AU2017237199B2 - Synthetic nucleic acid spike-ins - Google Patents

Synthetic nucleic acid spike-ins Download PDF

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Publication number
AU2017237199B2
AU2017237199B2 AU2017237199A AU2017237199A AU2017237199B2 AU 2017237199 B2 AU2017237199 B2 AU 2017237199B2 AU 2017237199 A AU2017237199 A AU 2017237199A AU 2017237199 A AU2017237199 A AU 2017237199A AU 2017237199 B2 AU2017237199 B2 AU 2017237199B2
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Prior art keywords
nucleic acids
sample
cases
synthetic nucleic
nucleic acid
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AU2017237199A1 (en
Inventor
Timothy A. Blauwkamp
Fred C. Christians
Michael Kertesz
Michael Rosen
Rene SIT
Shivkumar Venkatasubrahmanyam
Igor D. Vilfan
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Karius Inc
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Karius Inc
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Priority to AU2021200637A priority Critical patent/AU2021200637B2/en
Priority to AU2021215106A priority patent/AU2021215106A1/en
Priority to AU2024204822A priority patent/AU2024204822A1/en
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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING 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
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6869—Methods for sequencing
    • C12Q1/6874—Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING 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
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6869—Methods for sequencing
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1034—Isolating an individual clone by screening libraries
    • C12N15/1065—Preparation or screening of tagged libraries, e.g. tagged microorganisms by STM-mutagenesis, tagged polynucleotides, gene tags
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING 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
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6888—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms
    • C12Q1/689—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms for bacteria
    • C—CHEMISTRY; METALLURGY
    • C40—COMBINATORIAL TECHNOLOGY
    • C40B—COMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES
    • C40B50/00—Methods of creating libraries, e.g. combinatorial synthesis
    • C40B50/06—Biochemical methods, e.g. using enzymes or whole viable microorganisms
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G16B30/10—Sequence alignment; Homology search
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING 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
    • C12Q2545/00—Reactions characterised by their quantitative nature
    • C12Q2545/10—Reactions characterised by their quantitative nature the purpose being quantitative analysis
    • C12Q2545/101—Reactions characterised by their quantitative nature the purpose being quantitative analysis with an internal standard/control
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING 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
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/166—Oligonucleotides used as internal standards, controls or normalisation probes

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  • Life Sciences & Earth Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Organic Chemistry (AREA)
  • Engineering & Computer Science (AREA)
  • Physics & Mathematics (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biotechnology (AREA)
  • Genetics & Genomics (AREA)
  • Analytical Chemistry (AREA)
  • General Health & Medical Sciences (AREA)
  • Biophysics (AREA)
  • General Engineering & Computer Science (AREA)
  • Biochemistry (AREA)
  • Microbiology (AREA)
  • Molecular Biology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Immunology (AREA)
  • Medical Informatics (AREA)
  • Theoretical Computer Science (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Evolutionary Biology (AREA)
  • Biomedical Technology (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Plant Pathology (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • General Chemical & Material Sciences (AREA)
  • Medicinal Chemistry (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)
AU2017237199A 2016-03-25 2017-03-24 Synthetic nucleic acid spike-ins Active AU2017237199B2 (en)

Priority Applications (3)

Application Number Priority Date Filing Date Title
AU2021200637A AU2021200637B2 (en) 2016-03-25 2021-02-01 Synthetic nucleic acid spike-ins
AU2021215106A AU2021215106A1 (en) 2016-03-25 2021-08-09 Synthetic nucleic acid spike-ins
AU2024204822A AU2024204822A1 (en) 2016-03-25 2024-07-12 Synthetic nucleic acid spike-ins

Applications Claiming Priority (7)

Application Number Priority Date Filing Date Title
US201662313668P 2016-03-25 2016-03-25
US62/313,668 2016-03-25
US201662397873P 2016-09-21 2016-09-21
US62/397,873 2016-09-21
US201762451363P 2017-01-27 2017-01-27
US62/451,363 2017-01-27
PCT/US2017/024176 WO2017165864A1 (en) 2016-03-25 2017-03-24 Synthetic nucleic acid spike-ins

Related Child Applications (1)

Application Number Title Priority Date Filing Date
AU2021200637A Division AU2021200637B2 (en) 2016-03-25 2021-02-01 Synthetic nucleic acid spike-ins

Publications (2)

Publication Number Publication Date
AU2017237199A1 AU2017237199A1 (en) 2018-08-16
AU2017237199B2 true AU2017237199B2 (en) 2020-11-05

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Family Applications (4)

Application Number Title Priority Date Filing Date
AU2017237199A Active AU2017237199B2 (en) 2016-03-25 2017-03-24 Synthetic nucleic acid spike-ins
AU2021200637A Active AU2021200637B2 (en) 2016-03-25 2021-02-01 Synthetic nucleic acid spike-ins
AU2021215106A Abandoned AU2021215106A1 (en) 2016-03-25 2021-08-09 Synthetic nucleic acid spike-ins
AU2024204822A Pending AU2024204822A1 (en) 2016-03-25 2024-07-12 Synthetic nucleic acid spike-ins

Family Applications After (3)

Application Number Title Priority Date Filing Date
AU2021200637A Active AU2021200637B2 (en) 2016-03-25 2021-02-01 Synthetic nucleic acid spike-ins
AU2021215106A Abandoned AU2021215106A1 (en) 2016-03-25 2021-08-09 Synthetic nucleic acid spike-ins
AU2024204822A Pending AU2024204822A1 (en) 2016-03-25 2024-07-12 Synthetic nucleic acid spike-ins

Country Status (11)

Country Link
US (5) US9976181B2 (https=)
EP (3) EP3978627A1 (https=)
JP (4) JP6743268B2 (https=)
KR (3) KR102326769B1 (https=)
CN (2) CN109312400A (https=)
AU (4) AU2017237199B2 (https=)
BR (1) BR112018069557A2 (https=)
CA (2) CA3185611A1 (https=)
IL (2) IL260924B (https=)
MX (3) MX383493B (https=)
WO (1) WO2017165864A1 (https=)

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