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
expression level
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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

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  • 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)
  • General Health & Medical Sciences (AREA)
  • Bioinformatics & Cheminformatics (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 (https=)
EP (2) EP3510173A4 (https=)
JP (2) JP2019528697A (https=)
CN (1) CN109689892A (https=)
AU (1) AU2017324949B2 (https=)
CA (1) CA3033241A1 (https=)
WO (1) WO2018048960A1 (https=)

Families Citing this family (20)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP3211093A1 (en) 2005-04-14 2017-08-30 The Trustees of Boston University Diagnostic for lung disorders using class prediction
WO2007103541A2 (en) 2006-03-09 2007-09-13 The Trustees Of Boston University Diagnostic and prognostic methods for lung disorders using gene expression profiles from nose epithelial cells
CN101990577A (zh) 2007-09-19 2011-03-23 波士顿大学理事会 鉴定肺病药物开发的新途径
US10236078B2 (en) 2008-11-17 2019-03-19 Veracyte, Inc. Methods for processing or analyzing a sample of thyroid tissue
EP3360978A3 (en) 2009-05-07 2018-09-26 Veracyte, Inc. Methods for diagnosis of thyroid conditions
EP2968988A4 (en) 2013-03-14 2016-11-16 Allegro Diagnostics Corp METHOD FOR EVALUATING A 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
US20170335396A1 (en) 2014-11-05 2017-11-23 Veracyte, Inc. Systems and methods of diagnosing idiopathic pulmonary fibrosis on transbronchial biopsies using machine learning and high dimensional transcriptional data
WO2017197335A1 (en) 2016-05-12 2017-11-16 Trustees Of Boston University Nasal epithelium gene expression signature and classifier for the prediction of lung cancer
US10927417B2 (en) 2016-07-08 2021-02-23 Trustees Of Boston University Gene expression-based biomarker for the detection and monitoring of bronchial premalignant lesions
SG11202105063QA (en) * 2018-11-29 2021-06-29 Somalogic Inc Methods for determining disease risk combining downsampling of class-imbalanced sets with survival analysis
WO2020132520A2 (en) * 2018-12-20 2020-06-25 Veracyte, Inc. Methods and systems for detecting genetic fusions to identify a lung disorder
ES3043308T3 (en) 2019-02-26 2025-11-25 Tempus Ai Inc Systems and methods for using sequencing data for pathogen detection
US12205675B2 (en) 2019-07-03 2025-01-21 Bostongene Corporation Techniques for bias correction in sequence data
US20240186001A1 (en) * 2019-10-16 2024-06-06 Icahn School Of Medicine At Mount Sinai Systems and methods for detecting a disease condition
US20240087690A1 (en) * 2020-05-12 2024-03-14 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
US20240277807A1 (en) * 2021-06-11 2024-08-22 Acceleron Pharma Inc. Actrii proteins and uses thereof
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
US7258838B2 (en) 1999-06-22 2007-08-21 President And Fellows Of Harvard College Solid state molecular probe device
EP2383776B1 (en) 1999-06-22 2015-02-25 President and Fellows of Harvard College Solid state nanopore device for evaluating biopolymers
US7238485B2 (en) 2004-03-23 2007-07-03 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
US7972858B2 (en) 2004-08-13 2011-07-05 President And Fellows Of Harvard College 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
CA2858455A1 (en) * 2011-12-09 2013-06-13 Pronota N.V. Ltbp2 as a biomarker for lung injury
CN107099581B (zh) * 2012-03-27 2021-07-13 弗·哈夫曼-拉罗切有限公司 预测、诊断和治疗特发性肺纤维化的方法
CN105247075B (zh) * 2013-03-15 2019-02-15 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
US20170335396A1 (en) * 2014-11-05 2017-11-23 Veracyte, Inc. Systems and methods of diagnosing idiopathic pulmonary fibrosis on transbronchial biopsies using machine learning and high dimensional transcriptional data

Also Published As

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

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