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US 2023/0420077 A1Published application
Disease-associated isoform identifier
AssigneeKiromic BioPharma, Inc.
InventorsLeonardo Mirandola, Maurizio Chiriva-Internati, Lucia Piccotti, Michael Ryan
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Abstract
The technology relates in part to methods and systems for the identification of disease-associated transcript isoforms and peptides. In certain aspects, the technology relates to methods and systems for the identification of transcript isoforms and peptides preferentially expressed in tumor cells.
Claims20
A computer-implemented method for identifying a transcript of a gene that is expressed at a level in a defined subpopulation of diseased tissue samples higher than a level the transcript is expressed in non-diseased tissue samples, comprising:
- (a) receiving user input comprising:
- (i) a defined disease selected from a plurality of defined diseases, wherein each of the defined diseases corresponds to diseased tissue samples,
- (ii) a defined minimum transcript expression value threshold for diseased tissue samples,
- (iii) a defined maximum or defined median transcript expression value threshold for non-diseased tissues, wherein each of the non-diseased tissues corresponds to non-diseased tissue samples, and
- (iv) a defined minimum sample sub-population percentage;
- (b) identifying in a database comprising one or more tables that relate:
- (i) transcript identifiers to genes, wherein:
- at least a portion of the transcript identifiers correspond to transcript isoform sets, and each of the transcript isoform sets is encoded by a gene;
- (ii) transcript identifiers to corresponding transcript expression values in diseased tissue samples, and
- (iii) transcript identifiers to corresponding transcript expression values in non-diseased tissue samples;
- one or more transcript identifiers meeting the following criteria (1) and (2):
- (1) a corresponding transcript expression value in diseased tissue samples corresponding to the input defined disease of (a)(i) is greater than the input defined minimum transcript expression value threshold of (a)(ii), and
- (2) a corresponding transcript expression value in non-diseased tissue is less than the input defined maximum or defined median transcript expression value threshold of (a)(iii),
- for a percentage of diseased samples corresponding to the input defined disease of (a)(i) greater than the defined minimum sub-population percentage of (a)(iv);
- and
- (c) outputting a list comprising a transcript identifier for each of one or more transcripts identified in
- (b), thereby identifying a transcript of one or more genes that is expressed at a level in a defined subpopulation of diseased tissue samples higher than a level the transcript is expressed in non-diseased tissue samples.
14 more elements
A system comprising one or more microprocessors and memory, the memory comprising:
- a database comprising one or more tables that relate:
- (i) transcript identifiers to genes, wherein:
- at least a portion of the transcript identifiers correspond to transcript isoform sets, and each of the transcript isoform sets is encoded by a gene;
- (ii) transcript identifiers to corresponding transcript expression values in diseased tissue samples, and
- (iii) transcript identifiers to corresponding transcript expression values in non-diseased tissue samples;
- and
- instructions executable by the one or more microprocessors configured to perform the following method:
- (a) receiving user input comprising:
- (i) a defined disease selected from a plurality of defined diseases, wherein each of the defined diseases corresponds to diseased tissue samples,
- (ii) a defined minimum transcript expression value threshold for diseased tissue samples,
- (iii) a defined maximum or a defined median transcript expression value threshold for non-diseased tissues, wherein each of the non-diseased tissues corresponds to non-diseased tissue samples, and
- (iv) a defined minimum sample sub-population percentage;
- (b) identifying in the database one or more transcript identifiers meeting the following criteria (1) and (2):
- (1) a corresponding transcript expression value in diseased tissue samples corresponding to the input defined disease of (a)(i) is greater than the input defined minimum transcript expression value threshold of (a)(ii), and
- (2) a corresponding transcript expression value in non-diseased tissue is less than the input defined maximum or defined median transcript expression value threshold of (a)(iii),
- for a percentage of diseased samples corresponding to the input defined disease of (a)(i) greater than the defined minimum sub-population percentage of (a)(iv);
- and
- (c) outputting a list comprising a transcript identifier for each of one or more transcripts identified in (b).
