CA2929557C - Cell-free nucleic acids for the analysis of the human microbiome and components thereof - Google Patents

Cell-free nucleic acids for the analysis of the human microbiome and components thereof Download PDF

Info

Publication number
CA2929557C
CA2929557C CA2929557A CA2929557A CA2929557C CA 2929557 C CA2929557 C CA 2929557C CA 2929557 A CA2929557 A CA 2929557A CA 2929557 A CA2929557 A CA 2929557A CA 2929557 C CA2929557 C CA 2929557C
Authority
CA
Canada
Prior art keywords
transplant
nucleic acids
microbial
cell
host
Prior art date
Legal status (The legal status 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 status listed.)
Active
Application number
CA2929557A
Other languages
English (en)
French (fr)
Other versions
CA2929557A1 (en
Inventor
Iwijn De Vlaminck
Michael Kertesz
Kiran K. KHUSH
Mark Alec KOWARSKY
Lance MARTIN
Stephen R. Quake
Hannah Valantine
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Leland Stanford Junior University
Original Assignee
Leland Stanford Junior University
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 Leland Stanford Junior University filed Critical Leland Stanford Junior University
Priority to CA3207499A priority Critical patent/CA3207499A1/en
Publication of CA2929557A1 publication Critical patent/CA2929557A1/en
Application granted granted Critical
Publication of CA2929557C publication Critical patent/CA2929557C/en
Active legal-status Critical Current
Anticipated expiration legal-status Critical

Links

Classifications

    • 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
    • C12Q1/70—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving virus or bacteriophage
    • C12Q1/701—Specific hybridization probes
    • C12Q1/705—Specific hybridization probes for herpetoviridae, e.g. herpes simplex, varicella zoster
    • 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
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • 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
    • 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
    • C12Q1/6895—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms for plants, fungi or algae
    • 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
    • C12Q1/70—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving virus or bacteriophage
    • C12Q1/701—Specific hybridization probes
    • 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
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • 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
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/20—Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
    • 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
    • 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
    • G16B30/20—Sequence assembly
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
    • Y02A—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE
    • Y02A90/00—Technologies having an indirect contribution to adaptation to climate change
    • Y02A90/10—Information and communication technologies [ICT] supporting adaptation to climate change, e.g. for weather forecasting or climate simulation

Landscapes

  • Life Sciences & Earth Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Engineering & Computer Science (AREA)
  • Organic Chemistry (AREA)
  • Analytical Chemistry (AREA)
  • Physics & Mathematics (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biotechnology (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Biophysics (AREA)
  • General Health & Medical Sciences (AREA)
  • Genetics & Genomics (AREA)
  • Molecular Biology (AREA)
  • Immunology (AREA)
  • Microbiology (AREA)
  • Biochemistry (AREA)
  • General Engineering & Computer Science (AREA)
  • Evolutionary Biology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Medical Informatics (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Theoretical Computer Science (AREA)
  • Virology (AREA)
  • Pathology (AREA)
  • Botany (AREA)
  • Mycology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)
  • Medicines That Contain Protein Lipid Enzymes And Other Medicines (AREA)
CA2929557A 2013-11-07 2014-11-07 Cell-free nucleic acids for the analysis of the human microbiome and components thereof Active CA2929557C (en)

Priority Applications (1)

Application Number Priority Date Filing Date Title
CA3207499A CA3207499A1 (en) 2013-11-07 2014-11-07 Cell-free nucleic acids for the analysis of the human microbiome and components thereof

Applications Claiming Priority (5)

Application Number Priority Date Filing Date Title
US201361901114P 2013-11-07 2013-11-07
US61/901,114 2013-11-07
US201361901857P 2013-11-08 2013-11-08
US61/901,857 2013-11-08
PCT/US2014/064669 WO2015070086A1 (en) 2013-11-07 2014-11-07 Cell-free nucleic acids for the analysis of the human microbiome and components thereof

Related Child Applications (1)

Application Number Title Priority Date Filing Date
CA3207499A Division CA3207499A1 (en) 2013-11-07 2014-11-07 Cell-free nucleic acids for the analysis of the human microbiome and components thereof

Publications (2)

Publication Number Publication Date
CA2929557A1 CA2929557A1 (en) 2015-05-14
CA2929557C true CA2929557C (en) 2023-09-26

