WO2018198598A1 - Procédé d'isolement de gouttelettes pour analyse génomique, et procédé d'analyse génomique - Google Patents
Procédé d'isolement de gouttelettes pour analyse génomique, et procédé d'analyse génomique Download PDFInfo
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- WO2018198598A1 WO2018198598A1 PCT/JP2018/010970 JP2018010970W WO2018198598A1 WO 2018198598 A1 WO2018198598 A1 WO 2018198598A1 JP 2018010970 W JP2018010970 W JP 2018010970W WO 2018198598 A1 WO2018198598 A1 WO 2018198598A1
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- genome
- droplet
- amplification
- analysis
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
- C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
- C12N15/09—Recombinant DNA-technology
- C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
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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
- C12Q1/6806—Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12M—APPARATUS FOR ENZYMOLOGY OR MICROBIOLOGY; APPARATUS FOR CULTURING MICROORGANISMS FOR PRODUCING BIOMASS, FOR GROWING CELLS OR FOR OBTAINING FERMENTATION OR METABOLIC PRODUCTS, i.e. BIOREACTORS OR FERMENTERS
- C12M1/00—Apparatus for enzymology or microbiology
Definitions
- the present invention relates to a method for isolating a droplet for genome analysis and a method for genome analysis.
- sorting In the case where target cells are isolated from samples containing various cells and the target genome is analyzed, cell sorting has become common in recent years as a method for isolating target cells. In particular, in the method of forming droplets (droplets) containing cells by emulsification, sorting (sorting) of droplets containing target cells is performed using nucleic acid amplification.
- a sample containing cells is emulsified to form droplets in the emulsion.
- a short chain sequence derived from the target cell is amplified by a nucleic acid amplification method such as PCR, and the presence or absence of the amplification is detected using a probe or the like.
- the droplet by which amplification was confirmed is fractionated as a droplet containing a target cell, and this is made into samples, such as a genome analysis (nonpatent literature 1).
- the target genome of the target cell is further subjected to nucleic acid amplification, and the obtained target genome amplification product is subjected to next-generation sequencing (NGS) and assembled.
- NGS next-generation sequencing
- the target genome of the target cell can be analyzed (Non-patent Document 2).
- Nucleic acid amplification in the cell sorting is aimed at confirming the presence or absence of cells in the droplets. Therefore, as described above, for example, a short region in the genome (for example, about 80 to 300 bp) is set and amplification is performed. Done.
- the droplets collected by amplification detection contain a large amount of short-chain amplification products by cell sorting, and the amount is compared to the cell-derived genome contained in the droplets. Very many. For this reason, even if nucleic acid amplification of the target genome is further performed on the collected droplets for genome analysis, in addition to target amplification products derived from the target genome, samples to be analyzed are not subject to analysis. There is a problem that these short-chain amplification products are sequenced while a large amount of short-chain amplification products are not mixed, and the analysis result of the target genome of the target cell is affected.
- an object of the present invention is to provide a method for isolating a droplet that can be subjected to genome analysis without affecting subsequent genome analysis, and a method for genome analysis.
- the present invention is a method for isolating a droplet for genome analysis, Including an emulsion formation step, a nucleic acid amplification step, a detection step, and a fractionation step
- the emulsion forming step includes A step of contacting a sample containing cells with an emulsion-forming solvent to form a plurality of droplets containing cells in the sample in the emulsion-forming solvent;
- the nucleic acid amplification step includes The step of amplifying the target genome contained in the target cell for the droplet,
- the detection step includes Detecting the presence or absence of amplification of the target genome in the droplet,
- the preparative step is In this step, the droplet in which the amplification of the target genome is detected is sorted as a genome analysis droplet containing an amplification product derived from the target genome.
- the present invention is a genome analysis method derived from a target cell, Including a step of isolating a droplet for genome analysis containing an amplification product derived from a target genome, and an analysis step,
- the isolation step includes A step of isolating a droplet for genome analysis containing an amplification product derived from a target genome of a target cell from a sample containing cells by the isolation method of the present invention,
- the analysis step includes The amplification product contained in the isolated droplet for genome analysis is a step of performing genome analysis.
