CA3033241A1 - Methods and systems for detecting usual interstitial pneumonia - Google Patents

Methods and systems for detecting usual interstitial pneumonia Download PDF

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Publication number
CA3033241A1
CA3033241A1 CA3033241A CA3033241A CA3033241A1 CA 3033241 A1 CA3033241 A1 CA 3033241A1 CA 3033241 A CA3033241 A CA 3033241A CA 3033241 A CA3033241 A CA 3033241A CA 3033241 A1 CA3033241 A1 CA 3033241A1
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uip
sample
transcripts
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CA3033241A
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English (en)
French (fr)
Inventor
Giulia C. Kennedy
Jing Huang
Yoonha CHOI
Daniel PANKRATZ
Patric Sean Walsh
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Veracyte Inc
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Veracyte Inc
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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
    • C12Q1/6844—Nucleic acid amplification reactions
    • C12Q1/686—Polymerase chain reaction [PCR]
    • 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
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P11/00—Drugs for disorders of the respiratory system
    • 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
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6834—Enzymatic or biochemical coupling of nucleic acids to a solid phase
    • C12Q1/6837—Enzymatic or biochemical coupling of nucleic acids to a solid phase using probe arrays or probe chips
    • 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
    • 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
    • G16B40/00—ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
    • G16B40/20—Supervised data analysis
    • 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
    • C12Q2600/112—Disease subtyping, staging or classification
    • 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
    • C12Q2600/118—Prognosis of disease development
    • 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
    • C12Q2600/158—Expression markers
    • 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
    • G16B40/00—ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding

Landscapes

  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Organic Chemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Wood Science & Technology (AREA)
  • Zoology (AREA)
  • Physics & Mathematics (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • General Health & Medical Sciences (AREA)
  • Analytical Chemistry (AREA)
  • Biotechnology (AREA)
  • Biophysics (AREA)
  • Genetics & Genomics (AREA)
  • Microbiology (AREA)
  • Immunology (AREA)
  • General Engineering & Computer Science (AREA)
  • Biochemistry (AREA)
  • Molecular Biology (AREA)
  • Data Mining & Analysis (AREA)
  • Medical Informatics (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Public Health (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Evolutionary Biology (AREA)
  • Theoretical Computer Science (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Software Systems (AREA)
  • Evolutionary Computation (AREA)
  • Artificial Intelligence (AREA)
  • Bioethics (AREA)
  • Epidemiology (AREA)
  • Databases & Information Systems (AREA)
  • Nuclear Medicine, Radiotherapy & Molecular Imaging (AREA)
  • Veterinary Medicine (AREA)
  • Medicinal Chemistry (AREA)
  • Pathology (AREA)
  • Pulmonology (AREA)
CA3033241A 2016-09-07 2017-09-06 Methods and systems for detecting usual interstitial pneumonia Pending CA3033241A1 (en)

Applications Claiming Priority (5)

Application Number Priority Date Filing Date Title
US201662384609P 2016-09-07 2016-09-07
US62/384,609 2016-09-07
US201762528899P 2017-07-05 2017-07-05
US62/528,899 2017-07-05
PCT/US2017/050358 WO2018048960A1 (en) 2016-09-07 2017-09-06 Methods and systems for detecting usual interstitial pneumonia

Publications (1)

Publication Number Publication Date
CA3033241A1 true CA3033241A1 (en) 2018-03-15

Family

ID=61562790

Family Applications (1)

Application Number Title Priority Date Filing Date
CA3033241A Pending CA3033241A1 (en) 2016-09-07 2017-09-06 Methods and systems for detecting usual interstitial pneumonia

Country Status (7)

Country Link
US (2) US20190330680A1 (enExample)
EP (2) EP4424840A1 (enExample)
JP (2) JP2019528697A (enExample)
CN (1) CN109689892A (enExample)
AU (1) AU2017324949B2 (enExample)
CA (1) CA3033241A1 (enExample)
WO (1) WO2018048960A1 (enExample)