Family

ID=53042160

Family Applications (2)

Application Number Title Priority Date Filing Date
CA2929557A Active CA2929557C (en) 2013-11-07 2014-11-07 Cell-free nucleic acids for the analysis of the human microbiome and components thereof
CA3207499A Pending CA3207499A1 (en) 2013-11-07 2014-11-07 Cell-free nucleic acids for the analysis of the human microbiome and components thereof

Family Applications After (1)

Application Number Title Priority Date Filing Date
CA3207499A Pending CA3207499A1 (en) 2013-11-07 2014-11-07 Cell-free nucleic acids for the analysis of the human microbiome and components thereof

Country Status (12)

Country Link
US (6) US10450620B2 (https=)
EP (2) EP3066236B1 (https=)
JP (4) JP7451070B2 (https=)
KR (4) KR102930443B1 (https=)
CN (2) CN112877472A (https=)
AU (1) AU2014346562B2 (https=)
BR (1) BR112016010095A2 (https=)
CA (2) CA2929557C (https=)
GB (1) GB2535382A (https=)
IL (4) IL285106B (https=)
MX (5) MX383494B (https=)
WO (1) WO2015070086A1 (https=)

Families Citing this family (87)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US9424392B2 (en) 2005-11-26 2016-08-23 Natera, Inc. System and method for cleaning noisy genetic data from target individuals using genetic data from genetically related individuals
US11111543B2 (en) 2005-07-29 2021-09-07 Natera, Inc. System and method for cleaning noisy genetic data and determining chromosome copy number
US12152275B2 (en) 2010-05-18 2024-11-26 Natera, Inc. Methods for non-invasive prenatal ploidy calling
US20190010543A1 (en) 2010-05-18 2019-01-10 Natera, Inc. Methods for simultaneous amplification of target loci
US11939634B2 (en) 2010-05-18 2024-03-26 Natera, Inc. Methods for simultaneous amplification of target loci
US12221653B2 (en) 2010-05-18 2025-02-11 Natera, Inc. Methods for simultaneous amplification of target loci
US9677118B2 (en) 2014-04-21 2017-06-13 Natera, Inc. Methods for simultaneous amplification of target loci
US11322224B2 (en) 2010-05-18 2022-05-03 Natera, Inc. Methods for non-invasive prenatal ploidy calling
US11408031B2 (en) 2010-05-18 2022-08-09 Natera, Inc. Methods for non-invasive prenatal paternity testing
US10316362B2 (en) 2010-05-18 2019-06-11 Natera, Inc. Methods for simultaneous amplification of target loci
AU2011358564B9 (en) 2011-02-09 2017-07-13 Natera, Inc Methods for non-invasive prenatal ploidy calling
US20140100126A1 (en) 2012-08-17 2014-04-10 Natera, Inc. Method for Non-Invasive Prenatal Testing Using Parental Mosaicism Data
JP7451070B2 (ja) 2013-11-07 2024-03-18 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 ユニバーシティー ヒトミクロビオームおよびその成分の分析のための無細胞核酸
CN104946737B (zh) 2013-12-11 2019-02-22 安可济控股有限公司 用于检测罕见序列变体的组合物和方法
US11859246B2 (en) * 2013-12-11 2024-01-02 Accuragen Holdings Limited Methods and compositions for enrichment of amplification products
EP3957749A1 (en) 2014-04-21 2022-02-23 Natera, Inc. Detecting tumour specific mutations in biopsies with whole exome sequencing and in cell-free samples
US20180173845A1 (en) 2014-06-05 2018-06-21 Natera, Inc. Systems and Methods for Detection of Aneuploidy
US10410749B2 (en) 2014-10-21 2019-09-10 uBiome, Inc. Method and system for microbiome-derived characterization, diagnostics and therapeutics for cutaneous conditions
US10325685B2 (en) 2014-10-21 2019-06-18 uBiome, Inc. Method and system for characterizing diet-related conditions
AU2015335907A1 (en) 2014-10-21 2017-04-13 Psomagen, Inc. Method and system for microbiome-derived diagnostics and therapeutics
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
WO2016109939A1 (zh) * 2015-01-06 2016-07-14 深圳市海普洛斯生物科技有限公司 一种富集循环肿瘤dna的方法和试剂
US10893509B2 (en) 2015-02-11 2021-01-12 Qualcomm Incorporated Multiple tri-state HARQ processes
WO2016183106A1 (en) 2015-05-11 2016-11-17 Natera, Inc. Methods and compositions for determining ploidy
