SG11201908564RA - Devices, processes, and systems for determination of nucleic acid sequence, expression, copy number, or methylation changes using combined nuclease, ligase, polymerase, and sequencing reactions - Google Patents
Devices, processes, and systems for determination of nucleic acid sequence, expression, copy number, or methylation changes using combined nuclease, ligase, polymerase, and sequencing reactionsInfo
- Publication number
- SG11201908564RA SG11201908564RA SG11201908564RA SG11201908564RA SG 11201908564R A SG11201908564R A SG 11201908564RA SG 11201908564R A SG11201908564R A SG 11201908564RA SG 11201908564R A SG11201908564R A SG 11201908564RA
- Authority
- SG
- Singapore
- Prior art keywords
- international
- polymerase
- mmmmmmmmmmmmmmmmmmmmmmmm
- expression
- processes
- Prior art date
Links
- 238000000034 method Methods 0.000 title abstract 4
- 101710163270 Nuclease Proteins 0.000 title abstract 3
- 238000006243 chemical reaction Methods 0.000 title abstract 3
- 230000011987 methylation Effects 0.000 title abstract 3
- 238000007069 methylation reaction Methods 0.000 title abstract 3
- 102000003960 Ligases Human genes 0.000 title abstract 2
- 108090000364 Ligases Proteins 0.000 title abstract 2
- 108091028043 Nucleic acid sequence Proteins 0.000 title abstract 2
- 150000007523 nucleic acids Chemical group 0.000 title abstract 2
- 238000012163 sequencing technique Methods 0.000 title abstract 2
- 206010028980 Neoplasm Diseases 0.000 abstract 3
- 201000011510 cancer Diseases 0.000 abstract 3
- 239000003795 chemical substances by application Substances 0.000 abstract 2
- 208000005443 Circulating Neoplastic Cells Diseases 0.000 abstract 1
- 108020004414 DNA Proteins 0.000 abstract 1
- 206010061819 Disease recurrence Diseases 0.000 abstract 1
- 108700011259 MicroRNAs Proteins 0.000 abstract 1
- 210000004369 blood Anatomy 0.000 abstract 1
- 239000008280 blood Substances 0.000 abstract 1
- 210000000601 blood cell Anatomy 0.000 abstract 1
- 210000004027 cell Anatomy 0.000 abstract 1
- 238000001514 detection method Methods 0.000 abstract 1
- 210000001808 exosome Anatomy 0.000 abstract 1
- -1 exosomes Proteins 0.000 abstract 1
- 239000002679 microRNA Substances 0.000 abstract 1
- 238000007479 molecular analysis Methods 0.000 abstract 1
- 238000012544 monitoring process Methods 0.000 abstract 1
- 230000035772 mutation Effects 0.000 abstract 1
- 230000008520 organization Effects 0.000 abstract 1
- 238000004393 prognosis Methods 0.000 abstract 1
- 230000005945 translocation Effects 0.000 abstract 1
Classifications
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- B—PERFORMING OPERATIONS; TRANSPORTING
- B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
- B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
- B01L3/00—Containers or dishes for laboratory use, e.g. laboratory glassware; Droppers
- B01L3/50—Containers for the purpose of retaining a material to be analysed, e.g. test tubes
- B01L3/502—Containers for the purpose of retaining a material to be analysed, e.g. test tubes with fluid transport, e.g. in multi-compartment structures
- B01L3/5027—Containers for the purpose of retaining a material to be analysed, e.g. test tubes with fluid transport, e.g. in multi-compartment structures by integrated microfluidic structures, i.e. dimensions of channels and chambers are such that surface tension forces are important, e.g. lab-on-a-chip
- B01L3/502761—Containers for the purpose of retaining a material to be analysed, e.g. test tubes with fluid transport, e.g. in multi-compartment structures by integrated microfluidic structures, i.e. dimensions of channels and chambers are such that surface tension forces are important, e.g. lab-on-a-chip specially adapted for handling suspended solids or molecules independently from the bulk fluid flow, e.g. for trapping or sorting beads, for physically stretching molecules
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- B—PERFORMING OPERATIONS; TRANSPORTING
- B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
- B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
- B01L3/00—Containers or dishes for laboratory use, e.g. laboratory glassware; Droppers
- B01L3/50—Containers for the purpose of retaining a material to be analysed, e.g. test tubes
- B01L3/508—Containers for the purpose of retaining a material to be analysed, e.g. test tubes rigid containers not provided for above
- B01L3/5085—Containers for the purpose of retaining a material to be analysed, e.g. test tubes rigid containers not provided for above for multiple samples, e.g. microtitration plates
- B01L3/50851—Containers for the purpose of retaining a material to be analysed, e.g. test tubes rigid containers not provided for above for multiple samples, e.g. microtitration plates specially adapted for heating or cooling samples
