Legal-Ethical Challenges and Technological Solutions to e-Health Data Consent in the EU

e-Health data is sensitive and consenting to the collection, processing, and sharing involves compliance with legal requirements, ethical standards, and appropriate digital tools. We explore two legal-ethical challenges: 1) What are the scope and requirements of digital health data consent? 2) What are the legal-ethical reasons for obtaining consent beyond the GDPR’s legal basis, and how might such consent be obtained? We then propose human-centered solutions to help navigate standards of ethical and legal consent across the EU, purposefully addressing those use cases to compensate for human difficulties in managing consent without clear guidelines. These solutions – including ISO standards, ontologies, consent mechanisms, value-centered privacy assistants, and layered dynamic consent platforms – complement and aid humans to help uphold ethical and rigorous consent

Conciseness, interest, and unexpectedness: User attitudes towards infographic and comic consent mediums

Being asked to consent to data sharing is a ubiquitous experience in digital services - yet it is very rare to encounter a well designed consent experience. Considering the momentum and importance of a European data space where personal information freely and easily flows across organizations, sectors and Member States, solving the long-discussed thorny issue of "how to get consent right" cannot be postponed any further. In this paper, we describe the first findings from a study based on 24 semi-structured interviews investigating participants’ expectations and opinions toward consent in a data sharing scenario with a data trustee. We analyzed various dimensions of a consent form redesigned as a comic and an infographic, including language, information design, content and the writer-reader relationship. The results provide insights into the complexity of elements that should be considered when asking individuals to freely and mindfully disclose their data, especially sensitive information