CN107922971A (zh) * 2015-05-18 2018-04-17 凯锐思公司 用于富集核酸群体的组合物和方法
WO2017004379A1 (en) * 2015-06-30 2017-01-05 uBiome, Inc. Method and system for diagnostic testing
AU2016308283B2 (en) 2015-08-19 2022-04-21 Arc Bio, Llc Capture of nucleic acids using a nucleic acid-guided nuclease-based system
EP3347496A4 (en) * 2015-09-09 2019-08-07 Ubiome Inc. METHOD AND SYSTEM FOR DIAGNOSES DERIVED FROM MICROBIOMA AND THERAPEUTIC TREATMENTS FOR BUCCO-DENTAL HEALTH
EP3347495A4 (en) * 2015-09-09 2019-08-21 Ubiome, Inc. METHOD AND SYSTEM FOR MICROBIOMY-DERIVED DIAGNOSES AND THERAPEUTIC AGENTS FOR DISEASES ASSOCIATED WITH GASTROINTESTINAL HEALTH
EP3141612A1 (en) 2015-09-10 2017-03-15 Fraunhofer-Gesellschaft zur Förderung der angewandten Forschung e.V. Method and device for nucleic acid based diagnostic approaches including the determination of a deviant condtion, especially a health condition and/or pathogenic condition of a sample
EP3146974A1 (en) * 2015-09-25 2017-03-29 Universite Claude Bernard - Lyon 1 Biomarkers for early determination of severity of influenza related disease
AU2016334233B2 (en) 2015-10-09 2023-01-05 Accuragen Holdings Limited Methods and compositions for enrichment of amplification products
CN108699505A (zh) 2015-12-03 2018-10-23 安可济控股有限公司 用于形成连接产物的方法和组合物
CN105567831B (zh) * 2016-01-29 2019-07-23 江汉大学 一种食品微生物定性与定量的检测方法
CN105603074B (zh) * 2016-01-29 2019-11-15 江汉大学 一种非诊断目的微生物定性与定量的检测方法
CN105671150A (zh) * 2016-01-29 2016-06-15 江汉大学 一种人体微生物定性与定量的检测方法
CN105603076A (zh) * 2016-01-29 2016-05-25 江汉大学 一种土壤微生物定性与定量的检测方法
CN105603075A (zh) * 2016-01-29 2016-05-25 江汉大学 一种小麦微生物定性与定量的检测方法
CA3185611A1 (en) 2016-03-25 2017-09-28 Karius, Inc. Synthetic nucleic acid spike-ins
WO2017181202A2 (en) 2016-04-15 2017-10-19 Natera, Inc. Methods for lung cancer detection
CA3022294A1 (en) * 2016-04-25 2017-11-02 uBiome, Inc. Method and system for characterizing skin-related conditions
CA3024630A1 (en) 2016-05-16 2017-11-23 Accuragen Holdings Limited Method of improved sequencing by strand identification
FR3051482B1 (fr) * 2016-05-19 2021-01-29 Life & Soft Procede de determination de la presence et quantification d'au moins un micro-organisme dans un echantillon biologique
EP4257701A3 (en) * 2016-06-30 2023-12-20 Grail, LLC Differential tagging of rna for preparation of a cell-free dna/rna sequencing library
CA3033749C (en) 2016-08-15 2026-03-24 Accuragen Holdings Limited Compositions and methods for detecting rare sequence variants
US11485996B2 (en) 2016-10-04 2022-11-01 Natera, Inc. Methods for characterizing copy number variation using proximity-litigation sequencing
GB201618485D0 (en) 2016-11-02 2016-12-14 Ucl Business Plc Method of detecting tumour recurrence
WO2018094183A1 (en) * 2016-11-17 2018-05-24 Seracare Life Sciences, Inc. Methods for preparing dna reference material and controls
US10011870B2 (en) 2016-12-07 2018-07-03 Natera, Inc. Compositions and methods for identifying nucleic acid molecules
JP2020515278A (ja) * 2017-04-04 2020-05-28 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 ユニバーシティー ドナー遺伝子型の非存在下での移植由来循環セルフリーｄｎａの定量化
WO2018187521A2 (en) * 2017-04-06 2018-10-11 Cornell University Methods of detecting cell-free dna in biological samples
WO2018191563A1 (en) 2017-04-12 2018-10-18 Karius, Inc. Sample preparation methods, systems and compositions
EP3431610A1 (en) * 2017-07-19 2019-01-23 Noscendo GmbH Methods and devices for nucleic acid-based real-time determination of disease states
US11519024B2 (en) 2017-08-04 2022-12-06 Billiontoone, Inc. Homologous genomic regions for characterization associated with biological targets
US11430543B2 (en) 2017-08-04 2022-08-30 Billiontoone, Inc. Sequencing output determination and analysis with target-associated molecules in quantification associated with biological targets
