HRP20221116T1 - Postupci i uređaji za određivanje stanja bolesti u realnom vremenu na bazi nukleinske kiseline - Google Patents
Postupci i uređaji za određivanje stanja bolesti u realnom vremenu na bazi nukleinske kiseline Download PDFInfo
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- HRP20221116T1 HRP20221116T1 HRP20221116TT HRP20221116T HRP20221116T1 HR P20221116 T1 HRP20221116 T1 HR P20221116T1 HR P20221116T T HRP20221116T T HR P20221116TT HR P20221116 T HRP20221116 T HR P20221116T HR P20221116 T1 HRP20221116 T1 HR P20221116T1
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- 238000000034 method Methods 0.000 title claims 12
- 150000007523 nucleic acids Chemical class 0.000 title claims 8
- 201000010099 disease Diseases 0.000 title claims 7
- 208000037265 diseases, disorders, signs and symptoms Diseases 0.000 title claims 7
- 108020004707 nucleic acids Proteins 0.000 title claims 6
- 102000039446 nucleic acids Human genes 0.000 title claims 6
- 244000005700 microbiome Species 0.000 claims 33
- 241000894007 species Species 0.000 claims 17
- 230000002068 genetic effect Effects 0.000 claims 9
- 239000012472 biological sample Substances 0.000 claims 5
- 238000012163 sequencing technique Methods 0.000 claims 5
- 208000015181 infectious disease Diseases 0.000 claims 3
- 208000035473 Communicable disease Diseases 0.000 claims 2
- 108091028043 Nucleic acid sequence Proteins 0.000 claims 2
- 206010028980 Neoplasm Diseases 0.000 claims 1
- 201000011510 cancer Diseases 0.000 claims 1
- 238000013507 mapping Methods 0.000 claims 1
Classifications
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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
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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
- 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
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- 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
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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
- C12Q2535/00—Reactions characterised by the assay type for determining the identity of a nucleotide base or a sequence of oligonucleotides
- C12Q2535/122—Massive parallel sequencing
-
- 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
- G16B35/00—ICT specially adapted for in silico combinatorial libraries of nucleic acids, proteins or peptides
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- Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
- Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
- Y02A—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE
- Y02A90/00—Technologies having an indirect contribution to adaptation to climate change
- Y02A90/10—Information and communication technologies [ICT] supporting adaptation to climate change, e.g. for weather forecasting or climate simulation
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- Chemical & Material Sciences (AREA)
- Life Sciences & Earth Sciences (AREA)
- Proteomics, Peptides & Aminoacids (AREA)
- Analytical Chemistry (AREA)
- Organic Chemistry (AREA)
- Health & Medical Sciences (AREA)
- Engineering & Computer Science (AREA)
- Zoology (AREA)
- Wood Science & Technology (AREA)
- Physics & Mathematics (AREA)
- Immunology (AREA)
- Genetics & Genomics (AREA)
- Biotechnology (AREA)
- Bioinformatics & Cheminformatics (AREA)
- General Health & Medical Sciences (AREA)
- Biophysics (AREA)
- General Engineering & Computer Science (AREA)
- Microbiology (AREA)
- Molecular Biology (AREA)
- Biochemistry (AREA)
- Pathology (AREA)
- Theoretical Computer Science (AREA)
- Spectroscopy & Molecular Physics (AREA)
- Medical Informatics (AREA)
- Evolutionary Biology (AREA)
- Bioinformatics & Computational Biology (AREA)
- Hospice & Palliative Care (AREA)
- Oncology (AREA)
- Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
Claims (11)
1. Postupak za određivanje prisustva mikroorganizama u subjektu koji sadrži:
(a) sekvenciranje nukleinskih kiselina prisutnih u biološkom uzorku dobivenom od subjekta da bi se dobio veći broj očitavanja sekvence nukleinske kiseline;
(b) uspoređivanje očitavanja sekvence dobivene u koraku (a) sa jednom ili više baza podataka koje sadrže genetske informacije od kontrolnog subjekta iste vrste i genetičke informacije iz većeg broja mikroorganizama da bi se utvrdilo da li se uspoređeno očitavanje sekvence mapira u vrsti sadržanoj u jednoj ili više baza podataka;
(c) određivanje tijekom vremena broja uspoređenih očitavanja sekvence koja se mapiraju u određenom mikroorganizmu i broja uspoređenih očitavanja sekvence koja se mapiraju u vrsti; i
(d) izračunavanje ocijene značajnosti tijekom vremena za vjerojatnost pronalaženja kod subjekta uspoređenog očitavanja sekvence koje se mapira u određenom mikroorganizmu na temelju broja uspoređenih očitavanja sekvence koja se mapiraju u određenom mikroorganizmu i broja uspoređenih očitavanja sekvence koja se mapiraju u vrsti, pri čemu kada ocjena značajnosti za određeni mikroorganizam dostigne ili premaši graničnu vrijednost, utvrđuje se da je određeni mikroorganizam prisutan u subjektu.
