CA3010311A1 - Single cell genomic profiling of circulating tumor cells (ctcs) in metastatic disease to characterize disease heterogeneity - Google Patents

Single cell genomic profiling of circulating tumor cells (ctcs) in metastatic disease to characterize disease heterogeneity Download PDF

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Publication number
CA3010311A1
CA3010311A1 CA3010311A CA3010311A CA3010311A1 CA 3010311 A1 CA3010311 A1 CA 3010311A1 CA 3010311 A CA3010311 A CA 3010311A CA 3010311 A CA3010311 A CA 3010311A CA 3010311 A1 CA3010311 A1 CA 3010311A1
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Prior art keywords
ctcs
ctc
cancer
patient
heterogeneity
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CA3010311A
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English (en)
French (fr)
Inventor
Ryan DITTAMORE
Dena Marrinucci
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Epic Sciences Inc
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Epic Sciences 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
    • C12Q1/6876—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
    • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/575—Immunoassay; Biospecific binding assay; Materials therefor for cancer
    • G01N33/57555—Immunoassay; Biospecific binding assay; Materials therefor for cancer of the prostate
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N15/00—Investigating characteristics of particles; Investigating permeability, pore-volume or surface-area of porous materials
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N15/00—Investigating characteristics of particles; Investigating permeability, pore-volume or surface-area of porous materials
    • G01N15/10—Investigating individual particles
    • G01N15/14—Optical investigation techniques, e.g. flow cytometry
    • G01N15/1429—Signal processing
    • G01N15/1433—Signal processing using image recognition
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N21/00—Investigating or analysing materials by the use of optical means, i.e. using sub-millimetre waves, infrared, visible or ultraviolet light
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/5005—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/5005—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells
    • G01N33/5091—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells for testing the pathological state of an organism
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/52—Use of compounds or compositions for colorimetric, spectrophotometric or fluorometric investigation, e.g. use of reagent paper and including single- and multilayer analytical elements
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/575—Immunoassay; Biospecific binding assay; Materials therefor for cancer
    • G01N33/5758—Immunoassay; Biospecific binding assay; Materials therefor for cancer involving compounds serving as markers for tumours, cancers or neoplasias, e.g. cellular determinants, receptors, heat shock/stress proteins, A-protein, oligosaccharides or metabolites
    • G01N33/57585—Immunoassay; Biospecific binding assay; Materials therefor for cancer involving compounds serving as markers for tumours, cancers or neoplasias, e.g. cellular determinants, receptors, heat shock/stress proteins, A-protein, oligosaccharides or metabolites involving compounds identifiable in body fluids
    • 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
    • C12Q2537/00—Reactions characterised by the reaction format or use of a specific feature
    • C12Q2537/10—Reactions characterised by the reaction format or use of a specific feature the purpose or use of
    • C12Q2537/16—Assays for determining copy number or wherein the copy number is of special importance
    • 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
    • C12Q2600/106—Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism
    • 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
    • C12Q2600/156—Polymorphic or mutational markers
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N15/00—Investigating characteristics of particles; Investigating permeability, pore-volume or surface-area of porous materials
    • G01N15/10—Investigating individual particles
    • G01N2015/1006—Investigating individual particles for cytology

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  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Immunology (AREA)
  • Engineering & Computer Science (AREA)
  • Molecular Biology (AREA)
  • Pathology (AREA)
  • Analytical Chemistry (AREA)
  • Hematology (AREA)
  • Biomedical Technology (AREA)
  • Urology & Nephrology (AREA)
  • General Health & Medical Sciences (AREA)
  • Physics & Mathematics (AREA)
  • Biochemistry (AREA)
  • General Physics & Mathematics (AREA)
  • Microbiology (AREA)
  • Biotechnology (AREA)
  • Food Science & Technology (AREA)
  • Cell Biology (AREA)
  • Medicinal Chemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Organic Chemistry (AREA)
  • Zoology (AREA)
  • Genetics & Genomics (AREA)
  • Wood Science & Technology (AREA)
  • Dispersion Chemistry (AREA)
  • Tropical Medicine & Parasitology (AREA)
  • Hospice & Palliative Care (AREA)
  • Biophysics (AREA)
  • Oncology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • General Engineering & Computer Science (AREA)
  • Signal Processing (AREA)
  • Physiology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Investigating Or Analysing Biological Materials (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)
  • Computer Vision & Pattern Recognition (AREA)
CA3010311A 2016-01-06 2017-01-05 Single cell genomic profiling of circulating tumor cells (ctcs) in metastatic disease to characterize disease heterogeneity Pending CA3010311A1 (en)

Applications Claiming Priority (5)

Application Number Priority Date Filing Date Title
US201662275659P 2016-01-06 2016-01-06
US62/275,659 2016-01-06
US201662344703P 2016-06-02 2016-06-02
US62/344,703 2016-06-02
PCT/US2017/012317 WO2017120324A1 (en) 2016-01-06 2017-01-05 Single cell genomic profiling of circulating tumor cells (ctcs) in metastatic disease to characterize disease heterogeneity

Publications (1)

Publication Number Publication Date
CA3010311A1 true CA3010311A1 (en) 2017-07-13

Family

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Family Applications (1)

Application Number Title Priority Date Filing Date
CA3010311A Pending CA3010311A1 (en) 2016-01-06 2017-01-05 Single cell genomic profiling of circulating tumor cells (ctcs) in metastatic disease to characterize disease heterogeneity