EP3662480A4 (en) 2017-08-04 2021-05-19 BillionToOne, Inc. MOLECULES ASSOCIATED WITH A TARGET FOR A CHARACTERIZATION ASSOCIATED WITH BIOLOGICAL TARGETS
WO2019060716A1 (en) 2017-09-25 2019-03-28 Freenome Holdings, Inc. SAMPLE EXTRACTION METHODS AND SYSTEMS
JP2021506342A (ja) 2017-12-14 2021-02-22 ティーエーアイ ダイアグノスティックス インコーポレイテッドＴａｉ Ｄｉａｇｎｏｓｔｉｃｓ，Ｉｎｃ． 移植のための移植片適合性の評価
ES2970286T3 (es) 2018-01-05 2024-05-27 Billiontoone Inc Plantillas de control de calidad para garantizar la validez de ensayos basados en secuenciación
US12398389B2 (en) 2018-02-15 2025-08-26 Natera, Inc. Methods for isolating nucleic acids with size selection
JP2021518106A (ja) * 2018-03-13 2021-08-02 ガーダント ヘルス， インコーポレイテッド 治療用核酸構築物の非侵襲的な検出およびモニタリングのための方法
WO2019178157A1 (en) 2018-03-16 2019-09-19 Karius, Inc. Sample series to differentiate target nucleic acids from contaminant nucleic acids
EP3785269A4 (en) * 2018-03-29 2021-12-29 Freenome Holdings, Inc. Methods and systems for analyzing microbiota
CA3090426A1 (en) 2018-04-14 2019-10-17 Natera, Inc. Methods for cancer detection and monitoring by means of personalized detection of circulating tumor dna
CN108660199A (zh) * 2018-05-20 2018-10-16 北京宏微特斯生物科技有限公司 一种基于cfDNA高通量测序检测病原体的方法
US12049665B2 (en) 2018-06-12 2024-07-30 Accuragen Holdings Limited Methods and compositions for forming ligation products
US12234509B2 (en) 2018-07-03 2025-02-25 Natera, Inc. Methods for detection of donor-derived cell-free DNA
US12071651B2 (en) 2018-08-06 2024-08-27 Billiontoone, Inc. Dilution tagging for quantification of biological targets
KR102114758B1 (ko) * 2018-11-19 2020-05-26 경북대학교 산학협력단 멤브레인 구조물을 이용한 혈액 내 미생물의 핵산 추출을 위한 혈액 시료 전처리 방법
ES3059710T3 (en) 2018-11-21 2026-03-23 Karius Inc Direct-to-library methods, systems, and compositions
US11512349B2 (en) 2018-12-18 2022-11-29 Grail, Llc Methods for detecting disease using analysis of RNA
WO2020198664A1 (en) * 2019-03-28 2020-10-01 The Regents Of The University Of California Methods and systems for sequencing cell-free microbiome dna
AU2020283042B2 (en) 2019-05-31 2026-02-19 Freenome Holdings, Inc. Methods and systems for high-depth sequencing of methylated nucleic acid
KR102503766B1 (ko) * 2020-06-16 2023-02-23 씨제이바이오사이언스 주식회사 장내 마이크로바이옴 지수를 결정하기 위한 장치, 방법 및 명령을 기록한 기록 매체
US20240071616A1 (en) * 2020-11-12 2024-02-29 Micronoma, Inc. Systems and methods to improve therapeutic outcomes
US20220195496A1 (en) * 2020-12-17 2022-06-23 Karius, Inc. Sequencing microbial cell-free dna from asymptomatic individuals
EP4263866A4 (en) * 2020-12-21 2024-12-04 Karius, Inc. Sequencing microbial cell-free nucleic acids to detect inflammation, secondary infection, and disease severity
CN113061666A (zh) * 2020-12-30 2021-07-02 中南大学湘雅二医院 肝移植后巨细胞病毒的检测方法、应用及系统
CA3213399A1 (en) * 2021-03-18 2022-09-22 Natera, Inc. Methods for determination of transplant rejection
AU2022325908A1 (en) * 2021-08-11 2024-01-04 Immunosis Pty Ltd Methods for determining secondary immunodeficiency
CA3249869A1 (en) * 2022-01-24 2023-07-27 Gusto Global, Llc SINGLE-POINT TARGETED AMPLICO FRAGMENT SEQUENCING AT SINGLE AND MULTI-LOCI LOCI
JP2025509878A (ja) 2022-03-21 2025-04-11 ビリオントゥーワン，インコーポレイテッド 処置モニタリングのためのメチル化セルフリーｄｎａの分子計数
WO2025024111A1 (en) * 2023-07-25 2025-01-30 Gusto Global, Llc Single point amplicon fragment sequencing and methods for diagnosing and monitoring disease
TW202536192A (zh) * 2023-10-24 2025-09-16 創新診斷科技中心 用於疾病分類之微生物ｄｎａ分析
US20250191691A1 (en) * 2023-12-07 2025-06-12 California Institute Of Technology Methods for the translated alignment of transcriptomic data at single-cell resolution
WO2025175229A1 (en) * 2024-02-16 2025-08-21 Karius, Inc. Multi-step methods for detecting nucleic acids
WO2025231437A1 (en) * 2024-05-03 2025-11-06 Karius, Inc. Predicting cytokine release syndrome in car-t cell therapy

