WO2023147445A3 - Cell-free rna biomarkers for the detection of cancer or predisposition to cancer - Google Patents

Cell-free rna biomarkers for the detection of cancer or predisposition to cancer Download PDF

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Publication number
WO2023147445A3
WO2023147445A3 PCT/US2023/061410 US2023061410W WO2023147445A3 WO 2023147445 A3 WO2023147445 A3 WO 2023147445A3 US 2023061410 W US2023061410 W US 2023061410W WO 2023147445 A3 WO2023147445 A3 WO 2023147445A3
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WO
WIPO (PCT)
Prior art keywords
cancer
predisposition
biomarkers
cfrna
differential expression
Prior art date
Application number
PCT/US2023/061410
Other languages
French (fr)
Other versions
WO2023147445A2 (en
Inventor
Thuy NGO
Hyun Ji Kim
Josiah WAGNER
Breeshey ROSKAMS HIETER
Pavana ANUR
Original Assignee
Oregon Health & Science University
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Publication date
Application filed by Oregon Health & Science University filed Critical Oregon Health & Science University
Publication of WO2023147445A2 publication Critical patent/WO2023147445A2/en
Publication of WO2023147445A3 publication Critical patent/WO2023147445A3/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
    • C12Q1/6876—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
    • 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
    • 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
    • C12Q2600/16—Primer sets for multiplex assays
    • 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
    • G16B25/00—ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
    • G16B25/10—Gene or protein expression profiling; Expression-ratio estimation or normalisation
    • 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

Abstract

Methods of detecting or treating cancer or predisposition to cancer are provided, the methods including analyzing a level of one or more cell-free RNA (cfRNA) biomarkers selected from AIDA, CAI, CENPE, CPOX, ELL2, EPB42, HBG1, HBG2, NEK2, NUSAP1, APOE, C3, CP, DHCR24, EGA, FGB, EGG, HRG, IFITM3, ATP IB 1, FPR3, SMC4, TXNDC16, ASPM, WRN, ZRANB2-AS2, BMX, CDC42BPA, KNL1, CACNA1A, ABCB7, HIST1H2BF, PSIP1, TMEM150C, ZC3H6, C9orfl6, CPQ, DYNC1I2, ECM1, and HIST1H2AH, or any combination thereof, in the biological sample; and performing a differential expression analysis comparing the level of each of the one or more cfRNA biomarkers to a corresponding control value (CV); in which differential expression shown by the differential expression analysis between the one or more cfRNA biomarkers and corresponding CVs indicates cancer or a predisposition for cancer in the subject.
PCT/US2023/061410 2022-01-27 2023-01-26 Cell-free rna biomarkers for the detection of cancer or predisposition to cancer WO2023147445A2 (en)

Applications Claiming Priority (4)

Application Number Priority Date Filing Date Title
US202263303970P 2022-01-27 2022-01-27
US63/303,970 2022-01-27
US202263426258P 2022-11-17 2022-11-17
US63/426,258 2022-11-17

Publications (2)

Publication Number Publication Date
WO2023147445A2 WO2023147445A2 (en) 2023-08-03
WO2023147445A3 true WO2023147445A3 (en) 2023-10-19

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Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2023/061410 WO2023147445A2 (en) 2022-01-27 2023-01-26 Cell-free rna biomarkers for the detection of cancer or predisposition to cancer

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WO (1) WO2023147445A2 (en)

Citations (9)

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WO2002074961A1 (en) * 2001-03-15 2002-09-26 Hyseq, Inc. Novel nucleic acids and polypeptides
US20040053248A1 (en) * 2000-12-22 2004-03-18 Tang Y. Tom Novel nucleic acids and polypeptides
US20040171823A1 (en) * 2003-01-14 2004-09-02 Nadler Steven G. Polynucleotides and polypeptides associated with the NF-kappaB pathway
US7462453B2 (en) * 2004-06-01 2008-12-09 Sumitomo Chemical Company, Limited Common marmoset-derived glyceraldehyde-3-phosphate dehydrogenase gene and use thereof
US20100129874A1 (en) * 2008-09-05 2010-05-27 The Washington University Method for multiplexed nucleic acid patch polymerase chain reaction
US20160333415A1 (en) * 2013-01-22 2016-11-17 Otsuka Pharmaceutical Co., Ltd. QUANTIFICATION METHOD FOR EXPRESSION LEVEL OF WT1 mRNA
US20180057842A1 (en) * 2014-11-10 2018-03-01 Murdoch Childrens Research Institute Vectors and methods for targeted integration in loci comprising constitutively expressed genes
WO2020092259A1 (en) * 2018-10-29 2020-05-07 Molecular Stethoscope, Inc. Characterization of bone marrow using cell-free messenger-rna
US20210388451A1 (en) * 2020-06-16 2021-12-16 Grail, Inc. Methods for analysis of cell-free rna

Patent Citations (9)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20040053248A1 (en) * 2000-12-22 2004-03-18 Tang Y. Tom Novel nucleic acids and polypeptides
WO2002074961A1 (en) * 2001-03-15 2002-09-26 Hyseq, Inc. Novel nucleic acids and polypeptides
US20040171823A1 (en) * 2003-01-14 2004-09-02 Nadler Steven G. Polynucleotides and polypeptides associated with the NF-kappaB pathway
US7462453B2 (en) * 2004-06-01 2008-12-09 Sumitomo Chemical Company, Limited Common marmoset-derived glyceraldehyde-3-phosphate dehydrogenase gene and use thereof
US20100129874A1 (en) * 2008-09-05 2010-05-27 The Washington University Method for multiplexed nucleic acid patch polymerase chain reaction
US20160333415A1 (en) * 2013-01-22 2016-11-17 Otsuka Pharmaceutical Co., Ltd. QUANTIFICATION METHOD FOR EXPRESSION LEVEL OF WT1 mRNA
US20180057842A1 (en) * 2014-11-10 2018-03-01 Murdoch Childrens Research Institute Vectors and methods for targeted integration in loci comprising constitutively expressed genes
WO2020092259A1 (en) * 2018-10-29 2020-05-07 Molecular Stethoscope, Inc. Characterization of bone marrow using cell-free messenger-rna
US20210388451A1 (en) * 2020-06-16 2021-12-16 Grail, Inc. Methods for analysis of cell-free rna

Non-Patent Citations (1)

* Cited by examiner, † Cited by third party
Title
MATHIAS UHLEN, ZHANG CHENG, LEE SUNJAE, SJöSTEDT EVELINA, FAGERBERG LINN, BIDKHORI GHOLAMREZA, BENFEITAS RUI, ARIF MUHAMMAD, : "A pathology atlas of the human cancer transcriptome", SCIENCE, AMERICAN ASSOCIATION FOR THE ADVANCEMENT OF SCIENCE, US, vol. 357, no. 6352, 18 August 2017 (2017-08-18), US , pages 1 - 13, XP055693994, ISSN: 0036-8075, DOI: 10.1126/science.aan2507 *

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