2. Postupak za određivanje prisustva mikroorganizama u subjektu koji sadrži:
korak izračunavanja tijekom vremena ocjene značajnosti za vjerojatnost pronalaženja kod subjekta očitavanja sekvence koje se mapira u određenom mikroorganizmu na temelju broja očitavanja sekvence koja se mapiraju u određenom mikroorganizmu i broja očitavanja sekvence koja se mapiraju u vrsti, pri čemu kada ocjena značajnosti za određeni mikroorganizam dostiže ili premašuje graničnu vrijednost, utvrđeno je da je određeni mikroorganizam prisutan u subjektu,
pri čemu se očitavanja sekvence koja se mapiraju u određenom mikroorganizmu i očitavanja sekvence koja se mapiraju u vrsti dobivaju uspoređivanjem očitavanja sekvence sa jednom ili više baza podataka koje sadrže genetske informacije od kontrolnog subjekta iste vrste i genetske informacije od većeg broja mikroorganizama da bi se utvrdilo da li se uspoređeno očitavanje sekvence mapira ili ne u vrsti koja se nalazi u jednoj ili više baza podataka, i pri čemu se očitavanja sekvence generiraju sekvenciranjem nukleinskih kiselina prisutnih u biološkom uzorku dobivenom od subjekta.
3. Postupak za određivanje prisustva mikroorganizama u subjektu koji sadrži:
(a) korak određivanja tijekom vremena broja očitavanja sekvence koja se mapiraju u određenom mikroorganizmu i broja očitavanja sekvence koja se mapiraju u vrsti, pri čemu se očitavanja sekvence dobivaju uspoređivanjem očitavanja sekvence sa jednom ili više baza podataka koje sadrže genetske informacije iz kontrolnog subjekta iste vrste i genetske informacije iz većeg broja mikroorganizama da bi se utvrdilo da li se očitavanje sekvence mapira u vrsti koja se nalazi u jednoj ili više baza podataka, i pri čemu se očitavanja sekvence generiraju sekvenciranjem nukleinskih kiselina prisutnih u biološkom uzorku dobivenom od subjekta; i
(b) izračunavanje ocjene značajnosti tijekom vremena za vjerojatnost pronalaženja kod subjekta očitavanja sekvence koja se mapiraju određenom mikroorganizmu na temelju broja očitavanja sekvence koja se mapiraju u određenom mikroorganizmu i broja očitavanja sekvence koja se mapiraju u vrsti, pri čemu kada ocjena značajnosti za određeni mikroorganizam dostiže ili premašuje graničnu vrijednost, utvrđuje se da je određeni mikroorganizam prisutan u subjektu.
4. Postupak prema bilo kojem od zahtjeva 1 do 3, naznačen time što, kada ocjena značajnosti za određeni mikroorganizam dostigne ili premaši graničnu vrijednost, određeni mikroorganizam se utvrđuje kao relevantan za uzrokovanje bolesti kod subjekta.
5. Postupak prema zahtjevu 4, naznačen time što, kada ocjena značajnosti za određeni mikroorganizam premašuje graničnu vrijednost sa nekoliko očitavanja sekvence, smatra se da je bolest koja je posljedica prisustva mikroorganizma teška.
