Clinical Decision Support Documents Description
Generate professional clinical decision support (CDS) documents for pharmaceutical companies, clinical researchers, and medical decision-makers. This skill specializes in analytical, evidence-based documents that inform treatment strategies and drug development:
Patient Cohort Analysis - Biomarker-stratified group analyses with statistical outcome comparisons Treatment Recommendation Reports - Evidence-based clinical guidelines with GRADE grading and decision algorithms
All documents are generated as publication-ready LaTeX/PDF files optimized for pharmaceutical research, regulatory submissions, and clinical guideline development.
Note: For individual patient treatment plans at the bedside, use the treatment-plans skill instead. This skill focuses on group-level analyses and evidence synthesis for pharmaceutical/research settings.
Capabilities Document Types
Patient Cohort Analysis
Biomarker-based patient stratification (molecular subtypes, gene expression, IHC) Molecular subtype classification (e.g., GBM mesenchymal-immune-active vs proneural, breast cancer subtypes) Outcome metrics with statistical analysis (OS, PFS, ORR, DOR, DCR) Statistical comparisons between subgroups (hazard ratios, p-values, 95% CI) Survival analysis with Kaplan-Meier curves and log-rank tests Efficacy tables and waterfall plots Comparative effectiveness analyses Pharmaceutical cohort reporting (trial subgroups, real-world evidence)
Treatment Recommendation Reports
Evidence-based treatment guidelines for specific disease states Strength of recommendation grading (GRADE system: 1A, 1B, 2A, 2B, 2C) Quality of evidence assessment (high, moderate, low, very low) Treatment algorithm flowcharts with TikZ diagrams Line-of-therapy sequencing based on biomarkers Decision pathways with clinical and molecular criteria Pharmaceutical strategy documents Clinical guideline development for medical societies Clinical Features Biomarker Integration: Genomic alterations (mutations, CNV, fusions), gene expression signatures, IHC markers, PD-L1 scoring Statistical Analysis: Hazard ratios, p-values, confidence intervals, survival curves, Cox regression, log-rank tests Evidence Grading: GRADE system (1A/1B/2A/2B/2C), Oxford CEBM levels, quality of evidence assessment Clinical Terminology: SNOMED-CT, LOINC, proper medical nomenclature, trial nomenclature Regulatory Compliance: HIPAA de-identification, confidentiality headers, ICH-GCP alignment Professional Formatting: Compact 0.5in margins, color-coded recommendations, publication-ready, suitable for regulatory submissions Pharmaceutical and Research Use Cases
This skill is specifically designed for pharmaceutical and clinical research applications:
Drug Development
Phase 2/3 Trial Analyses: Biomarker-stratified efficacy and safety analyses Subgroup Analyses: Forest plots showing treatment effects across patient subgroups Companion Diagnostic Development: Linking biomarkers to drug response Regulatory Submissions: IND/NDA documentation with evidence summaries
Medical Affairs
KOL Education Materials: Evidence-based treatment algorithms for thought leaders Medical Strategy Documents: Competitive landscape and positioning strategies Advisory Board Materials: Cohort analyses and treatment recommendation frameworks Publication Planning: Manuscript-ready analyses for peer-reviewed journals
Clinical Guidelines
Guideline Development: Evidence synthesis with GRADE methodology for specialty societies Consensus Recommendations: Multi-stakeholder treatment algorithm development Practice Standards: Biomarker-based treatment selection criteria Quality Measures: Evidence-based performance metrics
Real-World Evidence
RWE Cohort Studies: Retrospective analyses of patient cohorts from EMR data Comparative Effectiveness: Head-to-head treatment comparisons in real-world settings Outcomes Research: Long-term survival and safety in clinical practice Health Economics: Cost-effectiveness analyses by biomarker subgroup When to Use
Use this skill when you need to:
Analyze patient cohorts stratified by biomarkers, molecular subtypes, or clinical characteristics Generate treatment recommendation reports with evidence grading for clinical guidelines or pharmaceutical strategies Compare outcomes between patient subgroups with statistical analysis (survival, response rates, hazard ratios) Produce pharmaceutical research documents for drug development, clinical trials, or regulatory submissions Develop clinical practice guidelines with GRADE evidence grading and decision algorithms Document biomarker-guided therapy selection at the population level (not individual patients) Synthesize evidence from multiple trials or real-world data sources Create clinical decision algorithms with flowcharts for treatment sequencing
Do NOT use this skill for:
Individual patient treatment plans (use treatment-plans skill) Bedside clinical care documentation (use treatment-plans skill) Simple patient-specific treatment protocols (use treatment-plans skill) Visual Enhancement with Scientific Schematics
⚠️ MANDATORY: Every clinical decision support document MUST include at least 1-2 AI-generated figures using the scientific-schematics skill.