- the present invention in the isolation of a droplet for genome analysis, in order to amplify a target genome to be analyzed later in confirming the presence or absence of cells in the droplet, for example, as described above, Short-chain amplification products that are not subject to analysis are not included. For this reason, if the droplets for genome analysis obtained by the isolation method of the present invention are used, for example, the influence of the short amplification product is avoided, and the genome analysis is performed by sequencing and assembly as it is. It can be carried out.
- the method for isolating a droplet for genome analysis of the present invention includes, for example, forming a droplet in the presence of the reagent for amplification of the target genome in the emulsion formation step, and including the droplet in the nucleic acid amplification step.
- the target genome is amplified using the amplification reagent.
- droplets are formed in the absence of the amplification reagent for the target genome, and in the nucleic acid amplification step, the amplification reagent And the target genome is amplified.
- the detection reagent for detection of amplification coexists in the amplification reagent, and the amplification reagent amplifies the target genome.
- the detection reagent includes an intercalator or a probe.
- the method for isolating a droplet for genome analysis of the present invention further includes, for example, an analysis step, and the analysis step analyzes an amplification product derived from a target genome contained in the analysis droplet.
- the emulsion-forming solvent contains a water-insoluble solvent, and the plurality of droplets are formed in the water-insoluble solvent.
- the plurality of droplets are water-soluble droplets containing the sample.
- a device having a flow path is used, and the emulsion formation process, the amplification process, and the detection process are performed in the flow path.
- the sorting step is further performed in the channel.
- the point is to amplify the target genome to be subjected to genome analysis as nucleic acid amplification for sorting the droplets for genome analysis.
- isolation method and analysis method of the present invention will be described by way of examples.
- the isolation method and analysis method of the present invention are not limited or restricted by the following embodiments. Moreover, the description of each embodiment can mutually be used.
- the isolation method of the present invention is a method for isolating droplets for genome analysis, Including an emulsion formation step, a nucleic acid amplification step, a detection step, and a fractionation step,
- the emulsion forming step includes A step of contacting a sample containing cells with an emulsion-forming solvent to form a plurality of droplets containing cells in the sample in the emulsion-forming solvent;
- the nucleic acid amplification step includes The step of amplifying the target genome contained in the target cell for the droplet,
- the detection step includes Detecting the presence or absence of amplification of the target genome in the droplet,
- the preparative step is In this step, the droplet in which the amplification of the target genome is detected is sorted as a genome analysis droplet containing an amplification product derived from the target genome.
- the emulsion forming step is a step of bringing a sample containing cells into contact with an emulsion forming solvent to form a plurality of droplets containing cells in the sample in the emulsion forming solvent.
- the sample can be divided and divided into a plurality of droplets. Then, various cells in the sample are distributed to each of the droplets.
- the type of the sample is not limited at all, and examples include samples that are considered to contain cells.
- Examples of the sample include a biological sample, and specific examples include blood, lymph, cerebrospinal fluid, semen, urine, nasal discharge, nasal swab, and the like.
- the species of the living body is not particularly limited, and examples thereof include humans; non-human mammals such as cows, pigs, sheep, mice, rats, rabbits and horses; birds; and animals such as fish.
- the emulsion-forming solvent is not particularly limited as long as it can form droplets containing the sample therein.
- the emulsion-forming solvent is, for example, a water-insoluble solvent, and water-soluble droplets containing the sample can be formed in the water-insoluble solvent.
- water-insoluble solvent examples include oil, mineral oil, chloroform, and aromatic compounds.
- the water-insoluble solvent for example, one kind may be used alone, or two or more kinds may be used in combination.
- a water-soluble solvent may be further present.
- the water-soluble solvent include water, a buffer solution, and a water-soluble polymer solution.
- the water-soluble solvent for example, one kind may be used alone, or two or more kinds may be used in combination.
- a reagent used in an amplification step described later may coexist.