Sage-Bionetworks/schematic: v23.9.2

What's Changed implement GE list rule by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/655 Develop initial rule pairs by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/802 Cross Manifest Validation: Value Level Comparisons and Reworked Warning Messages by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/751 Develop schema viz tool tests by @mialy-defelice in https://github.com/Sage-Bionetworks/schematic/pull/659 make sorting case insensitive by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/830 Develop fix submit keyerror by @mialy-defelice in https://github.com/Sage-Bionetworks/schematic/pull/831 updating the release documentation by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/817 Develop an endpoint to return data types of columns in a manifest by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/815 Develop rule combination by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/766 BugFix: Import dataType from CLI as list not string by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/836 BugFix: Manifest Import - Mask null cells as empty strings instead of NaNs by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/837 BugFix: list like behavior by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/840 Check type of 'url' entry when raising errors by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/844 Fix example data model list validation rule and update "list" in ManifestGenerator to handle both list strict and list like by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/847 add warning to validate_manifest endpoint by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/859 Develop NA string behavior by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/842 Develop blank annotation behavior by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/862 Develop Missing Entity Handling by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/871 rename manifest based on manifest_basename when submit to synapse by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/869 Output errors generated from jsonSchema (when submitting manifest) to the console by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/873 Develop manifest submission error handle by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/879 do not create dir if located in cwd by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/881 Update annotations unit test by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/880 Develop optional rule args by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/843 Containerizing schematic (and update dependencies as needed) by @BrunoGrandePhD in https://github.com/Sage-Bionetworks/schematic/pull/882 add endpoint find_class_specific_properties by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/890 add route get_subgraph_by_edge_type by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/891 create endpoint to return schema as a pickle file by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/892 poetry documentation by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/895 Add support for Schematic API to Dockerfile by @BrunoGrandePhD in https://github.com/Sage-Bionetworks/schematic/pull/887 Create project table manifests, move entities to new project by @mialy-defelice in https://github.com/Sage-Bionetworks/schematic/pull/829 add concurrency to github action by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/896 HOTFIX: Mixed type column manifest table upload by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/902 update asset view table endpoint to allow returning a json by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/912 added get_node_range endpoint by @andrewelamb in https://github.com/Sage-Bionetworks/schematic/pull/904 added get_property_label endpoint by @andrewelamb in https://github.com/Sage-Bionetworks/schematic/pull/905 added node_dependencies endpoint by @andrewelamb in https://github.com/Sage-Bionetworks/schematic/pull/906 Allow schema.org schema to be loaded and used by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/903 add example workbook to demo cli functions by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/916 change manifest name for censored manifest when upload by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/931 Add Restriction Flag to Make Synapse Table Method by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/935 Develop Table Uploads: Replace by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/917 allow users to upload csv or json file when submitting manifest using API endpoints by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/908 allow users to upload csv or json file when validating manifest using API endpoints by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/910 Develop table schema fix replacements by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/947 Fixing parsing of table schema parameters on table replace by @milen-sage in https://github.com/Sage-Bionetworks/schematic/pull/945 Develop schema viz tool cors by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/942 Move Schema Visualization to Schematic by @mialy-defelice in https://github.com/Sage-Bionetworks/schematic/pull/645 add default max size for columns missing this key by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/952 populate manifest as an excel spreadsheet without sending data to Google api by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/940 Skip Trashed Entities and Entities that "do not exist" by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/985 Reword conditional requirements for the attribute table by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/987 add tests related to manifest get by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/979 fix api endpoint for docker container by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/974 Remove unused libraries by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/991 Remove Manifest Table Submission Dependency on Project Scope when not Validating by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/989 HOTFIX: Extend table replacement sleep duration to ensure synapse deletion operation completes by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/999 Pass config.yml as an environment variable to docker container by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/975 update error messages in synapseStore when manifest_basename key is missing in config.yml by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/997 Added instructions for installing and using schematic and the schematic API docker containers to README by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/953 Develop pdoc by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/957 correct typo: master_basename to manifest_basename in error message by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1005 Fixed typo in conditional requirement for schema viz attribute table by adding quotes by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1003 Added tests for all API endpoints by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/995 Fixed an issue where the DCA would disconnect on manifest submission by casting UUIDs to type string by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1006 Reminded users to run synapse login --rememberMe after schematic init step in ReadMe by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1004 Added the option to populate manifest as an excel spreadsheet to avoid sending metadata to Google APIs by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/994 For schematic APIs, return excel file instead of excel file path by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/988 Emphasized that users should download the config.yml from develop branch in ReadMe by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1007 Removed validity requirement for unrequired attribute entries, allow users to specify validation rule conformity required for entries, fix DCA disconnect caused by JSON Schema validation errors by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1000 Strip hyphens from Synapse annotation keys by @milen-sage in https://github.com/Sage-Bionetworks/schematic/pull/1020 Fixed a bug where in some instances manifests would be uploaded with different display and downloadAs names by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1017 Added an API endpoint to check if a given node is required or not by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1024 added more instructions of running CLI in jupyter notebook by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1031 Added a slack bot to notify successful new releases by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1025 Turned service_account_creds.json as an environment variable and default way of authentication by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1015 Changed base docker image and removed package for security reasons by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1037 Add support for treating date entries as type datetime by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1041 Automatically updated CLI documentation on Readthedocs by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1047 Deprecated token pickle and credentials.json by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1040 Introduce tests to cover current table operations: creation and replacement by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1046 Skip api tests when rule combination tests are run by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1068 Added workflow to deploy schematic docker container in Github container registry by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1062 Remove schematic support for Python v3.7 and v3.8 by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1090 Refactor table operations structure in asset store by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1069 Added input_token as a parameter for /manifest/get endpoint to fix credential