This is not optional. Clinical decision documents require clear visual algorithms. Before finalizing any document:
Generate at minimum ONE schematic or diagram (e.g., clinical decision algorithm, treatment pathway, or biomarker stratification tree) For cohort analyses: include patient flow diagram For treatment recommendations: include decision flowchart
How to generate figures:
Use the scientific-schematics skill to generate AI-powered publication-quality diagrams Simply describe your desired diagram in natural language Nano Banana Pro will automatically generate, review, and refine the schematic
How to generate schematics:
python scripts/generate_schematic.py "your diagram description" -o figures/output.png
The AI will automatically:
Create publication-quality images with proper formatting Review and refine through multiple iterations Ensure accessibility (colorblind-friendly, high contrast) Save outputs in the figures/ directory
When to add schematics:
Clinical decision algorithm flowcharts Treatment pathway diagrams Biomarker stratification trees Patient cohort flow diagrams (CONSORT-style) Survival curve visualizations Molecular mechanism diagrams Any complex concept that benefits from visualization
For detailed guidance on creating schematics, refer to the scientific-schematics skill documentation.
Document Structure
CRITICAL REQUIREMENT: All clinical decision support documents MUST begin with a complete executive summary on page 1 that spans the entire first page before any table of contents or detailed sections.
Page 1 Executive Summary Structure
The first page of every CDS document should contain ONLY the executive summary with the following components:
Required Elements (all on page 1):
Document Title and Type
Main title (e.g., "Biomarker-Stratified Cohort Analysis" or "Evidence-Based Treatment Recommendations") Subtitle with disease state and focus
Report Information Box (using colored tcolorbox)
Document type and purpose Date of analysis/report Disease state and patient population Author/institution (if applicable) Analysis framework or methodology
Key Findings Boxes (3-5 colored boxes using tcolorbox)
Primary Results (blue box): Main efficacy/outcome findings Biomarker Insights (green box): Key molecular subtype findings Clinical Implications (yellow/orange box): Actionable treatment implications Statistical Summary (gray box): Hazard ratios, p-values, key statistics Safety Highlights (red box, if applicable): Critical adverse events or warnings
Visual Requirements:
Use \thispagestyle{empty} to remove page numbers from page 1 All content must fit on page 1 (before \newpage) Use colored tcolorbox environments with different colors for visual hierarchy Boxes should be scannable and highlight most critical information Use bullet points, not narrative paragraphs End page 1 with \newpage before table of contents or detailed sections
Example First Page LaTeX Structure:
\maketitle \thispagestyle{empty}
% Report Information Box \begin{tcolorbox}[colback=blue!5!white, colframe=blue!75!black, title=Report Information] \textbf{Document Type:} Patient Cohort Analysis\ \textbf{Disease State:} HER2-Positive Metastatic Breast Cancer\ \textbf{Analysis Date:} \today\ \textbf{Population:} 60 patients, biomarker-stratified by HR status \end{tcolorbox}
\vspace{0.3cm}
% Key Finding #1: Primary Results \begin{tcolorbox}[colback=blue!5!white, colframe=blue!75!black, title=Primary Efficacy Results] \begin{itemize} \item Overall ORR: 72\% (95\% CI: 59-83\%) \item Median PFS: 18.5 months (95\% CI: 14.2-22.8) \item Median OS: 35.2 months (95\% CI: 28.1-NR) \end{itemize} \end{tcolorbox}
\vspace{0.3cm}
% Key Finding #2: Biomarker Insights \begin{tcolorbox}[colback=green!5!white, colframe=green!75!black, title=Biomarker Stratification Findings] \begin{itemize} \item HR+/HER2+: ORR 68\%, median PFS 16.2 months \item HR-/HER2+: ORR 78\%, median PFS 22.1 months \item HR status significantly associated with outcomes (p=0.041) \end{itemize} \end{tcolorbox}
\vspace{0.3cm}
% Key Finding #3: Clinical Implications \begin{tcolorbox}[colback=orange!5!white, colframe=orange!75!black, title=Clinical Recommendations] \begin{itemize} \item Strong efficacy observed regardless of HR status (Grade 1A) \item HR-/HER2+ patients showed numerically superior outcomes \item Treatment recommended for all HER2+ MBC patients \end{itemize} \end{tcolorbox}