Family Cites Families (85)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5242794A (en) 1984-12-13 1993-09-07 Applied Biosystems, Inc. Detection of specific sequences in nucleic acids
US4988617A (en) 1988-03-25 1991-01-29 California Institute Of Technology Method of detecting a nucleotide change in nucleic acids
US5494810A (en) 1990-05-03 1996-02-27 Cornell Research Foundation, Inc. Thermostable ligase-mediated DNA amplifications system for the detection of genetic disease
US6287850B1 (en) 1995-06-07 2001-09-11 Affymetrix, Inc. Bioarray chip reaction apparatus and its manufacture
GB9704444D0 (en) 1997-03-04 1997-04-23 Isis Innovation Non-invasive prenatal diagnosis
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
US6787308B2 (en) 1998-07-30 2004-09-07 Solexa Ltd. Arrayed biomolecules and their use in sequencing
US20030022207A1 (en) 1998-10-16 2003-01-30 Solexa, Ltd. Arrayed polynucleotides and their use in genome analysis
US7056661B2 (en) 1999-05-19 2006-06-06 Cornell Research Foundation, Inc. Method for sequencing nucleic acid molecules
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
WO2001023610A2 (en) 1999-09-29 2001-04-05 Solexa Ltd. Polynucleotide sequencing
US6582938B1 (en) 2001-05-11 2003-06-24 Affymetrix, Inc. Amplification of nucleic acids
GB0002389D0 (en) 2000-02-02 2000-03-22 Solexa Ltd Molecular arrays
AU2001293163A1 (en) 2000-09-27 2002-04-08 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
US6996477B2 (en) 2001-04-19 2006-02-07 Dana Farber Cancer Institute, Inc. Computational subtraction method
DE10120797B4 (de) 2001-04-27 2005-12-22 Genovoxx Gmbh Verfahren zur Analyse von Nukleinsäureketten
AU2002337030A1 (en) 2001-08-29 2003-03-18 Genovoxx Gmbh Method for analyzing nucleic acid sequences and gene expression
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
DE10246005A1 (de) 2001-10-04 2003-04-30 Genovoxx Gmbh Gerät zur Sequenzierung von Nukleinsäuremolekülen
DE10149786B4 (de) 2001-10-09 2013-04-25 Dmitry Cherkasov Oberfläche für Untersuchungen aus Populationen von Einzelmolekülen
US20050124022A1 (en) 2001-10-30 2005-06-09 Maithreyan Srinivasan Novel sulfurylase-luciferase fusion proteins and thermostable sulfurylase
US6902921B2 (en) 2001-10-30 2005-06-07 454 Corporation 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
WO2003074740A1 (en) 2002-03-01 2003-09-12 Ravgen, Inc. Rapid analysis of variations in a genome
US6977162B2 (en) 2002-03-01 2005-12-20 Ravgen, Inc. Rapid analysis of variations in a genome
DE10214395A1 (de) 2002-03-30 2003-10-23 Dmitri Tcherkassov Verfahren zur Analyse von Einzelnukleotidpolymorphismen
US7727720B2 (en) 2002-05-08 2010-06-01 Ravgen, Inc. Methods for detection of genetic disorders
US7442506B2 (en) 2002-05-08 2008-10-28 Ravgen, Inc. Methods for detection of genetic disorders
CN1688719A (zh) * 2002-07-01 2005-10-26 瓦罗洛吉克公司 确定致病性病毒对蛋白酶抑制剂易感性的组合物和方法