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- B—PERFORMING OPERATIONS; TRANSPORTING
- B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
- B01F—MIXING, e.g. DISSOLVING, EMULSIFYING OR DISPERSING
- B01F33/00—Other mixers; Mixing plants; Combinations of mixers
- B01F33/30—Micromixers
- B01F33/301—Micromixers using specific means for arranging the streams to be mixed, e.g. channel geometries or dispositions
- B01F33/3017—Mixing chamber
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- B—PERFORMING OPERATIONS; TRANSPORTING
- B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
- B01F—MIXING, e.g. DISSOLVING, EMULSIFYING OR DISPERSING
- B01F33/00—Other mixers; Mixing plants; Combinations of mixers
- B01F33/80—Mixing plants; Combinations of mixers
- B01F33/81—Combinations of similar mixers, e.g. with rotary stirring devices in two or more receptacles
- B01F33/813—Combinations of similar mixers, e.g. with rotary stirring devices in two or more receptacles mixing simultaneously in two or more mixing receptacles
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- B—PERFORMING OPERATIONS; TRANSPORTING
- B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
- B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
- B01L7/00—Heating or cooling apparatus; Heat insulating devices
- B01L7/52—Heating or cooling apparatus; Heat insulating devices with provision for submitting samples to a predetermined sequence of different temperatures, e.g. for treating nucleic acid samples
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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
- C12Q1/6869—Methods for sequencing
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- B—PERFORMING OPERATIONS; TRANSPORTING
- B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
- B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
- B01L2200/00—Solutions for specific problems relating to chemical or physical laboratory apparatus
- B01L2200/02—Adapting objects or devices to another
- B01L2200/026—Fluid interfacing between devices or objects, e.g. connectors, inlet details
- B01L2200/027—Fluid interfacing between devices or objects, e.g. connectors, inlet details for microfluidic devices
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- B—PERFORMING OPERATIONS; TRANSPORTING
- B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
- B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
- B01L2200/00—Solutions for specific problems relating to chemical or physical laboratory apparatus
- B01L2200/06—Fluid handling related problems
- B01L2200/0605—Metering of fluids
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- B—PERFORMING OPERATIONS; TRANSPORTING
- B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
- B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
- B01L2200/00—Solutions for specific problems relating to chemical or physical laboratory apparatus
- B01L2200/06—Fluid handling related problems
- B01L2200/0642—Filling fluids into wells by specific techniques
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- B—PERFORMING OPERATIONS; TRANSPORTING
- B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
- B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
- B01L2200/00—Solutions for specific problems relating to chemical or physical laboratory apparatus
- B01L2200/06—Fluid handling related problems
- B01L2200/0647—Handling flowable solids, e.g. microscopic beads, cells, particles
- B01L2200/0668—Trapping microscopic beads
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- B—PERFORMING OPERATIONS; TRANSPORTING
- B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
- B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
- B01L2200/00—Solutions for specific problems relating to chemical or physical laboratory apparatus
- B01L2200/06—Fluid handling related problems
- B01L2200/0673—Handling of plugs of fluid surrounded by immiscible fluid
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- B—PERFORMING OPERATIONS; TRANSPORTING
- B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
- B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
- B01L2200/00—Solutions for specific problems relating to chemical or physical laboratory apparatus
- B01L2200/16—Reagents, handling or storing thereof
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- B—PERFORMING OPERATIONS; TRANSPORTING
- B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
- B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
- B01L2300/00—Additional constructional details
- B01L2300/06—Auxiliary integrated devices, integrated components
- B01L2300/0681—Filter
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- B—PERFORMING OPERATIONS; TRANSPORTING