Families Citing this family (20)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP2360278A1 (en) 2005-04-14 2011-08-24 Trustees Of Boston University Diagnostic for lung disorders using class prediction
EP1999472A2 (en) 2006-03-09 2008-12-10 The Trustees Of Boston University Diagnostic and prognostic methods for lung disorders using gene expression profiles from nose epithelial cells
AU2008302076B2 (en) 2007-09-19 2015-06-11 The Trustees Of Boston University Identification of novel pathways for drug development for lung disease
US10236078B2 (en) 2008-11-17 2019-03-19 Veracyte, Inc. Methods for processing or analyzing a sample of thyroid tissue
US8669057B2 (en) 2009-05-07 2014-03-11 Veracyte, Inc. Methods and compositions for diagnosis of thyroid conditions
WO2014186036A1 (en) 2013-03-14 2014-11-20 Allegro Diagnostics Corp. Methods for evaluating copd status
US11976329B2 (en) 2013-03-15 2024-05-07 Veracyte, Inc. Methods and systems for detecting usual interstitial pneumonia
US12297505B2 (en) 2014-07-14 2025-05-13 Veracyte, Inc. Algorithms for disease diagnostics
CN114606309A (zh) 2014-11-05 2022-06-10 威拉赛特公司 使用机器学习和高维转录数据的诊断系统和方法
EP4180531A3 (en) 2016-05-12 2023-08-23 Trustees of Boston University Nasal epithelium gene expression signature and classifier for the prediction of lung cancer
WO2018009915A1 (en) 2016-07-08 2018-01-11 Trustees Of Boston University Gene expression-based biomarker for the detection and monitoring of bronchial premalignant lesions
US20220015714A1 (en) * 2018-11-29 2022-01-20 Somalogic, Inc. Methods For Determining Disease Risk Combining Downsampling of Class-Imbalanced Sets With Survival Analysis
GB2596233B (en) * 2018-12-20 2023-10-11 Veracyte Inc Methods and systems for detecting genetic fusions to identify a lung disorder
WO2020176620A1 (en) * 2019-02-26 2020-09-03 Tempus Systems and methods for using sequencing data for pathogen detection
EP4567125A3 (en) 2019-07-03 2025-09-17 BostonGene Corporation Systems and methods for sample preparation, sample sequencing, and sequencing data bias correction and quality control
CA3155044A1 (en) * 2019-10-16 2021-04-22 Icahn School Of Medicine At Mount Sinai Systems and methods for detecting a disease condition
WO2021228342A2 (en) * 2020-05-12 2021-11-18 Synaptic Aps An individualized group testing method for medical test samples
US12093803B2 (en) * 2020-07-01 2024-09-17 International Business Machines Corporation Downsampling genomic sequence data
EP4351723A4 (en) * 2021-06-11 2025-04-16 Acceleron Pharma, Inc. ACTRII PROTEINS AND THEIR USES
WO2025117806A1 (en) * 2023-11-30 2025-06-05 Arizona Board Of Regents On Behalf Of Arizona State University Volatile biomarkers for discriminating valley fever from other lung infections

Family Cites Families (12)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5795782A (en) 1995-03-17 1998-08-18 President & Fellows Of Harvard College Characterization of individual polymer molecules based on monomer-interface interactions
AU5631200A (en) 1999-06-22 2001-01-09 President And Fellows Of Harvard College Control of solid state dimensional features
US7258838B2 (en) 1999-06-22 2007-08-21 President And Fellows Of Harvard College Solid state molecular probe device
WO2006028508A2 (en) 2004-03-23 2006-03-16 President And Fellows Of Harvard College Methods and apparatus for characterizing polynucleotides
JP4533015B2 (ja) 2004-06-15 2010-08-25 キヤノン株式会社 化合物及びそれを用いた有機エレクトロルミネッセンス素子
CA2577079C (en) 2004-08-13 2014-05-20 President And Fellows Of Harvard College An ultra high-throughput opti-nanopore dna readout platform
WO2011044142A1 (en) * 2009-10-05 2011-04-14 Duke University Peripheral blood biomarkers for idiopathic interstitial pneumonia and methods of use
AU2012347263A1 (en) * 2011-12-09 2014-07-24 Mycartis N.V. LTBP2 as a biomarker for lung injury
SG11201405830VA (en) * 2012-03-27 2014-10-30 Genentech Inc Methods of prognosing, diagnosing and treating idiopathic pulmonary fibrosis
CN109504768A (zh) * 2013-03-15 2019-03-22 威拉赛特公司 用于诊断肺病的生物标记物及其使用方法
BR112015022490A2 (pt) * 2013-03-15 2017-07-18 Veracyte Inc métodos e composições para classificação de amostras
CN114606309A (zh) * 2014-11-05 2022-06-10 威拉赛特公司 使用机器学习和高维转录数据的诊断系统和方法

Also Published As

Publication number Publication date
EP3510173A1 (en) 2019-07-17
US20190330680A1 (en) 2019-10-31
WO2018048960A1 (en) 2018-03-15
JP2022126644A (ja) 2022-08-30
US20210355524A1 (en) 2021-11-18
AU2017324949B2 (en) 2024-05-23
JP7394169B2 (ja) 2023-12-07
AU2017324949A1 (en) 2019-02-28
EP4424840A1 (en) 2024-09-04
EP3510173A4 (en) 2020-05-20
JP2019528697A (ja) 2019-10-17
CN109689892A (zh) 2019-04-26

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