# US 8,788,286 B2 · Side effects prediction using co-associating bioattributes > Agents: this data is available as JSON from the patentgrep API and MCP server — see https://patentgrep.com/llms.txt - Number: US 8,788,286 B2 - Document ID: US8788286B2 - Status: Granted - Kind: B2 - Application number: 11/969,027 - Filed: 2008-01-03 - Published: 2009-02-12 - Granted: 2014-07-22 - Earliest claimed: 2007-08-08 - Assignees: Expanse Bioinformatics, Inc. - Applicants: Andrew Alexander Kenedy; Charles Anthony Eldering - Inventors: Andrew Alexander Kenedy; Charles Anthony Eldering - Web page: https://patentgrep.com/patent/US8788286B2 ## CPC - G06Q 50/00: Information and communication technology [ICT] specially adapted for implementation of business processes of specific business sectors, e.g. utilities or tourism (healthcare informatics G16H) - G16B 20/20: Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection - G16H 50/20: for computer-aided diagnosis, e.g. based on medical expert systems - G16B 20/00: ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations - G06Q: INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR ADMINISTRATIVE, COMMERCIAL, FINANCIAL, MANAGERIAL OR SUPERVISORY PURPOSES; SYSTEMS OR METHODS SPECIALLY ADAPTED FOR ADMINISTRATIVE, COMMERCIAL, FINANCIAL, MANAGERIAL OR SUPERVISORY PURPOSES, NOT OTHERWISE PROVIDED FOR - G16B: BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY - G16H: HEALTHCARE INFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR THE HANDLING OR PROCESSING OF MEDICAL OR HEALTHCARE DATA ## Abstract A bioinformatics method, software, database and system for predicting side effects resulting from predisposition modification are presented in which a set of attributes is used to modify an individual's attribute profile to generate a modified attribute profile. The modified attribute profile is compared against a predetermined set of attribute combinations that are statistically associated with one or more candidate side effect attributes. Attribute combinations from the set that also occur in the modified attribute profile are identified, and those candidate side effect attributes that are statistically associated with the identified attribute combinations are stored as a set of predicted side effect attributes resulting from modification of the individual's attribute profile. ## Claims ### Claim 1 A bioinformatics computer for predicting future side effects that result from modifying an attribute profile of an individual, said computer including a data input device, a processor, a memory, and data output device, wherein a method performed on said computer is characterized as comprising: a) said processor accessing a previously modified attribute profile contained in said memory, wherein the previously modified attribute profile comprises an attribute profile of said individual that has been previously modified as to a set of pre-existing attributes associated with that individual, wherein the identity of the individual is masked or anonymized; b) said processor accessing a dataset in said memory containing attribute combinations and corresponding statistical results that indicate the strength of association of each of the attribute combinations with one or more candidate side effect attributes, wherein each of the attribute combinations comprises at least one pangenetic attribute and at least one non-pangenetic attribute, and wherein the one or more candidate side effect attributes comprise pangenetic attributes and non- pangenetic attributes that do not occur in the previously modified attribute profile, the candidate side effect attributes being filtered to exclude user specified attributes; c) said processor identifying attribute combinations contained in the dataset that also occur in the previously modified attribute profile; d) transmitting through said output device one or more candidate side effect attributes that are statistically associated with the identified attribute combinations as output, to generate a set of predicted cumulative future side effect attributes that result from modifying the attribute profile of the individual, wherein the candidate side effect attributes transmitted as output are transmitted as a rank-ordered tabulation containing corresponding statistical results that indicate: (i) the strength of association of the candidate side effect attributes in the tabulation with the identified attribute combinations, and (ii) the individual's potential for association with each of the predicted cumulative future side effect attributes; e) updating the modified attribute profile with the predicted cumulative future side effect attributes; and f) repeating steps (a)-(e) until no further attribute combinations can be identified in step (c); g) compiling the predicted cumulative future side effect attributes into at least two subgroups corresponding to desirable and undesirable side effects. ### Claim 2 (depends on 1) The bioinformatics computer of claim 1, wherein the output is transmitted to at least one destination selected from the group consisting of a user, a database, a dataset, a computer readable memory, a computer readable medium, a computer processor, a computer network, a printout device, a visual display, and a wireless receiver. ### Claim 3 (depends on 1) The bioinformatics computer of claim 1, wherein the corresponding statistical results meet at least one predetermined statistical threshold. ### Claim 4 (depends on 1) The bioinformatics computer of claim 1, wherein the strength of association of an identified attribute combination with said candidate side effect attribute must meet at least one predetermined statistical threshold in order for the candidate side effect attribute to be transmitted as output. ### Claim 5 (depends on 1) The bioinformatics computer of claim 1, further comprising: g) associating the set of predicted cumulative future side effect attributes with the individual and storing the association. ### Claim 6 A computer program tangibly embodied on a non-transitory computer readable medium which, when read by the computer, causes execution of a series of steps by said computer having an input device, a processor, a memory, and an output device, where said steps are a bioinformatics method for predicting future side effects that result from modifying an attribute profile of an individual, comprising: a) accessing a previously modified attribute profile, wherein the previously modified attribute profile comprises an attribute profile of an individual that has been previously modified as to a set of pre-existing attributes associated with that individual, wherein the identity of the individual is masked or anonymized; b) accessing a set containing attribute combinations and corresponding statistical results that indicate the strength of association of each of the attribute combinations with one or more candidate side effect