- B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
- B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
- B01L2300/00—Additional constructional details
- B01L2300/08—Geometry, shape and general structure
- B01L2300/0809—Geometry, shape and general structure rectangular shaped
- B01L2300/0819—Microarrays; Biochips
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- B—PERFORMING OPERATIONS; TRANSPORTING
- B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
- B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
- B01L2300/00—Additional constructional details
- B01L2300/08—Geometry, shape and general structure
- B01L2300/0809—Geometry, shape and general structure rectangular shaped
- B01L2300/0829—Multi-well plates; Microtitration plates
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- B—PERFORMING OPERATIONS; TRANSPORTING
- B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
- B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
- B01L2300/00—Additional constructional details
- B01L2300/08—Geometry, shape and general structure
- B01L2300/0861—Configuration of multiple channels and/or chambers in a single devices
- B01L2300/0864—Configuration of multiple channels and/or chambers in a single devices comprising only one inlet and multiple receiving wells, e.g. for separation, splitting
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- B—PERFORMING OPERATIONS; TRANSPORTING
- B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
- B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
- B01L2300/00—Additional constructional details
- B01L2300/08—Geometry, shape and general structure
- B01L2300/0861—Configuration of multiple channels and/or chambers in a single devices
- B01L2300/0867—Multiple inlets and one sample wells, e.g. mixing, dilution
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- B—PERFORMING OPERATIONS; TRANSPORTING
- B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
- B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
- B01L2300/00—Additional constructional details
- B01L2300/08—Geometry, shape and general structure
- B01L2300/0861—Configuration of multiple channels and/or chambers in a single devices
- B01L2300/087—Multiple sequential chambers
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- B—PERFORMING OPERATIONS; TRANSPORTING
- B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
- B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
- B01L2300/00—Additional constructional details
- B01L2300/16—Surface properties and coatings
- B01L2300/161—Control and use of surface tension forces, e.g. hydrophobic, hydrophilic
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- B—PERFORMING OPERATIONS; TRANSPORTING
- B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
- B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
- B01L2300/00—Additional constructional details
- B01L2300/16—Surface properties and coatings
- B01L2300/161—Control and use of surface tension forces, e.g. hydrophobic, hydrophilic
- B01L2300/165—Specific details about hydrophobic, oleophobic surfaces
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- B—PERFORMING OPERATIONS; TRANSPORTING
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- B01L2300/00—Additional constructional details
- B01L2300/18—Means for temperature control
- B01L2300/1805—Conductive heating, heat from thermostatted solids is conducted to receptacles, e.g. heating plates, blocks
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- B—PERFORMING OPERATIONS; TRANSPORTING
- B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
- B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
- B01L2400/00—Moving or stopping fluids
- B01L2400/06—Valves, specific forms thereof
- B01L2400/0622—Valves, specific forms thereof distribution valves, valves having multiple inlets and/or outlets, e.g. metering valves, multi-way valves
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- B—PERFORMING OPERATIONS; TRANSPORTING
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- B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
- B01L3/00—Containers or dishes for laboratory use, e.g. laboratory glassware; Droppers
- B01L3/52—Containers specially adapted for storing or dispensing a reagent
- B01L3/527—Containers specially adapted for storing or dispensing a reagent for a plurality of reagents
Abstract