6. Postupak za određivanje prisustva stanja bolesti kod subjekta koji sadrži:
korak izračunavanja tijekom vremena ocjene značajnosti za vjerojatnost pronalaženja u subjektu očitavanja sekvence koje se ne mapira u kontrolnom subjektu na temelju broja očitavanja sekvence koja se ne mapiraju u kontrolnom subjektu i broja očitavanja sekvence koja se mapiraju u kontrolnom subjektu, pri čemu kada ocjena značajnosti dostigne ili premaši graničnu vrijednost, utvrđuje se da je stanje bolesti prisutno kod subjekta,
pri čemu se očitavanja sekvence koja se mapiraju u kontrolnom subjektu i očitavanja sekvence koja se ne mapiraju u kontrolnom subjektu dobivaju uspoređivanjem očitavanja sekvence sa jednom ili više baza podataka koje sadrže genetske informacije od kontrolnog subjekta iste vrste da bi se utvrdilo da li se ili ne uspoređeno očitavanje sekvence mapira u kontrolnom subjektu, i pri čemu se očitavanja sekvence generiraju sekvenciranjem nukleinskih kiselina prisutnih u biološkom uzorku dobivenom od subjekta.
7. Postupak prema zahtjevu 6, naznačen time što, stanje bolesti je rak.
8. Postupak prema zahtjevu 6, naznačen time što, stanje bolesti je infekcija uzrokovana mikroorganizmom.
9. Postupak za dijagnosticiranje infektivne bolesti uzrokovane mikroorganizmima u subjektu koji sadrži:
(a) sekvenciranje nukleinskih kiselina prisutnih u biološkom uzorku dobivenom od subjekta da bi se dobio veći broj očitavanja sekvence nukleinske kiseline;
(b) uspoređivanje očitavanja sekvence dobivene u koraku (a) sa jednom ili više baza podataka koje sadrže genetske informacije od kontrolnog subjekta iste vrste i genetske informacije iz više mikroorganizama da bi se utvrdilo da li se uspoređeno očitavanje sekvence mapira u vrsti sadržanoj u jednoj ili više baza podataka;
(c) određivanje tijekom vremena broja uspoređenih očitavanja sekvence koja se mapiraju u određenom mikroorganizmu i broja uspoređenih očitavanja sekvence koja se mapiraju u vrsti; i
(d) izračunavanje ocjene značajnosti tijekom vremena za vjerojatnost pronalaženja kod subjekta uspoređenog očitavanja sekvence koje se mapira u određenom mikroorganizmu na temelju broja uspoređenih očitavanja sekvence koja se mapiraju u određenom mikroorganizmu i broja uspoređenih očitavanja sekvence koja se mapiraju u vrsti,
pri čemu kada ocjena značajnosti za određeni mikroorganizam dostigne ili premaši graničnu vrijednost, utvrđuje se da određeni mikroorganizam uzrokuje infektivnu bolest.
10. Kompjuterski čitljiv medij za skladištenje koji čuva programski kod koji sadrži instrukcije koje kada ih procesor izvršava, izvršavaju postupak prema bilo kojem od zahtjeva 1 do 9.
