: doi:10.2217/17435889.2.4.459
COCKROFT, S. L.; CHU, J.; AMORIN, M.; GHADIRI, M. R.: "A single-molecule nanopore device detects DNA polymerase activity with single-nucleotide resolution", J. AM. CHEM. SOC., vol. 130, 2008, pages 818 - 820, XP055097434, DOI: doi:10.1021/ja077082c
LEVENE, M. J. ET AL.: "Zero-mode waveguides for single-molecule analysis at high concentrations", SCIENCE, vol. 299, 2003, pages 682 - 686, XP002341055, DOI: doi:10.1126/science.1079700
LUNDQUIST, P. M. ET AL.: "Parallel confocal detection of single molecules in real time", OPT. LETT., vol. 33, 2008, pages 1026 - 1028, XP001522593, DOI: doi:10.1364/OL.33.001026
KORLACH, J. ET AL.: "Selective aluminum passivation for targeted immobilization of single DNA polymerase molecules in zero-mode waveguide nanostructures", PROC. NATL. ACAD. SCI. USA, vol. 105, 2008, pages 1176 - 1181, XP002632441, DOI: doi:10.1073/PNAS.0710982105
KORLACH J. ET AL.: "Long, processive enzymatic DNA synthesis using 100% dye-labeled terminal phosphate-linked nucleotides", NUCLEOSIDES, NUCLEOTIDES AND NUCLEIC ACIDS, vol. 27, 2008, pages 1072 - 1083
HARRIS T. D. ET AL.: "Single Molecule DNA Sequencing of a viral Genome", SCIENCE, vol. 320, 2008, pages 106 - 109, XP055412280, DOI: doi:10.1126/science.1150427
SODA ET AL., NATURE, 2007, pages 448561 - 6
RIKOVA ET AL., CELL, vol. 131, 2007, pages 1190 - 1203
KOHNO ET AL., NATURE MEDICINE, vol. 18, 2012, pages 375 - 7
TAKOUCHI ET AL., NATURE MEDICINE, vol. 18, 2012, pages 378 - 81
ZHENG Z. ET AL., NATURE MEDICINE, vol. 20, 2014, pages 1479 - 1484
See also references of EP 3545106A4
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