15 more elements
A computer-implemented method for identifying a transcript of a gene that is expressed at a level in a defined subpopulation of diseased tissue samples higher than a level the transcript is expressed in non-diseased tissue samples, comprising:
- (a) receiving user input comprising:
- (i) a defined disease selected from a plurality of defined diseases, wherein each of the defined diseases corresponds to diseased tissue samples,
- (ii) a defined transcript expression ratio threshold, wherein the transcript expression ratio is a ratio of a transcript expression value for diseased tissue samples to a transcript expression value for non-diseased tissues, wherein each of the non-diseased tissues corresponds to non-diseased tissue samples, and
- (iii) a defined minimum sample sub-population percentage;
- (b) identifying in a database comprising one or more tables that relate:
- (i) transcript identifiers to genes, wherein:
- at least a portion of the transcript identifiers correspond to transcript isoform sets, and each of the transcript isoform sets is encoded by a gene;
- and
- (ii) transcript identifiers to corresponding transcript expression ratios;
- one or more transcript identifiers having a corresponding transcript expression ratio for the input defined disease of (a)(i) that is greater than the input defined transcript expression ratio threshold of (a)(ii),
- for a percentage of diseased samples corresponding to the input defined disease of (a)(i) greater than the defined minimum sub-population percentage of (a)(iii);
- and
- (c) outputting a list comprising a transcript identifier for each of one or more transcripts identified in (b), thereby identifying a transcript of one or more genes that is expressed at a level in a defined subpopulation of diseased tissue samples higher than a level the transcript is expressed in non-diseased tissue samples.
10 more elements
A system comprising one or more microprocessors and memory, the memory comprising:
- a database comprising one or more tables that relate:
- (i) transcript identifiers to genes, wherein:
- at least a portion of the transcript identifiers correspond to transcript isoform sets, and each of the transcript isoform sets is encoded by a gene;
- (ii) transcript identifiers to corresponding transcript expression values in diseased tissue samples, and
- (iii) transcript identifiers to corresponding transcript expression values in non-diseased tissue samples;
- and
- instructions executable by the one or more microprocessors configured to perform the following method:
- (a) receiving user input comprising:
- (i) a defined disease selected from a plurality of defined diseases, wherein each of the defined diseases corresponds to diseased tissue samples,
- (ii) a defined transcript expression ratio threshold, wherein the transcript expression ratio is a ratio of a transcript expression value for diseased tissue samples to a transcript expression value for non-diseased tissues, wherein each of the non-diseased tissues corresponds to non-diseased tissue samples, and
- (iii) a defined minimum sample sub-population percentage;
- (b) identifying in the database one or more transcript identifiers having a corresponding transcript expression ratio for the input defined disease of (a)(i) that is greater than the input defined transcript expression ratio threshold of (a)(ii), for a percentage of diseased samples corresponding to the input defined disease of (a)(i) greater than the defined minimum sub-population percentage of (a)(iii);
- and
- (c) outputting a list comprising a transcript identifier for each of one or more transcripts identified in (b).
11 more elements
A computer-implemented method for analyzing a polypeptide comprising:
- (a) identifying one or more transcript identifiers in a database comprising one or more tables that relate:
- (i) transcript identifiers to genes, wherein:
- at least a portion of the transcript identifiers correspond to transcript isoform sets, and each of the transcript isoform sets is encoded by a gene;
- (ii) transcript identifiers to corresponding transcript expression values in diseased tissue samples, and
- (iii) transcript identifiers to corresponding transcript expression values in non-diseased tissue samples;
- (b) receiving user selection of a transcript identifier;
- and
- (c) outputting one or more of:
- (i) a three-dimensional structure corresponding to a polypeptide linear sequence corresponding to the selected transcript identifier, and
- (ii) functional polypeptide domain information for a polypeptide linear sequence corresponding to the selected transcript identifier, wherein the one or more tables of the database relate three-dimensional structure coordinates and functional polypeptide domain information to the polypeptide linear sequence.
7 more elements
A method for generating a database comprising:
- (i) relating transcript identifiers to genes, wherein:
- at least a portion of the transcript identifiers correspond to transcript isoform sets, and each of the transcript isoform sets is encoded by a gene;
- (ii) relating transcript identifiers to corresponding transcript expression values in diseased tissue samples for a plurality of defined diseases;
- and
- (iii) relating percentages of diseased tissue samples for each defined disease to corresponding transcript identifiers, wherein the percentages are based on an amount of diseased tissue samples corresponding to a defined disease for which transcript expression values of a corresponding transcript identifier exceed a defined minimum transcript expression value threshold, or
- (iii′) relating percentages of diseased tissue samples for each defined disease to corresponding transcript identifiers, wherein the percentages are based on an amount of diseased tissue samples corresponding to a defined disease for which transcript expression ratios of a corresponding transcript identifier exceed a defined transcript expression ratio threshold.
3 more elements
Dependencies are inferred from the claim text.