SG11201908571UA - Leveraging sequence-based fecal microbial community survey data to identify a composite biomarker for colorectal cancer - Google Patents

Leveraging sequence-based fecal microbial community survey data to identify a composite biomarker for colorectal cancer

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Publication number
SG11201908571UA
SG11201908571UA SG11201908571UA SG11201908571UA SG 11201908571U A SG11201908571U A SG 11201908571UA SG 11201908571U A SG11201908571U A SG 11201908571UA SG 11201908571U A SG11201908571U A SG 11201908571UA
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Singapore
Prior art keywords
international
rule
colorectal cancer
sequence
california
Prior art date
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Inventor
Todd Zachary Desantis
Thomas Weinmaier
Manasi Sanjay Shah
Emily Brooke Hollister-Branton
Original Assignee
Second Genome Inc
Baylor College Medicine
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Publication date
Application filed by Second Genome Inc, Baylor College Medicine filed Critical Second Genome Inc
Publication of SG11201908571UA publication Critical patent/SG11201908571UA/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
    • C12Q1/6888—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms
    • 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
    • G01N33/574—Immunoassay; Biospecific binding assay; Materials therefor for cancer
    • G01N33/57407—Specifically defined cancers
    • G01N33/57446—Specifically defined cancers of stomach or intestine
    • 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
    • C12Q1/6816—Hybridisation assays characterised by the detection means
    • 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
    • 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
    • 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
    • G01N33/574—Immunoassay; Biospecific binding assay; Materials therefor for cancer
    • G01N33/57407—Specifically defined cancers
    • 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
    • G01N33/574—Immunoassay; Biospecific binding assay; Materials therefor for cancer
    • G01N33/57407—Specifically defined cancers
    • G01N33/57419—Specifically defined cancers of colon
    • 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
    • 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
    • G16B50/00—ICT programming tools or database systems specially adapted for bioinformatics
    • 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

Abstract

Analysisflow: W O 18/ 17 0396 Al Advanm Search • r , ons) oriklge of ...aioaaal pre-oxieting studio (n.2) Rao sequence da/o evailabledared n.13 Saain Select - UPPRSE (SS4.1P) Saroples<100 isadi pa stook =mg axe n< learrOes Paftano rkomeeled to metre chemotherapy or Whammy IndiAchal OTIJ WoMP*. ly • :SUP as d CRA Pa DESeq2 - 7 OKI/motel. CRA Vs ill.dy*Olsoese_sitte control FIG. 1 Per ftry0ESeq2 7 ONet.thre nen mo DESeq2 result brat lest508.5er6orier ei CRC Miele ari or \ 4 Ckle: Rondo Ifieds model tuba duly as a Wan fled FOI ....iambs] pen coat V. ailiassery(Cia aCerhol,CKVsGRN k URN aholl (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (43) International Publication Date 20 September 2018 (20.09.2018) WIP0 I PCT omit VIII °nolo olomonoolioiliflo oimIE (10) International Publication Number WO 2018/170396 Al (51) International Patent Classification: C12Q 1/689 (2018.01) C12Q 1/04 (2006.01) C12Q 1/6888 (2018.01) (21) International Application Number: PCT/US2018/022862 (22) International Filing Date: 16 March 2018 (16.03.2018) (25) Filing Language: English (26) Publication Language: English (30) Priority Data: 62/472,863 17 March 2017 (17.03.2017) US (71) Applicants: SECOND GENOME, INC. [US/US]; 341 Allerton Avenue, South San Francisco, California 94080 (US). BAYLOR COLLEGE OF MEDICINE [US/US]; One Baylor Plaza, Houston, Texas 77030 (US). (72) Inventors: DESANTIS, Todd Zachary; 626 Salem Court, Livermore, California 94551 (US). WEINMAIER, Thomas; 728 Jamestown Avenue, San Francisco, Califor- nia 94124 (US). SHAH, Manasi Sanjay; 50 Washington St, Apt. 12, Santa Clara, California 95050 (US). HOL- LISTER-BRANTON, Emily Brooke; 5514 Willowbend Blvd., Houston, Texas 77096 (US). (74) Agent: HOLLY, David Christopher et al.; Cooley LLP, 1299 Pennsylvania Avenue, N.W., Suite 700, Washington, District of Columbia 20004 (US). (81) Designated States (unless otherwise indicated, for every kind of national protection available): AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IR, IS, JO, JP, KE, KG, KH, KN, KP, KR, KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (84) Designated States (unless otherwise indicated, for every kind of regional protection available): ARIPO (BW, GH, GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, TZ, UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, TJ, TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, DK, EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, LV, MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, SM, (54) Title: LEVERAGING SEQUENCE-BASED FECAL MICROBIAL COMMUNITY SURVEY DATA TO IDENTIFY A COM- POSITE BIOMARKER FOR COLORECTAL CANCER (57) : The present disclosure provides fecal microbial markers for di- agnosing colorectal cancer and colorectal adenoma. The present disclosure al- so provides methods for diagnosing colorectal cancer and colorectal adenoma using these intestinal microbial markers. [Continued on next page] WO 2018/170396 Al MIDEDIMOMOIDEIREEMOMMEHMOHOROMEMOIS TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, GW, KM, ML, MR, NE, SN, TD, TG). Declarations under Rule 4.17: as to applicant's entitlement to apply for and be granted a patent (Rule 4.17(11)) as to the applicant's entitlement to claim the priority of the earlier application (Rule 4.17(iii)) Published: with international search report (Art. 21(3)) before the expiration of the time limit for amending the claims and to be republished in the event of receipt of amendments (Rule 48.2(h)) with sequence listing part of description (Rule 5.2(a))
SG11201908571U 2017-03-17 2018-03-16 Leveraging sequence-based fecal microbial community survey data to identify a composite biomarker for colorectal cancer SG11201908571UA (en)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US201762472863P 2017-03-17 2017-03-17
PCT/US2018/022862 WO2018170396A1 (en) 2017-03-17 2018-03-16 Leveraging sequence-based fecal microbial community survey data to identify a composite biomarker for colorectal cancer