Country Status (8)

Country Link
US (2) US20190025312A1 (cg-RX-API-DMAC10.html)
EP (1) EP3400311A4 (cg-RX-API-DMAC10.html)
JP (3) JP2019502384A (cg-RX-API-DMAC10.html)
CN (2) CN108884494A (cg-RX-API-DMAC10.html)
AU (2) AU2017205443A1 (cg-RX-API-DMAC10.html)
CA (1) CA3010311A1 (cg-RX-API-DMAC10.html)
EA (1) EA201891571A1 (cg-RX-API-DMAC10.html)
WO (1) WO2017120324A1 (cg-RX-API-DMAC10.html)

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JP6352588B2 (ja) 2009-10-21 2018-07-04 ザ スクリプス リサーチ インスティテュート 希少ではない細胞を用いて希少細胞を検出する方法
WO2015112955A1 (en) 2014-01-27 2015-07-30 Epic Sciences, Inc. Circulating tumor cell diagnostics for prostate cancer biomarkers
US10545151B2 (en) 2014-02-21 2020-01-28 Epic Sciences, Inc. Methods for analyzing rare circulating cells
US11514289B1 (en) * 2016-03-09 2022-11-29 Freenome Holdings, Inc. Generating machine learning models using genetic data
WO2018122056A1 (en) * 2016-12-30 2018-07-05 Ventana Medical Systems, Inc. Automated system and method for creating and executing a scoring guide to assist in the analysis of tissue specimen
EP3431611A1 (en) 2017-07-21 2019-01-23 Menarini Silicon Biosystems S.p.A. Improved method and kit for the generation of dna libraries for massively parallel sequencing
US11348661B2 (en) 2018-05-14 2022-05-31 Tempus Labs, Inc. Predicting total nucleic acid yield and dissection boundaries for histology slides
US10957041B2 (en) 2018-05-14 2021-03-23 Tempus Labs, Inc. Determining biomarkers from histopathology slide images
CN109060989B (zh) * 2018-08-29 2021-07-30 重庆市肿瘤研究所 应用iTRAQ技术研究三阴性乳腺癌外泌体差异表达蛋白的方法
CN109658981B (zh) * 2018-12-10 2022-10-04 海南大学 一种单细胞测序的数据分类方法
SG11202109958SA (en) * 2019-03-26 2021-10-28 Tempus Labs Inc Determining biomarkers from histopathology slide images
KR102343947B1 (ko) * 2019-09-30 2021-12-27 주식회사 피디젠 환자 정보 분석을 이용한 암 재발 및 전이 모니터링 시스템을 이용한 비즈니스모델
EP3965119A1 (en) * 2020-09-04 2022-03-09 Koninklijke Philips N.V. Methods for estimating heterogeneity of a tumour based on values for two or more genome mutation and/or gene expression related parameter, as well as corresponding devices
CN112164420B (zh) * 2020-09-07 2021-07-20 厦门艾德生物医药科技股份有限公司 一种基因组瘢痕模型的建立方法
EP4327334A4 (en) * 2021-04-19 2025-04-30 F. Hoffmann-La Roche AG Methods and systems for predicting genetic alterations from pathology slide images
EP4445141A1 (en) * 2021-12-07 2024-10-16 Epic Sciences, Inc. Enhanced characterization of breast cancer
US20250157650A1 (en) * 2021-12-21 2025-05-15 Foundation Medicine, Inc. Methods and systems for predicting genomic profiling success

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CA2623405C (en) * 2005-09-20 2014-11-25 Immunivest Corporation Methods and composition to generate unique sequence dna probes labeling of dna probes and the use of these probes
DK2981624T3 (da) * 2013-04-05 2020-03-02 Myriad Genetics Inc Fremgangsmåder til vurdering af homolog rekombinationsdeficiens og forudsigelse af respons på cancerbehandling
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US10745760B2 (en) * 2014-01-17 2020-08-18 University Health Network Biopsy-driven genomic signature for prostate cancer prognosis
WO2015112955A1 (en) * 2014-01-27 2015-07-30 Epic Sciences, Inc. Circulating tumor cell diagnostics for prostate cancer biomarkers
WO2015112999A1 (en) * 2014-01-27 2015-07-30 Epic Sciences, Inc. Detection of prostate specific membrane antigen (psma) expression on circulating tumor cells (ctc)
EA201691499A1 (ru) * 2014-01-30 2017-02-28 Эпик Сайенсиз, Инк. Диагностика с помощью циркулирующих опухолевых клеток биомаркеров, позволяющих предсказывать резистентность по отношению к направленным на андрогеновый рецептор (ar) терапиям

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Publication number Publication date
WO2017120324A1 (en) 2017-07-13
EP3400311A4 (en) 2019-07-03
CN115323054A (zh) 2022-11-11
US20220390451A1 (en) 2022-12-08
JP2021118689A (ja) 2021-08-12
CN108884494A (zh) 2018-11-23
EP3400311A1 (en) 2018-11-14
EA201891571A1 (ru) 2019-01-31
JP2019502384A (ja) 2019-01-31
JP2023116530A (ja) 2023-08-22
AU2023202282A1 (en) 2023-05-11
AU2017205443A1 (en) 2018-07-19
US20190025312A1 (en) 2019-01-24

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