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)
  • Molecular Biology (AREA)
  • Microbiology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Immunology (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Theoretical Computer Science (AREA)
  • Evolutionary Biology (AREA)
  • Medical Informatics (AREA)
  • Biomedical Technology (AREA)
  • Plant Pathology (AREA)
  • Crystallography & Structural Chemistry (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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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 (enExample)
EP (3) EP3433382B1 (enExample)
JP (4) JP6743268B2 (enExample)
KR (3) KR102326769B1 (enExample)
CN (2) CN116987777A (enExample)
AU (4) AU2017237199B2 (enExample)
BR (1) BR112018069557A2 (enExample)
CA (2) CA3185611A1 (enExample)
IL (2) IL260924B (enExample)
MX (3) MX383493B (enExample)
WO (1) WO2017165864A1 (enExample)

Families Citing this family (43)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CA2971444A1 (en) 2014-12-20 2016-06-23 Arc Bio, Llc Compositions and methods for targeted depletion, enrichment, and partitioning of nucleic acids using crispr/cas system proteins
EP4450636A3 (en) 2015-05-18 2025-01-01 Karius, Inc. Compositions and methods for enriching populations of nucleic acids
CA2995983A1 (en) 2015-08-19 2017-02-23 Arc Bio, Llc Capture of nucleic acids using a nucleic acid-guided nuclease-based system
CN116987777A (zh) 2016-03-25 2023-11-03 凯锐思公司 合成核酸掺入物
EP3610034B1 (en) 2017-04-12 2022-06-08 Karius, Inc. Sample preparation methods, systems and compositions
CA3071855C (en) 2017-08-04 2021-09-14 Billiontoone, Inc. Target-associated molecules for characterization associated with biological targets
ES2923478T3 (es) 2017-08-04 2022-09-27 Billiontoone Inc Determinación y análisis de resultados de una secuenciación con moléculas asociadas a una diana en una cuantificación asociada con dianas biológicas
US11519024B2 (en) 2017-08-04 2022-12-06 Billiontoone, Inc. Homologous genomic regions for characterization associated with biological targets
CN109680343B (zh) * 2017-10-18 2022-02-18 深圳华大生命科学研究院 一种外泌体微量dna的建库方法
EP4335928B1 (en) * 2018-01-05 2025-10-29 BillionToOne, Inc. Quality control templates for ensuring validity of sequencing-based assays
EP3752636A4 (en) * 2018-02-15 2022-01-26 Thrive Earlier Detection Corp. Barcoded molecular standards
US11970786B2 (en) * 2018-02-15 2024-04-30 Bioo Scientific Corporation Methods and kits for detecting contamination and sample misidentification
CA3082601A1 (en) 2018-03-16 2019-09-19 Karius, Inc. Sample series to differentiate target nucleic acids from contaminant nucleic acids
GB201805676D0 (en) * 2018-04-05 2018-05-23 Imperial Innovations Ltd Compositions
US11702653B2 (en) 2018-05-21 2023-07-18 Battelle Memorial Institute Control compositions and methods for sequencing
TWI852936B (zh) * 2018-06-29 2024-08-21 美商格瑞爾有限責任公司 核酸重組及整合分析
DE102018213027A1 (de) * 2018-08-03 2020-02-06 Robert Bosch Gmbh Reaktionsgemisch, Verfahren und Kit zur Durchführung einer quantitativen Echtzeit-PCR
WO2020033425A1 (en) * 2018-08-06 2020-02-13 Billiontoone, Inc. Dilution tagging for quantification of biological targets
AU2019356016A1 (en) * 2018-10-04 2021-05-13 Arc Bio, Llc Normalization controls for managing low sample inputs in next generation sequencing
