Patent application EP22179854A (EP), filed 2022-06-20
Publication number: EP4109333A1
Title: METHOD FOR ANALYSING BIOLOGICAL SAMPLES
Abstract: A method is provided for analysing a biological sample (200) with a plurality of analytes, comprises the following steps: Determining information about the biological sample (200) and its analytes, the analytes being marked by a plurality of markers; Generating a probabilistic model (400, 600) of the distribution of the analytes within the biological sample based on the determined information; Generating at least one optical readout of the biological sample (200); Determining the presence, in particular, the location and/or co-location, of at least one analyte in the readout based at least partially on the probabilistic model (400, 600) of the distribution of the analytes within the biological sample (200).
IPC codes: G06K   9/    00            A I
G01N  15/    14            A I
G01N  33/   533            A I
G01N  33/    58            A I
G06K  19/    06            A I
G06V  20/    69            A I
G01N  15/  1433            A I
Claims: number: 1
text: A method for analysing a biological sample (200) with a plurality of analytes, comprising the following steps:
number: 2
text: The method according to claim 1, wherein the information about the sample is determined from at least one of the following sources: generic databases or data generated from the biological sample.
number: 3
text: The method according to one of the preceding claims, wherein the information about the sample comprises at least one of the following types: genomic, transcriptomic, proteomic, metabolomic, interactomic, localisomic, or epigenomic.
number: 4
text: The method according to one of the preceding claims, wherein the information about the sample is determined for at least one of the following levels: subcellular, organellular, cellular, or tissular.
number: 5
text: The method according to one of the preceding claims, wherein the information about the sample is at least determined prior to generating the one optical readout.
number: 6
text: The method according to one of the preceding claims, wherein the at least one optical readout is segmented in order to determine the information about the sample from the segmented optical readout.
number: 7
text: The method according to one of the preceding claims, wherein the information about the sample is determined from the optical readout pixel-per-pixel.
number: 8
text: The method according to one of the preceding claims, wherein the probabilistic model is modified based on information about the biological sample determined from the at least one optical readout, preferably, the probabilistic model is iteratively modified based on information about the biological sample determined from a plurality of generated optical readouts.
number: 9
text: The method according to one of the preceding claims, wherein at least one further optical readout is generated and the analytes are marked by a further plurality of markers for the further optical readout.
number: 10
text: The method according to one of the preceding claims, wherein at least the plurality of markers is based on the probabilistic model of the distribution of the analytes.
number: 11
text: The method according to one of the preceding claims, wherein generating the optical readout comprises:
number: 12
text: The method according to claim 11, further comprising at least one of:
number: 13
text: The method according to claim 12, further comprising:
providing at least one dye and/or dye combination of dyes for the second plurality of combinations of dyes and/or rules for the second mapping, based on the at least one first optical readout.
number: 14
text: The method according to claims 12 or 13, further comprising iteratively repeating the steps of claim 12 and/or claim 13 for at least one of: a number of pluralities of combinations of dyes; or a number of mappings, until all affinity reagents attached to analytes in the sample are determined.
number: 15
text: A computer program for performing the method according to one of the preceding claims.
number: 16
text: A computer readable storage medium storing the computer program according to claim 15.
Office action: search_report, dated 2022-12-28
Rejection reasons: novelty_epc_54
inventive_step_epc_56
Prior art cited: ref_id: EP2021066645W
ref_type: patent
severity: background
ref_id: EP2021073819W
ref_type: patent
severity: background
ref_id: EP2021063310W
ref_type: patent
severity: background
ref_id: EP2021087551W
ref_type: patent
severity: background
ref_id: EP2021087558W
ref_type: patent
severity: background
ref_id: - RODRIGUEZ ET AL., TRENDS BIOCHEM SCI., vol. 42, no. 2, February 2017 (2017-02-01), pages 111 - 129
ref_type: npl
severity: background
ref_id: - YAN ET AL., MICROCHIMICA ACTA, vol. 186, 2019, pages 583
ref_type: npl
severity: background
ref_id: - IRAVANIVARMA, ENVIRON CHEM LETT., 10 March 2020 (2020-03-10)
ref_type: npl
severity: background
ref_id: - KACENAUSKAITE ET AL., J. AM. CHEM. SOC., vol. 143, 2021, pages 1377 - 1385
ref_type: npl
severity: background
ref_id: US2021166380A1
ref_type: patent
severity: background
ref_id: US2018030504A1
ref_type: patent
severity: background
ref_id: [XYI]     - GARAPATI HITA SONY ET AL: "Predicting subcellular localization of proteins using protein-protein interaction data", GENOMICS, ACADEMIC PRESS, SAN DIEGO, US, vol. 112, no. 3, 14 January 2020 (2020-01-14), pages 2361 - 2368, XP086089674, ISSN: 0888-7543, [retrieved on 20200114], DOI: 10.1016/J.YGENO.2020.01.007
ref_type: npl
severity: background
ref_id: US2018030504
ref_type: patent
severity: obviousness
ref_id: US2021166380
ref_type: patent
severity: novelty_destroying
ref_id: - GARAPATI HITA SONY ET AL, "Predicting subcellular localization of proteins using protein-protein interaction data", GENOMICS, ACADEMIC PRESS, SAN DIEGO, US, vol. 112, no. 3, doi:10.1016/J.YGENO.2020.01.007, ISSN 0888-7543, (20200114), pages 2361 - 2368, (20200114), XP086089674 [X] 1-5,10,11,15,16 * section 3.1, section 3.3, section 4 (last sentence), page 2366, RC, last paragraph - page 2367, LC, first paragraph; figure 2; table 1 * [Y] 12-14 [I] 6-9
ref_type: npl
severity: novelty_destroying
Final disposition: pending (2022-12-28)