\newpage \tableofcontents % TOC on page 2 \newpage % Detailed content starts page 3
Patient Cohort Analysis (Detailed Sections - Page 3+) Cohort Characteristics: Demographics, baseline features, patient selection criteria Biomarker Stratification: Molecular subtypes, genomic alterations, IHC profiles Treatment Exposure: Therapies received, dosing, treatment duration by subgroup Outcome Analysis: Response rates (ORR, DCR), survival data (OS, PFS), DOR Statistical Methods: Kaplan-Meier survival curves, hazard ratios, log-rank tests, Cox regression Subgroup Comparisons: Biomarker-stratified efficacy, forest plots, statistical significance Safety Profile: Adverse events by subgroup, dose modifications, discontinuations Clinical Recommendations: Treatment implications based on biomarker profiles Figures: Waterfall plots, swimmer plots, survival curves, forest plots Tables: Demographics table, biomarker frequency, outcomes by subgroup Treatment Recommendation Reports (Detailed Sections - Page 3+)
Page 1 Executive Summary for Treatment Recommendations should include:
Report Information Box: Disease state, guideline version/date, target population Key Recommendations Box (green): Top 3-5 GRADE-graded recommendations by line of therapy Biomarker Decision Criteria Box (blue): Key molecular markers influencing treatment selection Evidence Summary Box (gray): Major trials supporting recommendations (e.g., KEYNOTE-189, FLAURA) Critical Monitoring Box (orange/red): Essential safety monitoring requirements
Detailed Sections (Page 3+):
Clinical Context: Disease state, epidemiology, current treatment landscape Target Population: Patient characteristics, biomarker criteria, staging Evidence Review: Systematic literature synthesis, guideline summary, trial data Treatment Options: Available therapies with mechanism of action Evidence Grading: GRADE assessment for each recommendation (1A, 1B, 2A, 2B, 2C) Recommendations by Line: First-line, second-line, subsequent therapies Biomarker-Guided Selection: Decision criteria based on molecular profiles Treatment Algorithms: TikZ flowcharts showing decision pathways Monitoring Protocol: Safety assessments, efficacy monitoring, dose modifications Special Populations: Elderly, renal/hepatic impairment, comorbidities References: Full bibliography with trial names and citations Output Format
MANDATORY FIRST PAGE REQUIREMENT:
Page 1: Full-page executive summary with 3-5 colored tcolorbox elements Page 2: Table of contents (optional) Page 3+: Detailed sections with methods, results, figures, tables
Document Specifications:
Primary: LaTeX/PDF with 0.5in margins for compact, data-dense presentation Length: Typically 5-15 pages (1 page executive summary + 4-14 pages detailed content) Style: Publication-ready, pharmaceutical-grade, suitable for regulatory submissions First Page: Always a complete executive summary spanning entire page 1 (see Document Structure section)
Visual Elements:
Colors: Page 1 boxes: blue=data/information, green=biomarkers/recommendations, yellow/orange=clinical implications, red=warnings Recommendation boxes (green=strong recommendation, yellow=conditional, blue=research needed) Biomarker stratification (color-coded molecular subtypes) Statistical significance (color-coded p-values, hazard ratios) Tables: Demographics with baseline characteristics Biomarker frequency by subgroup Outcomes table (ORR, PFS, OS, DOR by molecular subtype) Adverse events by cohort Evidence summary tables with GRADE ratings Figures: Kaplan-Meier survival curves with log-rank p-values and number at risk tables Waterfall plots showing best response by patient Forest plots for subgroup analyses with confidence intervals TikZ decision algorithm flowcharts Swimmer plots for individual patient timelines Statistics: Hazard ratios with 95% CI, p-values, median survival times, landmark survival rates Compliance: De-identification per HIPAA Safe Harbor, confidentiality notices for proprietary data Integration
This skill integrates with:
scientific-writing: Citation management, statistical reporting, evidence synthesis clinical-reports: Medical terminology, HIPAA compliance, regulatory documentation scientific-schematics: TikZ flowcharts for decision algorithms and treatment pathways treatment-plans: Individual patient applications of cohort-derived insights (bidirectional) Key Differentiators from Treatment-Plans Skill