CN113227393B (zh) * 2018-10-31 2025-02-11 夸登特健康公司 用于校准表观遗传分区测定的方法、组合物和系统
CA3118990A1 (en) 2018-11-21 2020-05-28 Karius, Inc. Direct-to-library methods, systems, and compositions
WO2020106987A1 (en) * 2018-11-21 2020-05-28 Karius, Inc. Detection and prediction of infectious disease
WO2020124003A1 (en) * 2018-12-13 2020-06-18 Battelle Memorial Institute Methods and control compositions for a quantitative polymerase chain reaction
CN113454218A (zh) * 2018-12-20 2021-09-28 夸登特健康公司 用于改进核酸分子的回收的方法、组合物和系统
EP3931356A1 (en) * 2019-02-28 2022-01-05 Inivata Ltd. Method for quantifying the amount of a target sequence in a nucleic acid sample
WO2020263921A1 (en) * 2019-06-28 2020-12-30 Biota Technology, Inc. Estimating a quantity of molecules in a sample
WO2021042235A1 (zh) * 2019-09-02 2021-03-11 北京哲源科技有限责任公司 疾病类型自动确定方法及电子设备
CA3153350A1 (en) * 2019-10-16 2021-04-22 Barbara ANDRE Determination of nucleic acid sequence concentrations
CN115087744A (zh) * 2019-11-06 2022-09-20 大学健康网络 用于无细胞MeDIP测序的合成加标对照及其使用方法
CN111599409B (zh) * 2020-05-20 2022-05-20 电子科技大学 基于MapReduce并行的circRNA识别方法
WO2021243045A1 (en) * 2020-05-29 2021-12-02 Natera, Inc. Methods for detection of donor-derived cell-free dna
KR20220045451A (ko) 2020-10-05 2022-04-12 주식회사 엘지에너지솔루션 배터리 상태 진단 장치 및 방법
CN112266978A (zh) * 2020-10-22 2021-01-26 深圳国际旅行卫生保健中心(深圳海关口岸门诊部) 引物探针组合、检测试剂盒及其应用
US20220195496A1 (en) * 2020-12-17 2022-06-23 Karius, Inc. Sequencing microbial cell-free dna from asymptomatic individuals
US20220282321A1 (en) * 2021-03-01 2022-09-08 The Broad Institute, Inc. Amplicon-based sequencing using dna spike-ins
CN115109840B (zh) * 2021-03-18 2025-08-12 厦门大学 一种分析目标核酸中突变的存在及其类型的方法
JP2024513187A (ja) * 2021-03-29 2024-03-22 イルミナ インコーポレイテッド ライブラリー中のｄｎａ損傷を評価し、アンプリコンサイズバイアスを正規化するための組成物及び方法
CA3241776A1 (en) * 2021-12-30 2023-07-06 Dom Zichi Next-generation sequencing for protein measurement
AU2023240345A1 (en) * 2022-03-21 2024-10-10 Billion Toone, Inc. Molecule counting of methylated cell-free dna for treatment monitoring
JP2024100144A (ja) 2023-01-13 2024-07-26 国立研究開発法人産業技術総合研究所 ゲノムまたはメタゲノム解析のための内部標準核酸
AU2024257509A1 (en) 2023-04-18 2025-10-30 Karius, Inc. Sample processing to enrich for select species of nucleic acids
CN117008647A (zh) * 2023-06-15 2023-11-07 深圳赛陆医疗科技有限公司 控制方法、基因测序仪和存储介质
WO2025160484A1 (en) 2024-01-25 2025-07-31 Karius, Inc. Microbial and human cell-free dna biomarkers for diagnosing and assessing the severity of inflammatory bowel disease

Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2014082032A1 (en) * 2012-11-26 2014-05-30 The University Of Toledo Methods for standardized sequencing of nucleic acids and uses thereof
WO2016094947A1 (en) * 2014-12-16 2016-06-23 Garvan Institute Of Medical Research Sequencing controls

Family Cites Families (106)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US6969488B2 (en) 1998-05-22 2005-11-29 Solexa, Inc. System and apparatus for sequential processing of analytes
USRE39920E1 (en) 1997-05-30 2007-11-13 Xenomics, Inc. Methods for detection of nucleic acid sequences in urine
US20030022207A1 (en) 1998-10-16 2003-01-30 Solexa, Ltd. Arrayed polynucleotides and their use in genome analysis
US20040106110A1 (en) 1998-07-30 2004-06-03 Solexa, Ltd. Preparation of polynucleotide arrays