11. Kompjuterski sustav koji sadrži procesor konfiguriran da izvrši postupak prema bilo kojem od zahtjeva 1 do 9.
Applications Claiming Priority (3)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| EP17182104.4A EP3431610A1 (en) | 2017-07-19 | 2017-07-19 | Methods and devices for nucleic acid-based real-time determination of disease states |
| EP18743760.3A EP3655540B1 (en) | 2017-07-19 | 2018-07-18 | Methods and devices for nucleic acid-based real-time determination of disease states |
| PCT/EP2018/069493 WO2019016258A1 (en) | 2017-07-19 | 2018-07-18 | METHODS AND DEVICES FOR THE DETERMINATION OF REAL-TIME PATHOLOGICAL CONDITIONS BASED ON NUCLEIC ACIDS |
Publications (1)
| Publication Number | Publication Date |
|---|---|
| HRP20221116T1 true HRP20221116T1 (hr) | 2022-11-25 |
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Family Applications (1)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| HRP20221116TT HRP20221116T1 (hr) | 2017-07-19 | 2018-07-18 | Postupci i uređaji za određivanje stanja bolesti u realnom vremenu na bazi nukleinske kiseline |
Country Status (21)
| Country | Link |
|---|---|
| US (1) | US11749378B2 (hr) |
| EP (2) | EP3431610A1 (hr) |
| JP (1) | JP7220711B2 (hr) |
| KR (1) | KR102521642B1 (hr) |
| CN (1) | CN110914451A (hr) |
| AU (1) | AU2018303179A1 (hr) |
| CA (1) | CA3069349A1 (hr) |
| DK (1) | DK3655540T3 (hr) |
| ES (1) | ES2927022T3 (hr) |
| HR (1) | HRP20221116T1 (hr) |
| HU (1) | HUE059856T2 (hr) |
| IL (1) | IL272068A (hr) |
| LT (1) | LT3655540T (hr) |
| NZ (1) | NZ759783A (hr) |
| PL (1) | PL3655540T3 (hr) |
| PT (1) | PT3655540T (hr) |
| RS (1) | RS63553B1 (hr) |
| RU (1) | RU2763969C2 (hr) |
| SG (1) | SG11202000365QA (hr) |
| SI (1) | SI3655540T1 (hr) |
| WO (1) | WO2019016258A1 (hr) |
Families Citing this family (2)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| EP3431610A1 (en) | 2017-07-19 | 2019-01-23 | Noscendo GmbH | Methods and devices for nucleic acid-based real-time determination of disease states |
| JP6590417B2 (ja) * | 2017-11-21 | 2019-10-16 | 株式会社バイオーム | 判別装置、判別方法、判別プログラム、判別システム |
Family Cites Families (13)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| GB0601302D0 (en) * | 2006-01-23 | 2006-03-01 | Semikhodskii Andrei | Diagnostic methods and apparatus |
| GB2477439B (en) | 2008-11-07 | 2012-02-15 | Sequenta Inc | Methods for correlating clonotypes with a disease in a patient |
| US9689044B2 (en) * | 2011-01-26 | 2017-06-27 | The Brigham And Women's Hospital, Inc. | Assays and methods to sequence microbes directly from immune complexes |
| CN103403186B (zh) * | 2011-01-26 | 2015-09-16 | 雷蒙特亚特特拉维夫大学有限公司 | 利用小rna测序消减和组装检测微生物感染 |
| AU2012308092A1 (en) * | 2011-09-13 | 2014-04-17 | Commonwealth Scientific And Industrial Research Organisation | Detection of viral infection |
| CN103305607B (zh) * | 2013-05-22 | 2015-04-15 | 宁波大学 | 一种基于微生物群落变化的水产养殖病害预测方法 |
| KR102649364B1 (ko) * | 2013-11-07 | 2024-03-20 | 더 보드 어브 트러스티스 어브 더 리랜드 스탠포드 주니어 유니버시티 | 인간 마이크로바이옴 및 그의 성분의 분석을 위한 무세포 핵산 |
| JP2017510871A (ja) * | 2014-01-10 | 2017-04-13 | セブン ブリッジズ ジェノミクス インコーポレイテッド | リードマッピングにおける公知の対立遺伝子の使用のためのシステム及び方法 |
| WO2016127944A1 (en) * | 2015-02-10 | 2016-08-18 | The Chinese University Of Hong Kong | Detecting mutations for cancer screening and fetal analysis |