issues when getting an existing manifest on AWS by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1080 Fixed getProjectManifests function in synapse storage by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1084 Develop api node display names by @mialy-defelice in https://github.com/Sage-Bionetworks/schematic/pull/1094 Create API endpoint for get_node_validation_rules by @mialy-defelice in https://github.com/Sage-Bionetworks/schematic/pull/1095 Update schematic dependencies by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1092 Raise errors for wrong schema errors by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1073 Set default of "table_manipulation" as "replace" in API endpoint when users enter None and updated tests by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1115 Update synapseClient dependency and api for manifest table uploads by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1101 set pyopenssl = "^23.0.0" by @andrewelamb in https://github.com/Sage-Bionetworks/schematic/pull/1125 added date GE rule by @andrewelamb in https://github.com/Sage-Bionetworks/schematic/pull/1103 Implement table upsert feature by using schematic-db by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1081 Add use_schema_label parameter to manifest submission endpoint, separate manifest submission and table upsert tests by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1129 Delete GE checkpoint after completion of GE validation by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1136 Remove try: catch: block from manifest submission command function by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1130 Save all properties that are Included in the domain of a Class by @mialy-defelice in https://github.com/Sage-Bionetworks/schematic/pull/1134 Display exceptions raised during validation with Great expectations, allow exclusion of upper bound OR lower bound for inRange rule by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1131 Update Documentation - python/package versions and POCs by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1139 Increase buffer size to a higher limit to deal with long token by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1144 lock schematic-db to version 0.0.6 by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1145 use try: finally: to delete checkpoint even if running the checkpoint fails or errors out by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1155 Allowed CORS on given routes instead of all routes by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1168 Added restrict rules param to manifest/validate by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1178 Bug Fix: remedy negation of table manipulation specification by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1186 Added an endpoint to check entity type on Synapse and an endpoint to check if an entity is in the asset view by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1078 add restrict rules control to manifest validate by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1189 Added a parameter to control if GE gets used when using manifest/validate endpoint by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1177 Propagate logger level entered in from command line to other schematic submodules by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1180 Add timing of validation operations to DEBUG log by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1181 Standardize validation error format and type by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1183 Added function to calculate and clear cache by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1190 Develop add file only manifest submission option by @mialy-defelice in https://github.com/Sage-Bionetworks/schematic/pull/1175 Create example data model for single rule benchmarking by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1193 Develop api tests for benchmarking single rule validation performance by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1184 Fixed column headers problem when generating an Excel spreadsheet for getting an existing manifest by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1164 Do not index attribute visualization dataframe when converting to csv for component viz endpoint by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1196 Remove restrictions on rule number and allowed combinations by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1203 Start checking mypy and black by @andrewelamb in https://github.com/Sage-Bionetworks/schematic/pull/1204 Add IsNA rule to validation suite | FDS-81 FDS-232 by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1200 Add API endpoint to visualize attributes for a specific component by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1195 Added functionality to download a manifest by using the manifest id by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1192 Introduce workflow for API tests by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1208 Remove requirement for .synapseConfig file to use upsert feature by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1207 Parallelize operations in load_df by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1100 Id Column - fix bug preventing table updates by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1214 Id Column - fix bug where there would be two columns with uuid values by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1215 Merge AWS deployment branch to develop by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1142 Id Column - fix bug preventing upserts by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1216 Downloaded manifests to temporary folders on AWS by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1210 FDS-293 Fix column mismatch for Excel File Based Manifest Generation by @mialy-defelice in https://github.com/Sage-Bionetworks/schematic/pull/1213 Feature fds 361 pylint by @andrewelamb in https://github.com/Sage-Bionetworks/schematic/pull/1212 Changed workflow to run poetry version 1.2.0 by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1222 remove breakpoint from command by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1224 Restrict typing-extensions package to versions before v4.6.0 by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1228 Make aws group dependencies optional and restrict typing_extensions package version by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1227 Change Uuid column name to Id by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1211 Avoided publishing minor releases to Docker Hub by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1231 Remove lock on schematic_db version - FDS-287 by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1232 feat: added nginx to encrypt the communication between ALB and API by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1202 Installed schematic in docker file by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1230 fix: Fixed unit test in test_manifest by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1233 Fix formatting issues when pulling data from Synapse to Excel Manifest by @mialy-defelice in https://github.com/Sage-Bionetworks/schematic/pull/1234 fix: fixed tests in test_api.py by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1225 Added test manifest by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1238 [Bug fix]: Tried install pdoc again in github action workflow pdoc.yml by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1239 Replaced synapse API calls with synapse Python client call by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1235 Feat: allowed production tag, staging tag, and manual run on existing tags to trigger building docker images for AWS deployment by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1241 Added hide-blanks parameter when submitting manifest through API by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1242 Revert "Feat: allowed production tag, staging tag, and manual run on existing tags to trigger building docker images for AWS deployment" by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1243 feat: allowed production tag, staging tag, and manual run on existing tags to trigger building docker images for AWS deployment by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1244 [Bug fix]: Fix regex in docker build workflow by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1246 Revert "[Bug fix]: Fix regex in docker build workflow" by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1248 [Bug fix]: Fix regex in docker build workflow by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1249 Feature fds 273 coniguration by @andrewelamb in https://github.com/Sage-Bionetworks/schematic/pull/1219 Expose strict_validation option for manifest/generate endpoint by @mialy-defelice in https://github.com/Sage-Bionetworks/schematic/pull/1253 Optimize performance in table upsert backwards compatibility scenarios by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1229 Fix df_utils/load_df so it more accurately captures integers to prevent Regex Errors. by @mialy-defelice in https://github.com/Sage-Bionetworks/schematic/pull/1240 Use FAIR Data service desk for issues by @afwillia in https://github.com/Sage-Bionetworks/schematic/pull/1257 Update Black to 2023 version: 23.7.0 by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1262 Update mypy to latest version by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1263 Updated cli help text for parameter json_schema by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1264 Modified Nginx parameters to fix submission issue by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1255 modify tag by @linglp in https://github.com/Sage-Bionetworks/schematic/pull/1251 BugFix: Fixed an issue where files on synapse were not being annotated correctly by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1254 [bug fix] Fixed errors when calling get_empty_manifest by @linglp in https://github.com/Sage-Bionetwork