US6787308B2 (en) 1998-07-30 2004-09-07 Solexa Ltd. Arrayed biomolecules and their use in sequencing
US7211390B2 (en) 1999-09-16 2007-05-01 454 Life Sciences 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
EP1218543A2 (en) 1999-09-29 2002-07-03 Solexa Ltd. Polynucleotide sequencing
GB0002389D0 (en) 2000-02-02 2000-03-22 Solexa Ltd Molecular arrays
WO2002027029A2 (en) 2000-09-27 2002-04-04 Lynx Therapeutics, Inc. Method for determining relative abundance of nucleic acid sequences
US6753137B2 (en) 2001-01-31 2004-06-22 The Chinese University Of Hong Kong Circulating epstein-barr virus DNA in the serum of patients with gastric carcinoma
JP2003101204A (ja) 2001-09-25 2003-04-04 Nec Kansai Ltd 配線基板及び配線基板の製造方法並びに電子部品
US6902921B2 (en) 2001-10-30 2005-06-07 454 Corporation Sulfurylase-luciferase fusion proteins and thermostable sulfurylase
US20050124022A1 (en) 2001-10-30 2005-06-09 Maithreyan Srinivasan Novel sulfurylase-luciferase fusion proteins and thermostable sulfurylase
US20050202414A1 (en) 2001-11-15 2005-09-15 The Regents Of The University Of California Apparatus and methods for detecting a microbe in a sample
WO2003052101A1 (en) * 2001-12-14 2003-06-26 Rosetta Inpharmatics, Inc. Sample tracking using molecular barcodes
CA2513535C (en) 2003-01-29 2012-06-12 454 Corporation Bead emulsion nucleic acid amplification
EP1606417A2 (en) 2003-03-07 2005-12-21 Rubicon Genomics Inc. In vitro dna immortalization and whole genome amplification using libraries generated from randomly fragmented dna
US7108979B2 (en) * 2003-09-03 2006-09-19 Agilent Technologies, Inc. Methods to detect cross-contamination between samples contacted with a multi-array substrate
US20070111233A1 (en) 2003-10-30 2007-05-17 Bianchi Diana W Prenatal diagnosis using cell-free fetal DNA in amniotic fluid
US7169560B2 (en) 2003-11-12 2007-01-30 Helicos Biosciences Corporation Short cycle methods for sequencing polynucleotides
US20060024711A1 (en) 2004-07-02 2006-02-02 Helicos Biosciences Corporation Methods for nucleic acid amplification and sequence determination
US7276720B2 (en) 2004-07-19 2007-10-02 Helicos Biosciences Corporation Apparatus and methods for analyzing samples
US20060012793A1 (en) 2004-07-19 2006-01-19 Helicos Biosciences Corporation Apparatus and methods for analyzing samples
US20060024678A1 (en) 2004-07-28 2006-02-02 Helicos Biosciences Corporation Use of single-stranded nucleic acid binding proteins in sequencing
EP1647600A3 (en) * 2004-09-17 2006-06-28 Affymetrix, Inc. (A US Entity) Methods for identifying biological samples by addition of nucleic acid bar-code tags
ITRM20050067A1 (it) 2005-02-17 2006-08-18 Istituto Naz Per Le Malattie I Metodo per la rivelazione di acidi nucleici virali o di origine virale nelle urine.
AU2006214444B8 (en) 2005-02-17 2012-04-05 Trovagene, Inc. Compositions and methods for detecting pathogen specific nucleic acids in urine
US7914982B2 (en) 2005-02-17 2011-03-29 Trovagene, Inc. Methods for detecting pathogen specific nucleic acids in urine
EP1856295B1 (en) 2005-02-17 2013-04-03 TrovaGene, Inc. Compositions and methods for detecting viral specific nucleic acids in urine
ITRM20050068A1 (it) 2005-02-17 2006-08-18 Istituto Naz Per Le Malattie I Metodo per la rivelazione di acidi nucleici di agenti patogeni batterici o di parassiti nelle urine.