WO2005003375A2 (en) 2003-01-29 2005-01-13 454 Corporation Methods of amplifying and sequencing nucleic acids
US20040209299A1 (en) 2003-03-07 2004-10-21 Rubicon Genomics, Inc. In vitro DNA immortalization and whole genome amplification using libraries generated from randomly fragmented DNA
CA2522007A1 (en) 2003-04-11 2004-10-28 Medimmune, Inc. Methods of preventing or treating respiratory conditions
EP1725572B1 (de) 2003-11-05 2017-05-31 AGCT GmbH Makromolekulare nukleotidverbindungen und methoden zu deren anwendung
DE10356837A1 (de) 2003-12-05 2005-06-30 Dmitry Cherkasov Modifizierte Nukleotide und Nukleoside
US7169560B2 (en) 2003-11-12 2007-01-30 Helicos Biosciences Corporation Short cycle methods for sequencing polynucleotides
JP2007515414A (ja) 2003-12-16 2007-06-14 パレンテラル アー エス 血漿置換剤およびその製造方法
DE102004009704A1 (de) 2004-02-27 2005-09-15 Dmitry Cherkasov Makromolekulare Nukleotidverbindungen und Methoden zu deren Anwendung
DE102004025744A1 (de) 2004-05-26 2005-12-29 Dmitry Cherkasov Oberfläche für die Analysen an einzelnen Nukleinsäuremolekülen
DE102004025746A1 (de) 2004-05-26 2005-12-15 Dmitry Cherkasov Verfahren, Oberfläche und Substrate zur hochparallelen Sequenzierung von Nukleinsäureketten
DE102004025695A1 (de) 2004-05-26 2006-02-23 Dmitry Cherkasov Verfahren und Oberfläche zur parallelen Sequenzierung von Nukleinsäureketten
DE102004025745A1 (de) 2004-05-26 2005-12-15 Cherkasov, Dmitry Oberfläche für die Analysen an einzelnen Molekülen
DE102004025694A1 (de) 2004-05-26 2006-02-23 Dmitry Cherkasov Verfahren und Oberfläche zu hochparallelen Analysen von Nukleinsäureketten
DE102004025696A1 (de) 2004-05-26 2006-02-23 Dmitry Cherkasov Verfahren, Oberfläche und Substrate zu hochparallelen Analysen von Nukleinsäureketten
US20060002471A1 (en) 2004-06-30 2006-01-05 Lippincott Louis A Motion estimation unit
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
WO2006089203A2 (en) 2005-02-17 2006-08-24 Istituto Nazionale Per Le Malattie Infettive Irccs Lazzaro Spallanzani Compositions and methods for detecting viral specific nucleic acids in urine
US7914982B2 (en) 2005-02-17 2011-03-29 Trovagene, Inc. Methods for detecting pathogen 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.
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
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
IES20090464A2 (en) * 2008-06-13 2010-03-03 Nat Univ Ireland SWI5 gene as a diagnostic target for the identification of fungal and yeast species
ES2595489T3 (es) 2008-07-18 2016-12-30 Trovagene, Inc. Métodos para la detección de secuencias de ácidos nucleicos "ultracortos" basados en PCR
US20120190663A1 (en) 2009-08-06 2012-07-26 Cedars-Sinai Medical Center Use of free dna as an early predictor of severity in acute pancreatitis
HUE052213T2 (hu) 2009-11-06 2021-04-28 Univ Leland Stanford Junior Grafitkilökõdés nem invazív diagnosztizálása szervátültetett betegekben