Publications (1)

Publication Number Publication Date
SG11201908571UA true SG11201908571UA (en) 2019-10-30

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US (1) US20200011873A1 (en)
EP (1) EP3596237A4 (en)
JP (1) JP2020513856A (en)
KR (1) KR20190140925A (en)
CN (1) CN110637097A (en)
AU (1) AU2018234737A1 (en)
CA (1) CA3056789A1 (en)
SG (1) SG11201908571UA (en)
WO (1) WO2018170396A1 (en)

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WO2020178297A1 (en) * 2019-03-04 2020-09-10 Fundación Para La Investigación Biomédica Del Hospital Ramón Y Cajal Anal bacterial biomarkers for the diagnosis of anal precancerous lesions
CN109943636B (en) * 2019-04-11 2020-01-24 上海宝藤生物医药科技股份有限公司 Colorectal cancer microbial marker and application thereof
CN110512015A (en) * 2019-09-11 2019-11-29 苏州普瑞森基因科技有限公司 A kind of intestinal cancer biomarker combinations object and its application
CN117305487A (en) * 2020-05-27 2023-12-29 微度(苏州)生物科技有限公司 Biomarker composition for early diagnosis of colorectal cancer and application
KR102623834B1 (en) * 2020-07-13 2024-01-12 서울대학교병원 Composition for preventing or treating colon cancer in male through changes in gut microbiota comprising estrogen
CN112029882B (en) * 2020-09-17 2022-09-09 中国农业科学院植物保护研究所 Method for separating beneficial microorganisms from environment
KR102241357B1 (en) * 2020-10-20 2021-04-16 주식회사 에이치이엠 Method and apparatus for diagnosing colon plyp using machine learning model
CN112410449A (en) * 2021-01-25 2021-02-26 天津奇云诺德生物医学有限公司 Microbial marker related to colorectal cancer and application thereof
CN112725457B (en) * 2021-03-08 2022-09-02 温州医科大学 Intestinal flora marker for judging intestinal cancer and detection method thereof
CN112863606B (en) * 2021-03-08 2022-07-26 杭州微数生物科技有限公司 Genome database for bacterium identification and typing analysis and identification and typing analysis method
KR102304402B1 (en) * 2021-03-26 2021-09-24 주식회사 에이치이엠파마 Method and diagnostic apparatus for determining obesity using machine learning model
CN114032278A (en) * 2021-03-26 2022-02-11 上海交通大学医学院 Microbial marker of colorectal cancer and application thereof
KR102304399B1 (en) * 2021-03-26 2021-09-24 주식회사 에이치이엠파마 Method and diagnostic apparatus for determining hyperglycemia using machine learning model
KR20220158948A (en) * 2021-05-25 2022-12-02 주식회사 에이치이엠파마 Method and diagnostic apparatus for determining gasbloating using machine learning model
WO2023049842A1 (en) * 2021-09-23 2023-03-30 Flagship Pioneering Innovations Vi, Llc Diagnosis and treatment of diseases and conditions of the intestinal tract
CN114369673B (en) * 2022-01-06 2023-07-14 同济大学 Colorectal adenoma biomarker, kit and screening method of biomarker
CN114373508B (en) * 2022-01-24 2024-02-02 浙江天科高新技术发展有限公司 Strain identification method based on 16S rDNA sequence
CN114496088B (en) * 2022-01-27 2023-06-20 中国农业科学院兰州兽医研究所 Echinococcosis microbial marker, screening method and application thereof
WO2023242413A1 (en) * 2022-06-17 2023-12-21 Barcelona Supercomputing Center - Centro Nacional De Supercomputación Method for screening for colorectal cancer using fecal microbiome profiling

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WO2015018307A1 (en) * 2013-08-06 2015-02-12 Bgi Shenzhen Co., Limited Biomarkers for colorectal cancer

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WO2018170396A1 (en) 2018-09-20
AU2018234737A1 (en) 2019-10-10
EP3596237A1 (en) 2020-01-22
KR20190140925A (en) 2019-12-20
CA3056789A1 (en) 2018-09-20
CN110637097A (en) 2019-12-31
JP2020513856A (en) 2020-05-21
US20200011873A1 (en) 2020-01-09
EP3596237A4 (en) 2021-01-27

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