US8785130B2 (en) * 2005-07-07 2014-07-22 Bio-Id Diagnostic Inc. Use of markers including nucleotide sequence based codes to monitor methods of detection and identification of genetic material
US8532930B2 (en) 2005-11-26 2013-09-10 Natera, Inc. Method for determining the number of copies of a chromosome in the genome of a target individual using genetic data from genetically related individuals
US8101353B2 (en) 2007-12-18 2012-01-24 Advanced Analytical Technologies, Inc. System and method for nucleotide sequence profiling for sample identification
WO2009099602A1 (en) * 2008-02-04 2009-08-13 Massachusetts Institute Of Technology Selection of nucleic acids by solution hybridization to oligonucleotide baits
US20110160290A1 (en) * 2008-05-21 2011-06-30 Muneesh Tewari Use of extracellular rna to measure disease
ES2532153T3 (es) 2008-07-18 2015-03-24 Trovagene, Inc. Métodos para la detección de secuencias de ácidos nucleicos "ultracortos" basados en PCR
US20100062494A1 (en) * 2008-08-08 2010-03-11 President And Fellows Of Harvard College Enzymatic oligonucleotide pre-adenylation
HUE031848T2 (en) 2008-09-20 2017-08-28 Univ Leland Stanford Junior Non-invasive diagnosis of fetal aneuploidy by sequencing
WO2011015944A2 (en) 2009-08-06 2011-02-10 Cedars-Sinai Medical Center Use of free dna as an early predictor of severity in acute pancreatitis
JP2013509883A (ja) 2009-11-06 2013-03-21 ザ ボード オブ トラスティーズ オブ ザ リーランド スタンフォード ジュニア ユニバーシティ 臓器移植患者における移植片拒絶反応の非侵襲的診断方法
US8835358B2 (en) * 2009-12-15 2014-09-16 Cellular Research, Inc. Digital counting of individual molecules by stochastic attachment of diverse labels
US20130261196A1 (en) * 2010-06-11 2013-10-03 Lisa Diamond Nucleic Acids For Multiplex Organism Detection and Methods Of Use And Making The Same
WO2012012703A2 (en) 2010-07-23 2012-01-26 Esoterix Genetic Laboratories, Llc Identification of differentially represented fetal or maternal genomic regions and uses thereof
US20120077185A1 (en) 2010-08-06 2012-03-29 Tandem Diagnostics, Inc. Detection of genetic abnormalities and infectious disease
ES2690753T3 (es) * 2010-09-21 2018-11-22 Agilent Technologies, Inc. Aumento de la confianza en las identificaciones de alelos con el recuento molecular
WO2012078792A2 (en) 2010-12-07 2012-06-14 Stanford University Non-invasive determination of fetal inheritance of parental haplotypes at the genome-wide scale
US9260753B2 (en) 2011-03-24 2016-02-16 President And Fellows Of Harvard College Single cell nucleic acid detection and analysis
AU2012236109A1 (en) 2011-04-01 2013-11-21 Occam Biolabs, Inc. Methods and kits for detecting cell-free pathogen-specific nucleic acids
US9809904B2 (en) * 2011-04-21 2017-11-07 University Of Washington Through Its Center For Commercialization Methods for retrieval of sequence-verified DNA constructs
WO2012159023A2 (en) 2011-05-19 2012-11-22 Virginia Commonwealth University Gut microflora as biomarkers for the prognosis of cirrhosis and brain dysfunction
SG194745A1 (en) * 2011-05-20 2013-12-30 Fluidigm Corp Nucleic acid encoding reactions
EP2718862B1 (en) 2011-06-06 2018-10-31 Koninklijke Philips N.V. Method for assembly of nucleic acid sequence data
MX345557B (es) 2011-07-06 2017-02-02 Quest Diagnostics Invest Inc Amplificacion y deteccion directa de patogenos virales y bacteriales.