EP2325312A1 (de) 2009-11-19 2011-05-25 Qiagen GmbH Verfahren zur selektiven Anreicherung und Isolierung mikrobieller und optional zusätzlich viraler Nukleinsäuren
CN102071261A (zh) * 2009-11-24 2011-05-25 上海复星医学科技发展有限公司 一种单纯疱疹病毒核酸检测方法及试剂盒
WO2011111966A2 (en) 2010-03-08 2011-09-15 Celltrion, Inc. Human monoclonal antibodies derived from human b cells and having neutralizing activity against influenza a viruses
US20120077185A1 (en) 2010-08-06 2012-03-29 Tandem Diagnostics, Inc. Detection of genetic abnormalities and infectious disease
AU2012236109A1 (en) 2011-04-01 2013-11-21 Occam Biolabs, Inc. Methods and kits for detecting cell-free pathogen-specific nucleic acids
US20140179726A1 (en) * 2011-05-19 2014-06-26 Virginia Commonwealth University Gut microflora as biomarkers for the prognosis of cirrhosis and brain dysfunction
EP2718862B1 (en) 2011-06-06 2018-10-31 Koninklijke Philips N.V. Method for assembly of nucleic acid sequence data
US20130024127A1 (en) 2011-07-19 2013-01-24 John Stuelpnagel Determination of source contributions using binomial probability calculations
CA2850785C (en) 2011-10-06 2022-12-13 Sequenom, Inc. Methods and processes for non-invasive assessment of genetic variations
WO2013113012A2 (en) 2012-01-27 2013-08-01 The Board Of Trustees Of The Leland Stanford Junior University Methods for profiling and quantitating cell-free rna
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
JP6411995B2 (ja) 2012-03-13 2018-10-24 ザ チャイニーズ ユニバーシティー オブ ホンコン 非侵襲的出生前診断のために大量並列シークエンシング・データを分析する方法
AU2013249012B2 (en) * 2012-04-19 2019-03-28 The 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
WO2013188846A1 (en) 2012-06-15 2013-12-19 Harry Stylli Methods of detecting diseases or conditions
GB2533006B (en) 2012-09-04 2017-06-07 Guardant Health Inc Systems and methods to detect 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
EP2728014B1 (en) 2012-10-31 2015-10-07 Genesupport SA Non-invasive method for detecting a fetal chromosomal aneuploidy
US20140242582A1 (en) 2013-02-28 2014-08-28 Ariosa Diagnostics, Inc. Detection of genetic abnormalities using ligation-based detection and digital pcr
GB2528205B (en) 2013-03-15 2020-06-03 Guardant Health Inc Systems and methods to detect rare mutations and copy number variation
US10017807B2 (en) 2013-03-15 2018-07-10 Verinata Health, Inc. Generating cell-free DNA libraries directly from blood
JP7451070B2 (ja) 2013-11-07 2024-03-18 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 ユニバーシティー ヒトミクロビオームおよびその成分の分析のための無細胞核酸
WO2015085105A1 (en) 2013-12-04 2015-06-11 University Of Alaska Fairbanks Methods and compositions for enriching non-host sequences in host samples
US10450650B2 (en) 2015-09-24 2019-10-22 The United States of America as represented by the Admininstrator of the National Aeronautics and Space Administration Method of manufacturing large area graphene and graphene-based photonics devices
JP7577928B2 (ja) 2019-06-19 2024-11-06 株式会社リコー トナー及び現像剤