- the droplet containing the said reagent is formed, in the amplification process mentioned later, the amplification reaction in an amplification process can be performed, without adding a reagent newly, for example.
- the reagent will be described later.
- the size of the droplets to be formed is not particularly limited, and the average volume has a lower limit of, for example, 4 pL or more and an upper limit of, for example, 10 nL or less.
- the number of cells contained in the droplet is not particularly limited.
- the number of cells contained in one droplet is, for example, 5 or less, 2 or less, and preferably 1 cell.
- the method for forming droplets in the emulsion forming solvent is not particularly limited, and a plurality of droplets can be formed in the emulsion forming solvent by bringing the emulsion forming solvent into contact with the sample.
- the sample may be brought into contact with the emulsion-forming solvent, or the emulsion-forming solvent may be brought into contact with the sample.
- a known droplet manufacturing method can be applied as the droplet forming method.
- an emulsification device having a microchannel can be used.
- the device includes, as the microchannel, for example, a sample channel, an emulsion-forming solvent channel, a connecting portion thereof, and a lead-out channel derived from the connecting portion.
- droplets are formed as follows. First, the emulsion forming solvent is introduced into the connecting portion from the emulsion forming solvent flow path, and then toward the connecting portion into which the emulsion forming solvent is introduced, from the sample flow path, The sample (eg, optionally containing the water-soluble solvent) is introduced.
- the emulsion-forming solvent and the sample come into contact with each other to be emulsified, and from the connecting portion to the outlet channel, an emulsion (a state in which droplets are dispersed in the emulsion-forming solvent) Derived.
- the sample and the water-soluble solvent may be introduced into the channel of the device as a mixed liquid mixed in advance as described above, or may be separately introduced into the channel. In the latter case, the sample channel and the reagent channel are provided upstream of the connecting portion, and the sample is introduced from the sample channel toward the connecting portion, and the reagent channel. To the water-soluble solvent and optionally the reagent or the like.
- the amplification step is a step of amplifying the target genome contained in the target cell with respect to the droplets formed in the emulsion formation step as described above.
- the target genome to be amplified is not particularly limited and can be appropriately determined according to the purpose of genome analysis.
- the present invention apart from the purpose of genome analysis, the present invention is not intended to amplify short-chain sequences but only to detect the presence or absence of cells in the droplets. The point is to amplify the genome. Therefore, the genome to be amplified in the amplification step is a target genome to be analyzed later, and the region to be amplified in the target genome is a region necessary for so-called genome analysis.
- genome analysis is performed by amplifying a plurality of regions where a part of a target genome overlaps, decoding the sequence, assembling the decoded sequence results, and analyzing the entire target genome.
- the amplification of the target genome in the amplification step is preferably amplification of a plurality of regions necessary for genome analysis.
- the length of each region to be amplified in the target genome is, for example, 400 bp to 60 kbp, and the total length to be analyzed is, for example, 246 bp to 1.5 ⁇ 107 bp.
- Examples of genome analysis in the present invention include whole genome analysis. In this case, for example, a plurality of regions including a plurality of gene loci may be amplified, or the full length or partial region of each gene may be amplified for all genes.
- the nucleic acid amplification method is not particularly limited, and a known method such as a PCR method can be employed.
- the amplification reagent is not particularly limited, and examples thereof include a polymerase, a primer, and dNTP.
- the amplification reagent used in the amplification step may be previously contained in the droplet, for example, or may be added to the droplet during the amplification step, and the operation is easy. preferable.
- a droplet is formed in the presence of the amplification reagent, and in the nucleic acid amplification step, the amplification reagent contained in the droplet is used to form the target genome.
- Amplification may be performed.
- droplets are formed in the absence of the amplification reagent, and in the nucleic acid amplification step, the amplification reagent is added to amplify the target genome. Just do it.
- the amplification step is preferably performed in the microchannel of the device as well.
- the device has, for example, an amplification channel connected downstream of the outlet channel, and the amplification can be performed in the amplification channel.