Sage-Bionetworks/schematic: v23.9.3

What's Changed BugFix: is_class_in_schema no longer errors out when a class is not in schema by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1287 BugFix: Fix error when use_annotations=True for record based metadata where there are no existing annotations by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1285 Bug Fix: Adding annotations to files with -mrt file_only parameter by @mialy-defelice in https://github.com/Sage-Bionetworks/schematic/pull/1290 Develop markers for api tests according to credentials required FDS-1026 by @GiaJordan in https://github.com/Sage-Bionetworks/schematic/pull/1289 Full Changelog: https://github.com/Sage-Bionetworks/schematic/compare/v23.9.2...v23.9.

Key Parameters of Tumor Epitope Immunogenicity Revealed Through a Consortium Approach Improve Neoantigen Prediction

Many approaches to identify therapeutically relevant neoantigens couple tumor sequencing with bioinformatic algorithms and inferred rules of tumor epitope immunogenicity. However, there are no reference data to compare these approaches, and the parameters governing tumor epitope immunogenicity remain unclear. Here, we assembled a global consortium wherein each participant predicted immunogenic epitopes from shared tumor sequencing data. 608 epitopes were subsequently assessed for T cell binding in patient-matched samples. By integrating peptide features associated with presentation and recognition, we developed a model of tumor epitope immunogenicity that filtered out 98% of non-immunogenic peptides with a precision above 0.70. Pipelines prioritizing model features had superior performance, and pipeline alterations leveraging them improved prediction performance. These findings were validated in an independent cohort of 310 epitopes prioritized from tumor sequencing data and assessed for T cell binding. This data resource enables identification of parameters underlying effective anti-tumor immunity and is available to the research community

Key Parameters of Tumor Epitope Immunogenicity Revealed Through a Consortium Approach Improve Neoantigen Prediction

Many approaches to identify therapeutically relevant neoantigens couple tumor sequencing with bioinformatic algorithms and inferred rules of tumor epitope immunogenicity. However, there are no reference data to compare these approaches, and the parameters governing tumor epitope immunogenicity remain unclear. Here, we assembled a global consortium wherein each participant predicted immunogenic epitopes from shared tumor sequencing data. 608 epitopes were subsequently assessed for T cell binding in patient-matched samples. By integrating peptide features associated with presentation and recognition, we developed a model of tumor epitope immunogenicity that filtered out 98% of non-immunogenic peptides with a precision above 0.70. Pipelines prioritizing model features had superior performance, and pipeline alterations leveraging them improved prediction performance. These findings were validated in an independent cohort of 310 epitopes prioritized from tumor sequencing data and assessed for T cell binding. This data resource enables identification of parameters underlying effective anti-tumor immunity and is available to the research community

Key Parameters of Tumor Epitope Immunogenicity Revealed Through a Consortium Approach Improve Neoantigen Prediction

Many approaches to identify therapeutically relevant neoantigens couple tumor sequencing with bioinformatic algorithms and inferred rules of tumor epitope immunogenicity. However, there are no reference data to compare these approaches, and the parameters governing tumor epitope immunogenicity remain unclear. Here, we assembled a global consortium wherein each participant predicted immunogenic epitopes from shared tumor sequencing data. 608 epitopes were subsequently assessed for T cell binding in patient-matched samples. By integrating peptide features associated with presentation and recognition, we developed a model of tumor epitope immunogenicity that filtered out 98% of non-immunogenic peptides with a precision above 0.70. Pipelines prioritizing model features had superior performance, and pipeline alterations leveraging them improved prediction performance. These findings were validated in an independent cohort of 310 epitopes prioritized from tumor sequencing data and assessed for T cell binding. This data resource enables identification of parameters underlying effective anti-tumor immunity and is available to the research community