| US10724110B2 (en) | 2015-09-01 | 2020-07-28 | Seven Bridges Genomics Inc. | Systems and methods for analyzing viral nucleic acids |
| EP3141612A1 (en) * | 2015-09-10 | 2017-03-15 | Fraunhofer-Gesellschaft zur Förderung der angewandten Forschung e.V. | Method and device for nucleic acid based diagnostic approaches including the determination of a deviant condtion, especially a health condition and/or pathogenic condition of a sample |
| CN106636423A (zh) * | 2017-01-12 | 2017-05-10 | 杨俊杰 | 口腔菌群多样性的分析方法及与疾病相关的菌群标志物 |
| EP3431610A1 (en) | 2017-07-19 | 2019-01-23 | Noscendo GmbH | Methods and devices for nucleic acid-based real-time determination of disease states |
-
2017
- 2017-07-19 EP EP17182104.4A patent/EP3431610A1/en not_active Withdrawn
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2018
- 2018-07-18 RU RU2020103728A patent/RU2763969C2/ru active
- 2018-07-18 JP JP2020524679A patent/JP7220711B2/ja active Active
- 2018-07-18 KR KR1020207001521A patent/KR102521642B1/ko active IP Right Grant
- 2018-07-18 WO PCT/EP2018/069493 patent/WO2019016258A1/en unknown
- 2018-07-18 SI SI201830760T patent/SI3655540T1/sl unknown
- 2018-07-18 AU AU2018303179A patent/AU2018303179A1/en active Pending
- 2018-07-18 CA CA3069349A patent/CA3069349A1/en active Pending
- 2018-07-18 CN CN201880047711.0A patent/CN110914451A/zh active Pending
- 2018-07-18 HR HRP20221116TT patent/HRP20221116T1/hr unknown
- 2018-07-18 PT PT187437603T patent/PT3655540T/pt unknown
- 2018-07-18 NZ NZ759783A patent/NZ759783A/en unknown
- 2018-07-18 RS RS20220846A patent/RS63553B1/sr unknown
- 2018-07-18 HU HUE18743760A patent/HUE059856T2/hu unknown
- 2018-07-18 SG SG11202000365QA patent/SG11202000365QA/en unknown
- 2018-07-18 US US16/631,523 patent/US11749378B2/en active Active
- 2018-07-18 LT LTEPPCT/EP2018/069493T patent/LT3655540T/lt unknown
- 2018-07-18 EP EP18743760.3A patent/EP3655540B1/en active Active
- 2018-07-18 DK DK18743760.3T patent/DK3655540T3/da active
- 2018-07-18 ES ES18743760T patent/ES2927022T3/es active Active
- 2018-07-18 PL PL18743760.3T patent/PL3655540T3/pl unknown
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2020
- 2020-01-15 IL IL272068A patent/IL272068A/en unknown
Also Published As
| Publication number | Publication date |
|---|---|
| KR102521642B1 (ko) | 2023-04-14 |
| EP3655540B1 (en) | 2022-08-31 |
| EP3655540A1 (en) | 2020-05-27 |
| SG11202000365QA (en) | 2020-02-27 |
| IL272068A (en) | 2020-03-31 |
| EP3431610A1 (en) | 2019-01-23 |
| LT3655540T (lt) | 2022-10-10 |
| US20200176079A1 (en) | 2020-06-04 |
| WO2019016258A1 (en) | 2019-01-24 |
| KR20200029472A (ko) | 2020-03-18 |
| JP2020527364A (ja) | 2020-09-10 |
| NZ759783A (en) | 2023-02-24 |
| HUE059856T2 (hu) | 2023-01-28 |
| PT3655540T (pt) | 2022-09-20 |
| JP7220711B2 (ja) | 2023-02-10 |
| RU2020103728A (ru) | 2021-08-19 |
| RS63553B1 (sr) | 2022-09-30 |
| RU2020103728A3 (hr) | 2021-08-19 |
| ES2927022T3 (es) | 2022-11-02 |
| PL3655540T3 (pl) | 2022-10-03 |
| SI3655540T1 (sl) | 2022-11-30 |
| AU2018303179A1 (en) | 2020-01-02 |
| CA3069349A1 (en) | 2019-01-24 |
| DK3655540T3 (da) | 2022-09-19 |
| RU2763969C2 (ru) | 2022-01-12 |
| CN110914451A (zh) | 2020-03-24 |
| US11749378B2 (en) | 2023-09-05 |
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