- the detection step is a step of detecting the presence or absence of amplification of the target genome in the droplet as described above.
- the method for detecting the presence or absence of the amplification is not particularly limited, and can be appropriately set depending on, for example, the amplification method, the type of the amplification reagent used, and the like.
- the presence / absence of the amplification is detected for each droplet, for example.
- the method for detecting the presence or absence of amplification is not particularly limited, and examples thereof include a general intercalator method and probe method.
- a detection reagent such as an intercalator or a probe can be used according to the detection method.
- the type of the probe is not particularly limited, and for example, a TaqMan (registered trademark) probe or the like can be used.
- the detection reagent may coexist with the amplification reagent, for example.
- the detection reagent used in the detection step may be previously contained in the droplet, for example, or may be added to the droplet during the detection step, and is easy to operate. preferable.
- a droplet is formed in the presence of the amplification reagent and the detection reagent, and in the nucleic acid amplification step, the amplification reagent contained in the droplet is used.
- the target genome may be amplified, and in the detection step, the presence or absence of the amplification may be detected using the detection reagent contained in the droplet.
- droplets are formed in the absence of the amplification reagent and the detection reagent, and in the nucleic acid amplification step, the amplification reagent is added, and the target Amplification of the genome is performed, and in the detection step, the detection reagent may be dropped to detect the presence or absence of the amplification.
- the detection step is preferably performed in the microchannel of the device as well.
- the device has a detection channel downstream of the amplification channel, and can perform the amplification in the detection channel.
- the amplification step and the detection step may be performed sequentially, for example, but can be performed simultaneously. In the latter case, for example, the amplification step and the detection step may be performed in the presence of the amplification reagent and the detection reagent.
- the device When using a device having the microchannel, the device has, for example, an amplification channel connected downstream of the outlet channel, and performs the amplification and the detection in the amplification channel. be able to.
- the sorting step is a step of sorting the droplet in which the amplification of the target genome is detected as a genome analysis droplet containing an amplification product derived from the target genome of the target cell.
- the detection process when the detection process is performed using the device, it can be isolated by, for example, deriving the droplet from the device and collecting it in another container (such as a microtube). .
- the present invention releases intracellular components such as nucleic acids from the cells contained in the droplets in the emulsion after the emulsion formation step, before the nucleic acid amplification step, or simultaneously with the nucleic acid amplification step.
- the release of the intracellular component is not particularly limited, and for example, a general cell lysis reagent can be used.
- the cell lysis reagent for example, may be added to the droplets in the emulsion after the emulsion formation step, or in the emulsion formation step, by contacting the sample and the emulsion formation solvent, You may make it contain in the droplet in the said emulsion formation solvent.
- the reagent examples include a solution containing a surfactant, a salt, and a solvent.
- the surfactant include anionic surfactants such as sodium deoxycholate and sodium lauryl sulfate.
- the salt examples include sodium chloride.
- the solvent include various buffers. Liquid. Specific examples of the composition of the reagent include, for example, 50 mmol / L Tris-HCl, 150 mmol / L NaCl, 0.5 w / v% sodium deoxycholate, 0.1 w / v% sodium lauryl sulfate, and 1.0 w / An example is v% NIP-40.
- the present invention may further include an analysis step.
- the analysis step is, for example, a step of analyzing an amplification product derived from a target genome contained in the analysis droplet. The analysis will be described later.
- the analysis method of the present invention is a genome analysis method derived from a target cell, Including a step of isolating a droplet for genome analysis containing an amplification product derived from a target genome, and an analysis step,
- the isolation step includes A step of isolating a droplet for genome analysis containing an amplification product derived from a target genome of a target cell from a sample containing cells by the isolation method of the present invention,
- the analysis step includes The amplification product contained in the isolated droplet for genome analysis is a step of performing genome analysis.
- the point of the analysis method of the present invention is that the droplet for genome analysis is isolated by the isolation method of the present invention, and other steps and conditions are not particularly limited.
- the description of the method for isolating a droplet for genome analysis of the present invention can be used as the isolation method of the isolation step.