US20130024127A1 (en) 2011-07-19 2013-01-24 John Stuelpnagel Determination of source contributions using binomial probability calculations
CA3067612A1 (en) 2011-09-22 2013-03-28 Lineage Biosciences, Inc. Compositions and methods for analyzing heterogeneous samples
KR101272017B1 (ko) * 2011-09-23 2013-06-07 주식회사 랩 지노믹스 비뇨생식기 감염 질환 진단용 ｄｎａ칩
CA2850785C (en) 2011-10-06 2022-12-13 Sequenom, Inc. Methods and processes for non-invasive assessment of genetic variations
EP2788506A2 (en) * 2011-11-01 2014-10-15 Pathogenica, Inc. Method and system for detection of an organism
CA2861856C (en) 2012-01-20 2020-06-02 Sequenom, Inc. Diagnostic processes that factor experimental conditions
HK1211624A1 (en) 2012-01-27 2016-05-27 The Board Of Trustees Of The University Of The Leland Stanford Junior University Methods for profiling and quantitating cell-free rna
EP2814959B1 (en) * 2012-02-17 2018-01-17 Fred Hutchinson Cancer Research Center Compositions and methods for accurately identifying mutations
US9892230B2 (en) 2012-03-08 2018-02-13 The Chinese University Of Hong Kong Size-based analysis of fetal or tumor DNA fraction in plasma
EP3573066B1 (en) 2012-03-13 2023-09-27 The Chinese University Of Hong Kong Methods for analyzing massively parallel sequencing data for noninvasive prenatal diagnosis
WO2013159035A2 (en) 2012-04-19 2013-10-24 Medical College Of Wisconsin, Inc. Highly sensitive surveillance using detection of cell free dna
EP2653562A1 (en) 2012-04-20 2013-10-23 Institut Pasteur Anellovirus genome quantification as a biomarker of immune suppression
JP2015522260A (ja) 2012-06-15 2015-08-06 ハリー スティリ， 疾患または状態を検出する方法
US20160040229A1 (en) 2013-08-16 2016-02-11 Guardant Health, Inc. Systems and methods to detect rare mutations and copy number variation
US20140066317A1 (en) 2012-09-04 2014-03-06 Guardant Health, Inc. Systems and methods to detect rare mutations and copy number variation
WO2014149134A2 (en) 2013-03-15 2014-09-25 Guardant Health Inc. Systems and methods to detect rare mutations and copy number variation
KR102393608B1 (ko) 2012-09-04 2022-05-03 가던트 헬쓰, 인크. 희귀 돌연변이 및 카피수 변이를 검출하기 위한 시스템 및 방법
EP3026124A1 (en) 2012-10-31 2016-06-01 Genesupport SA Non-invasive method for detecting a fetal chromosomal aneuploidy
WO2014127484A1 (en) * 2013-02-21 2014-08-28 British Columbia Cancer Agency Branch Spike-in control nucleic acids for sample tracking
US20140242582A1 (en) 2013-02-28 2014-08-28 Ariosa Diagnostics, Inc. Detection of genetic abnormalities using ligation-based detection and digital pcr
EP3409791B1 (en) 2013-03-15 2021-06-30 Verinata Health, Inc. Generating cell-free dna libraries directly from blood
EP4187543A1 (en) 2013-04-03 2023-05-31 Sequenom, Inc. Methods and processes for non-invasive assessment of genetic variations
US9422551B2 (en) * 2013-05-29 2016-08-23 New England Biolabs, Inc. Adapters for ligation to RNA in an RNA library with reduced bias
CN105705515B (zh) * 2013-11-07 2021-05-25 安捷伦科技有限公司 多种用于dna操作的转座酶适体
KR20240038168A (ko) 2013-11-07 2024-03-22 더 보드 어브 트러스티스 어브 더 리랜드 스탠포드 주니어 유니버시티 인간 마이크로바이옴 및 그의 성분의 분석을 위한 무세포 핵산
AU2014346399A1 (en) * 2013-11-11 2016-06-02 Arizona Board Of Regents On Behalf Of Northern Arizona University Systems and methods for universal tail-based indexing strategies for amplicon sequencing
WO2015073080A1 (en) * 2013-11-12 2015-05-21 Life Technologies Corporation Reagents and methods for sequencing
US11035000B2 (en) 2013-12-04 2021-06-15 University Of Alaska Fairbanks Methods and compositions for enriching non-host sequences in host samples
EP3495506B1 (en) 2013-12-11 2023-07-12 AccuraGen Holdings Limited Methods for detecting rare sequence variants