Also Published As

Publication number Publication date
GB2535382A (en) 2016-08-17
BR112016010095A2 (pt) 2017-09-12
US20210301356A1 (en) 2021-09-30
CN105829589A (zh) 2016-08-03
JP7451070B2 (ja) 2024-03-18
EP3066236B1 (en) 2022-08-24
EP3066236A1 (en) 2016-09-14
MX2021006895A (es) 2021-07-07
KR20160069519A (ko) 2016-06-16
JP7739349B2 (ja) 2025-09-16
IL278349B (en) 2021-09-30
MX2016005798A (es) 2016-11-28
IL245446A0 (en) 2016-06-30
US20150133391A1 (en) 2015-05-14
JP7813512B2 (ja) 2026-02-13
JP2025106376A (ja) 2025-07-15
IL285106B (en) 2022-09-01
EP4130350A1 (en) 2023-02-08
MX2021006897A (es) 2021-07-07
MX2021006893A (es) 2021-07-07
CN105829589B (zh) 2021-02-02
IL272714A (en) 2020-04-30
CN112877472A (zh) 2021-06-01
US20210310085A1 (en) 2021-10-07
US10450620B2 (en) 2019-10-22
US20230349011A1 (en) 2023-11-02
US11365453B2 (en) 2022-06-21
EP3066236A4 (en) 2017-05-24
MX383494B (es) 2025-03-14
KR102930443B1 (ko) 2026-02-25
JP2023071944A (ja) 2023-05-23
AU2014346562A1 (en) 2016-05-26
US20200017926A1 (en) 2020-01-16
CA2929557A1 (en) 2015-05-14
CA3207499A1 (en) 2015-05-14
KR20210008941A (ko) 2021-01-25
US12195814B2 (en) 2025-01-14
US20210310084A1 (en) 2021-10-07
KR20240038168A (ko) 2024-03-22
JP2017500015A (ja) 2017-01-05
US11427876B2 (en) 2022-08-30
MX2020004247A (es) 2020-07-29
GB201608448D0 (en) 2016-06-29
IL285106A (en) 2021-08-31
AU2014346562B2 (en) 2018-11-29
WO2015070086A1 (en) 2015-05-14
IL245446B (en) 2020-04-30
KR102205950B1 (ko) 2021-01-22
US11401562B2 (en) 2022-08-02
JP2021072777A (ja) 2021-05-13
KR20260035294A (ko) 2026-03-12
KR102649364B1 (ko) 2024-03-20
IL272714B (en) 2020-11-30

Similar Documents

Publication Publication Date Title
US11427876B2 (en) Cell-free nucleic acids for the analysis of the human microbiome and components thereof
De Vlaminck et al. Temporal response of the human virome to immunosuppression and antiviral therapy
US11767559B2 (en) Methods of monitoring immunosuppressive therapies in a transplant recipient
JP2018527938A (ja) サンプルの逸脱状態、特に健康状態および／または病原性状態の決定を含む核酸ベースの診断アプローチのための方法およびデバイス
Boudreault et al. Risk factors for late‐onset cytomegalovirus disease in donor seropositive/recipient seronegative kidney transplant recipients who receive antiviral prophylaxis
US11987844B2 (en) Use of CFDNA fragments as biomarkers in patients after organ transplantation
HK40082336A (en) Cell-free nucleic acids for the analysis of the human microbiome and components thereof
JP2025509966A (ja) 異種間移植における臓器の健康を非侵襲的に監視する方法

Legal Events

Date Code Title Description
EEER Examination request

Effective date: 20171219

MPN Maintenance fee for patent paid

Free format text: FEE DESCRIPTION TEXT: MF (PATENT, 10TH ANNIV.) - STANDARD

Year of fee payment: 10

U00 Fee paid

Free format text: ST27 STATUS EVENT CODE: A-4-4-U10-U00-U101 (AS PROVIDED BY THE NATIONAL OFFICE); EVENT TEXT: MAINTENANCE REQUEST RECEIVED

Effective date: 20241102

U11 Full renewal or maintenance fee paid

Free format text: ST27 STATUS EVENT CODE: A-4-4-U10-U11-U102 (AS PROVIDED BY THE NATIONAL OFFICE); EVENT TEXT: MAINTENANCE FEE PAYMENT PAID IN FULL

Effective date: 20241102

MPN Maintenance fee for patent paid

Free format text: FEE DESCRIPTION TEXT: MF (PATENT, 11TH ANNIV.) - STANDARD

Year of fee payment: 11

U00 Fee paid

Free format text: ST27 STATUS EVENT CODE: A-4-4-U10-U00-U101 (AS PROVIDED BY THE NATIONAL OFFICE); EVENT TEXT: MAINTENANCE REQUEST RECEIVED

Effective date: 20251014

U11 Full renewal or maintenance fee paid

Free format text: ST27 STATUS EVENT CODE: A-4-4-U10-U11-U102 (AS PROVIDED BY THE NATIONAL OFFICE); EVENT TEXT: MAINTENANCE FEE PAYMENT PAID IN FULL

Effective date: 20251014