attributes, wherein each of the attribute combinations comprises at least one pangenetic attribute and at least one non-pangenetic attribute, and wherein the one or more candidate side effect attributes comprise pangenetic attributes and non-pangenetic attributes that do not occur in the previously modified attribute profile, the candidate side effect attributes being filtered to exclude user specified attributes; c) said processor identifying attribute combinations contained in the dataset that also occur in the previously modified attribute profile; d) transmitting one or more candidate side effect attributes that are statistically associated with the identified attribute combinations as output, to generate a set of predicted cumulative future side effect attributes that result from modifying the attribute profile of the individual, wherein the candidate side effect attributes transmitted as output are transmitted as a rank-ordered tabulation containing corresponding statistical results that indicate: i) the strength of association of the candidate side effect attributes in the tabulation with the identified attribute combinations, and ii) the individual's potential for association with each of the predicted cumulative future side effect attributes; e) updating the modified attribute profile with the predicted cumulative future side effect attributes; f) repeating steps (a)-(e) until no further attribute combinations can be identified in step (c); and g) compiling the predicted cumulative future side effect attributes into at least two subgroups corresponding to desirable and undesirable side effects. ### Claim 7 A bioinformatics database system, including a computer having a data input device, a processor, a memory, and a data output device, for predicting future side effects that result from modifying an attribute profile of an individual, comprising: a) said memory containing: i) a first data structure containing a previously modified attribute profile, wherein the previously modified attribute profile comprises an attribute profile of an individual that has been previously modified as to a set of pre-existing attributes associated with that individual, wherein the identity of the individual is masked or anonymized, wherein each of the attribute combinations comprises at least one pangenetic attribute and at least one non-pangenetic attribute, and wherein the one or more candidate side effect attributes comprise pangenetic attributes and non-pangenetic attributes that do not occur in the previously modified attribute profile, the candidate side effect attributes being filtered to exclude user specified attributes; ii) a second data structure in said memory containing attribute combinations and corresponding statistical results that indicate the strength of association of each of the attribute combinations with one or more candidate side effect attributes; b) said processor further: i) accessing the first data structure; ii) accessing the second data structure; iii) identifying attribute combinations contained in the second data structure that also occur in the previously modified attribute profile contained in the first data structure: iv) transmitting through said output device one or more candidate side effect attributes that are statistically associated with the identified attribute combinations as output, to generate a set of predicted cumulative future side effect attributes that result from modifying the attribute profile of the individual, wherein the candidate side effect attributes transmitted as output are transmitted as a rank-ordered tabulation containing corresponding statistical results that indicate: (a) the strength of association of the candidate side effect attributes in the tabulation with the identified attribute combinations, and (b) the individual's potential for association with each of the predicted cumulative future side effect attributes; v) updating the modified attribute profile with the predicted cumulative future side effect attributes; vi) repeating steps (i)-(iv) until no further attribute combinations can be identified in step (iii); and vii) compiling the predicted cumulative future side effect attributes into at least two subgroups corresponding to desirable and undesirable side effects. ### Claim 8 A bioinformatics computer-based system, including a computer having a data input device, a processor, a memory, and a data output device, for predicting side effects that result from modifying an attribute profile of an individual, comprising: a) said processor comprising a first data accessing subsystem for accessing a previously modified attribute profile contained in said memory, wherein the previously modified attribute profile comprises an attribute profile of an individual that has been previously modified as to a set of pre-existing attributes associated with that individual, wherein the identity of the individual is masked or anonymized; b) said processor also comprising a second data accessing subsystem for accessing a set in said memory containing attribute combinations and corresponding statistical results that indicate the strength of association of each of the attribute combinations with one or more candidate side effect attributes, wherein each of the attribute combinations comprises at least one pangenetic attribute and at least one non-pangenetic attribute, and wherein the one or more candidate side effect attributes comprise pangenetic attributes and non-pangenetic attributes that do not occur in the modified attribute profile, the candidate side effect attributes being filtered to exclude user specified attributes; c) said processor identifying attribute combinations contained in the set that also occur in the previously modified attribute profile; and d) said output device comprising a data communications subsystem for transmitting one or more candidate side effect attributes that are statistically associated with the identified attribute combinations as output, to generate a set of predicted cumulative future side effect attributes that result from modifying the attribute profile of the individual, wherein the candidate side effect attributes transmitted as output are transmitted as a rank-ordered tabulation containing corresponding statistical results that indicate: i) the strength of association of the candidate side effect attributes in the tabulation with the identified attribute combinations, and ii) the individual's potential for association with each of the predicted cumulative future side effect attributes; e) updating the modified attribute profile with the predicted cumulative future side effect ,attributes; f) repeating steps (a)-(e) until no further attribute combinations can be identified in step (c); and g) compiling the predicted cumulative future side effect attributes into at least two subgroups corresponding to desirable and undesirable side effects.