US20170002397A1 (en) * 2014-01-28 2017-01-05 Qiagen Gmbh Internal amplification control
CN106103713B (zh) 2014-02-03 2021-05-28 赛默飞世尔科技波罗的海封闭股份公司 用于经控制dna片段化的方法
GB201405226D0 (en) 2014-03-24 2014-05-07 Cambridge Entpr Ltd Nucleic acid preparation method
ES2777529T3 (es) * 2014-04-17 2020-08-05 Adaptive Biotechnologies Corp Cuantificación de genomas de células inmunitarias adaptativas en una mezcla compleja de células
GB201411603D0 (en) * 2014-06-30 2014-08-13 Vela Operations Pte Ltd Compositions for quantitative and/or semiquantitative mutation detection methods
EP3913066A1 (en) * 2014-09-09 2021-11-24 Igenomx International Genomics Corporation Compositions for rapid nucleic acid library preparation
EP4450636A3 (en) 2015-05-18 2025-01-01 Karius, Inc. Compositions and methods for enriching populations of nucleic acids
CN105112569B (zh) * 2015-09-14 2017-11-21 中国医学科学院病原生物学研究所 基于宏基因组学的病毒感染检测及鉴定方法
EP3405573A4 (en) * 2016-01-22 2019-09-18 Grail, Inc. METHOD AND SYSTEMS FOR HIGH-FIDELITY SEQUENCING
CN116987777A (zh) 2016-03-25 2023-11-03 凯锐思公司 合成核酸掺入物
EP3246412A1 (en) * 2016-05-17 2017-11-22 DName-iT NV Methods for identification of samples
JP7448310B2 (ja) 2016-07-06 2024-03-12 ガーダント ヘルス， インコーポレイテッド セルフリー核酸のフラグメントームプロファイリングのための方法
CA3031231A1 (en) 2016-08-08 2018-02-15 Karius, Inc. Reduction of signal from contaminant nucleic acids
WO2018045359A1 (en) 2016-09-02 2018-03-08 Karius, Inc. Detection and treatment of infection during pregnancy
SG11201903509QA (en) 2016-10-24 2019-05-30 Univ Hong Kong Chinese Methods and systems for tumor detection
WO2018187521A2 (en) 2017-04-06 2018-10-11 Cornell University Methods of detecting cell-free dna in biological samples
EP3610034B1 (en) 2017-04-12 2022-06-08 Karius, Inc. Sample preparation methods, systems and compositions
US12104205B2 (en) * 2017-06-20 2024-10-01 Mgi Tech Co., Ltd. PCR primer pair and application thereof
US11254980B1 (en) * 2017-11-29 2022-02-22 Adaptive Biotechnologies Corporation Methods of profiling targeted polynucleotides while mitigating sequencing depth requirements
CA3082601A1 (en) 2018-03-16 2019-09-19 Karius, Inc. Sample series to differentiate target nucleic acids from contaminant nucleic acids
WO2020106987A1 (en) 2018-11-21 2020-05-28 Karius, Inc. Detection and prediction of infectious disease
CA3118990A1 (en) 2018-11-21 2020-05-28 Karius, Inc. Direct-to-library methods, systems, and compositions
US20220195496A1 (en) 2020-12-17 2022-06-23 Karius, Inc. Sequencing microbial cell-free dna from asymptomatic individuals

Patent Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2014082032A1 (en) * 2012-11-26 2014-05-30 The University Of Toledo Methods for standardized sequencing of nucleic acids and uses thereof
WO2016094947A1 (en) * 2014-12-16 2016-06-23 Garvan Institute Of Medical Research Sequencing controls

Non-Patent Citations (3)

* Cited by examiner, † Cited by third party
Title
DAVIDE RISSO ET AL, "Normalization of RNA-seq data using factor analysis of control genes or samples", NATURE BIOTECHNOLOGY, New York, (2014-08-24), vol. 32, no. 9, doi:10.1038/nbt.2931, ISSN 1087-0156, pages 896 - 902 *
Fu et al. (Molecular indexing enables quantitative targeted RNA sequencing and reveals poor efficiencies in standard library preparations, Proc Natl Acad Sci U S A. Feb. 4, 2014;111(5):1891-6. Epub Jan. 21, 2014) (Year: 2014). *
OLIVER STEGLE ET AL, "Computational and analytical challenges in single-cell transcriptomics", NATURE REVIEWS GENETICS, GB, (2015-01-28), vol. 16, no. 3, doi:10.1038/nrg3833, ISSN 1471-0056, pages 133 - 145 *

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