MOTIVATION: Aberrant DNA methylation is a fundamental epigenetic hallmark of cancer. However, existing resources often lack technological diversity and comprehensive cancer coverage. Furthermore, most platforms fail to achieve deep multi-omics integration and tend to ignore cancer-type-specific methylation features, limiting their utility in precision oncology and drug discovery. RESULTS: We developed Cancer Methylation Atlas (CMAtlas), a comprehensive platform integrating 13 753 samples across 34 cancer types. By applying technology-tailored pipelines to data from various profiling technologies, we identified 830 725 tumor-specific differentially methylated elements (DMEs) and 1 480 098 differentially methylated regions (DMRs), alongside 1 154 256 cancer-type-specific DMEs and 329 154 DMRs. The platform demonstrates high cross-platform consistency and strong concordance between tumor tissues and cell lines, ensuring the robustness of our findings. All DMEs and DMRs are annotated with multi-omics data (RNA expression, somatic mutations, and chromatin accessibility) and clinical relevance (survival associations and cell-free DNA profiling). We further demonstrate the utility of CMAtlas by identifying prognostic aberrant methylation in colorectal cancer driver genes. AVAILABILITY AND IMPLEMENTATION: CMAtlas is freely accessible at {{https://cmatlas.renlab.cn/}}. The platform offers an intuitive web interface supporting gene-centric and cancer-centric queries, alongside customizable analysis modules designed to facilitate user-specific research needs.

OBJECTIVES: Direct electronic access to multiple electronic health record (EHR) systems through patient portals offers a novel avenue for decentralized research. Given the critical value of patient characterization, we sought to compare computable evaluation of health conditions from patient-portal EHR against the traditional self-report. MATERIALS AND METHODS: In the nationwide Innovative Support for Patients with SARS-CoV-2 Infections Registry (INSPIRE) study, which linked self-reported questionnaires with multiplatform patient-portal EHR data, we compared self-reported health conditions across different clinical domains against computable definitions based on diagnosis codes, medications, vital signs, and laboratory testing. We assessed their concordance using Cohen's Kappa and the prognostic significance of differentially captured features as predictors of 1-year all-cause hospitalization risk. RESULTS: Among 1683 participants (mean age 41 ± 15 years, 67% female, 63% non-Hispanic Whites), the prevalence of conditions varied substantially between EHR and self-report (-13.2% to +11.6% across definitions). Compared with comprehensive EHR phenotypes, self-report under-captured all conditions, including hypertension (27.9% vs 16.2%), diabetes (10.1% vs 6.2%), and heart disease (8.5% vs 4.3%). However, diagnosis codes alone were insufficient. The risk for 1-year hospitalization was better defined by the same features from patient-portal EHR (area under the receiver operating curve [AUROC] 0.79) than from self-report (AUROC 0.68). DISCUSSION: EHR-derived computable phenotypes identified a higher prevalence of comorbidities than self-report, with prognostic value of additionally identified features. However, definitions based solely on diagnosis codes often undercaptured self-reported conditions, suggesting a role of broader EHR elements. CONCLUSION: In this nationwide study, patient-portal-derived EHR data enabled extensive capture of patient characteristics across multiple EHR platforms, allowing better disease phenotyping compared with self-report.