- the target genome for analysis is amplified in the isolation step, and the isolated droplet for genome analysis is subjected to, for example, sequencing without further amplification processing. Can be analyzed. And since the sequence which is not the object of analysis is not amplified in the said isolation process, the target genome analysis can be performed avoiding the influence of the amplification product of a short chain like the past.
- the analysis step is a step of performing genome analysis on the amplification product contained in the isolated genome analysis droplet.
- the genome analysis include known methods, and specific examples include Fluorescence In Situ Hybridization (FISH), G-Band, Next-Generation Sequencing (NGS), and the like.
- the target genome to be analyzed later is amplified. Does not include short-chain amplification products that are not subject to genome analysis. For this reason, if the droplets for genome analysis obtained by the isolation method of the present invention are used, for example, the influence of the short amplification product is avoided, and the genome analysis is performed by sequencing and assembly as it is. It can be carried out.
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Abstract
L'invention concerne un procédé d'isolement de gouttelettes pour une analyse génomique sans affecter l'analyse génomique ultérieure, et un procédé d'analyse génomique. Ce procédé d'isolement de gouttelettes pour l'analyse génomique est caractérisé en ce qu'il comprend une étape de formation d'émulsion, une étape d'amplification d'acide nucléique, une étape de détection et une étape de tri. A l'étape de formation d'émulsion, un échantillon qui contient des cellules et un solvant de formation d'émulsion sont mis en contact pour former de multiples gouttelettes qui contiennent les cellules de l'échantillon dans le solvant de formation d'émulsion. A l'étape d'amplification d'acide nucléique, le génome cible contenu dans les cellules cibles est amplifié dans les gouttelettes. A l'étape de détection, il est détecté si le génome cible dans les gouttelettes a été amplifié ou non. A l'étape de tri, les gouttelettes dans lesquelles l'amplification du génome cible a été détectée sont triées en tant que gouttelettes pour une analyse génomique contenant un produit d'amplification dérivé du génome cible dans les cellules cibles.
Applications Claiming Priority (2)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| JP2017087235A JP2018183096A (ja) | 2017-04-26 | 2017-04-26 | ゲノム解析用液滴の単離方法、およびゲノム解析方法 |
| JP2017-087235 | 2017-04-26 |
Publications (1)
| Publication Number | Publication Date |
|---|---|
| WO2018198598A1 true WO2018198598A1 (fr) | 2018-11-01 |
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Family Applications (1)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| PCT/JP2018/010970 Ceased WO2018198598A1 (fr) | 2017-04-26 | 2018-03-20 | Procédé d'isolement de gouttelettes pour analyse génomique, et procédé d'analyse génomique |
Country Status (2)
| Country | Link |
|---|---|
| JP (1) | JP2018183096A (fr) |
| WO (1) | WO2018198598A1 (fr) |
Citations (1)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| WO2016182034A1 (fr) * | 2015-05-12 | 2016-11-17 | 株式会社オンチップ・バイオテクノロジーズ | Procédé d'analyse de particules individuelles, et système pour sa mise en œuvre |
-
2017
- 2017-04-26 JP JP2017087235A patent/JP2018183096A/ja active Pending
-
2018
- 2018-03-20 WO PCT/JP2018/010970 patent/WO2018198598A1/fr not_active Ceased
Patent Citations (1)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| WO2016182034A1 (fr) * | 2015-05-12 | 2016-11-17 | 株式会社オンチップ・バイオテクノロジーズ | Procédé d'analyse de particules individuelles, et système pour sa mise en œuvre |
Non-Patent Citations (1)
| Title |
|---|
| EASTBURN D.J. ET AL.: "Identification and genetic analysis of cancer cells with PCR-activated cell sorting", NUCLEIC ACIDS RESEARCH, vol. 42, no. 16, 15 September 2014 (2014-09-15), pages 1 - 10, XP055527394, ISSN: 0305-1048 * |
Also Published As
| Publication number | Publication date |
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| JP2018183096A (ja) | 2018-11-22 |
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