m ▪ m (70 m m 0(70a7 1111111111111111111111111111111111111111111111 mmmmmmmmmmmmmmmmmmmmmmmm mmmmmmmmmmmmmmmmmmmmmmmm mmmmmmmmmmmmmmmmmmmmmmmm 1.1.1.11.1.1111111.1.1•11. mmmmmmmmmmmmmmmmmmmmmmmm m ▪ mmmmmmmmmmmmmmmmmmmmmmm m ▪ mmmmmmmmmmmmmmmmmmmmmmm E Nmmmmmmmmmmmmmmmmmmmmm J 26 22 24a 24b 11111111111111111010111111111 131111311111111111311113 IIIIIIIIIIIIIIIIIIIIIII A AAA Z AAAAAAA 14 10 2 .... 12 .... 20 16 18a Figure 2 INEEMENIENEMEMENNESEMENE 11111111111111111111111111111111111111 30 28 32 (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (43) International Publication Date 04 October 2018 (04.10.2018) W I PO I PCT Hu omits °nolo HE mil Kim °mono ow (10) International Publication Number WO 2018/183723 Al 1-1 N co 1-1 00 O C 1-1 (51) International Patent Classification: B01F 13/00 (2006.01) Cl 2M 1/34 (2006.01) BOIL 3/00 (2006.01) Cl 2M 1/40 (2006.01) C12M 1/00 (2006.01) (21) International Application Number: PCT/US2018/025213 (22) International Filing Date: 29 March 2018 (29.03.2018) (25) Filing Language: English (26) Publication Language: English (30) Priority Data: 62/478,412 29 March 2017 (29.03.2017) US (71) Applicant: CORNELL UNIVERSITY [US/US]; Center for Technology Licensing at Cornell University (CTL), 395 Pine Tree Road, Suite 310, Ithaca, NY 14850 (US). (72) Inventor: BARANY, Francis; 450 E. 63rd Street, Apt. 12C, New York, NY 10021 (US). (74) Agent: GOLDMAN, Michael, L. et al.; LECLAIRRYAN PLLC, 70 Linden Oaks, Suite 210, Rochester, NY 14625 (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. (54) Title: DEVICES, PROCESSES, AND SYSTEMS FOR DETERMINATION OF NUCLEIC ACID SEQUENCE, EXPRESSION, = COPY NUMBER, OR METHYLATION CHANGES USING COMBINED NUCLEASE, LIGASE, POLYMERASE, AND SE- QUENCING REACTIONS (57) : The present invention relates to methods, devices, instruments, processes, and systems for the highly specific, targeted molecular analysis of regions of human genomes and transcriptomes from the blood, i.e. from cell free circulating DNA, exosomes, microRNA, IncRNA, circulating tumor cells, or total blood cells. The technology enables highly sensitive identification and enumera- tion of mutation, expression, copy number, translocation, alternative splicing, and methylation changes using spatial multiplexing and combined nuclease, ligation, polymerase, and sequencing reactions. Such technology may be used for non-invasive early detection of cancer, non-invasive cancer prognosis, and monitoring both treatment efficacy and disease recurrence of cancer. [Continued on next page] WO 2018/183723 Al MIDEDIMOMOIDEIREEMOMMENEEMOMOVOIMIE (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, TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, GW, KM, ML, MR, NE, SN, TD, TG). Declarations under Rule 4.17: — of inventorship (Rule 4.17(iv)) Published: — with international search report (Art. 21(3))
Applications Claiming Priority (2)
Application Number | Priority Date | Filing Date | Title |
---|---|---|---|
US201762478412P | 2017-03-29 | 2017-03-29 | |
PCT/US2018/025213 WO2018183723A1 (en) | 2017-03-29 | 2018-03-29 | Devices, processes, and systems for determination of nucleic acid sequence, expression, copy number, or methylation changes using combined nuclease, ligase, polymerase, and sequencing reactions |
Publications (1)
Publication Number | Publication Date |
---|---|
SG11201908564RA true SG11201908564RA (en) | 2019-10-30 |
Family
ID=63676873
Family Applications (1)
Application Number | Title | Priority Date | Filing Date |
---|---|---|---|
SG11201908564R SG11201908564RA (en) | 2017-03-29 | 2018-03-29 | Devices, processes, and systems for determination of nucleic acid sequence, expression, copy number, or methylation changes using combined nuclease, ligase, polymerase, and sequencing reactions |
Country Status (10)
Country | Link |
---|---|
US (2) | US11305282B2 (en) |
EP (1) | EP3600671A4 (en) |
JP (2) | JP7131836B2 (en) |
CN (1) | CN110769925A (en) |
AU (1) | AU2018243360B2 (en) |
BR (1) | BR112019019347A2 (en) |
CA (1) | CA3056256A1 (en) |
IL (2) | IL269415B2 (en) |
SG (1) | SG11201908564RA (en) |
WO (1) | WO2018183723A1 (en) |
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2018
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- 2018-03-29 CN CN201880034449.6A patent/CN110769925A/en active Pending
- 2018-03-29 CA CA3056256A patent/CA3056256A1/en active Pending
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2022
- 2022-02-14 US US17/671,033 patent/US20220168742A1/en active Pending
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CN113092461A (en) * | 2021-04-09 | 2021-07-09 | 四川大学华西医院 | Homogeneous two-dimensional visualization/fluorescence analysis method for circulating tumor cells by selectively recognizing folate receptor and application |
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AU2018243360B2 (en) | 2023-10-26 |
IL269415B1 (en) | 2023-11-01 |
JP2020511983A (en) | 2020-04-23 |
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EP3600671A1 (en) | 2020-02-05 |
JP7131836B2 (en) | 2022-09-06 |
JP2022166216A (en) | 2022-11-01 |
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