Clinical Decision Support (this skill):
Audience: Pharmaceutical companies, clinical researchers, guideline committees, medical affairs Scope: Population-level analyses, evidence synthesis, guideline development Focus: Biomarker stratification, statistical comparisons, evidence grading Output: Multi-page analytical documents (5-15 pages typical) with extensive figures and tables Use Cases: Drug development, regulatory submissions, clinical practice guidelines, medical strategy Example: "Analyze 60 HER2+ breast cancer patients by hormone receptor status with survival outcomes"
Treatment-Plans Skill:
Audience: Clinicians, patients, care teams Scope: Individual patient care planning Focus: SMART goals, patient-specific interventions, monitoring plans Output: Concise 1-4 page actionable care plans Use Cases: Bedside clinical care, EMR documentation, patient-centered planning Example: "Create treatment plan for a 55-year-old patient with newly diagnosed type 2 diabetes"
When to use each:
Use clinical-decision-support for: cohort analyses, biomarker stratification studies, treatment guideline development, pharmaceutical strategy documents Use treatment-plans for: individual patient care plans, treatment protocols for specific patients, bedside clinical documentation Example Usage Patient Cohort Analysis
Example 1: NSCLC Biomarker Stratification
Analyze a cohort of 45 NSCLC patients stratified by PD-L1 expression (<1%, 1-49%, ≥50%) receiving pembrolizumab. Include outcomes: ORR, median PFS, median OS with hazard ratios comparing PD-L1 ≥50% vs <50%. Generate Kaplan-Meier curves and waterfall plot.
Example 2: GBM Molecular Subtype Analysis
Generate cohort analysis for 30 GBM patients classified into Cluster 1 (Mesenchymal-Immune-Active) and Cluster 2 (Proneural) molecular subtypes. Compare outcomes including median OS, 6-month PFS rate, and response to TMZ+bevacizumab. Include biomarker profile table and statistical comparison.
Example 3: Breast Cancer HER2 Cohort
Analyze 60 HER2-positive metastatic breast cancer patients treated with trastuzumab-deruxtecan, stratified by prior trastuzumab exposure (yes/no). Include ORR, DOR, median PFS with forest plot showing subgroup analyses by hormone receptor status, brain metastases, and number of prior lines.
Treatment Recommendation Report
Example 1: HER2+ Metastatic Breast Cancer Guidelines
Create evidence-based treatment recommendations for HER2-positive metastatic breast cancer including biomarker-guided therapy selection. Use GRADE system to grade recommendations for first-line (trastuzumab+pertuzumab+taxane), second-line (trastuzumab-deruxtecan), and third-line options. Include decision algorithm flowchart based on brain metastases, hormone receptor status, and prior therapies.
Example 2: Advanced NSCLC Treatment Algorithm
Generate treatment recommendation report for advanced NSCLC based on PD-L1 expression, EGFR mutation, ALK rearrangement, and performance status. Include GRADE-graded recommendations for each molecular subtype, TikZ flowchart for biomarker-directed therapy selection, and evidence tables from KEYNOTE-189, FLAURA, and CheckMate-227 trials.
Example 3: Multiple Myeloma Line-of-Therapy Sequencing
Create treatment algorithm for newly diagnosed multiple myeloma through relapsed/refractory setting. Include GRADE recommendations for transplant-eligible vs ineligible, high-risk cytogenetics considerations, and sequencing of daratumumab, carfilzomib, and CAR-T therapy. Provide flowchart showing decision points at each line of therapy.
Key Features Biomarker Classification Genomic: Mutations, CNV, gene fusions Expression: RNA-seq, IHC scores Molecular subtypes: Disease-specific classifications Clinical actionability: Therapy selection guidance Outcome Metrics Survival: OS (overall survival), PFS (progression-free survival) Response: ORR (objective response rate), DOR (duration of response), DCR (disease control rate) Quality: ECOG performance status, symptom burden Safety: Adverse events, dose modifications Statistical Methods Survival analysis: Kaplan-Meier curves, log-rank tests Group comparisons: t-tests, chi-square, Fisher's exact Effect sizes: Hazard ratios, odds ratios with 95% CI Significance: p-values, multiple testing corrections Evidence Grading
GRADE System
1A: Strong recommendation, high-quality evidence 1B: Strong recommendation, moderate-quality evidence 2A: Weak recommendation, high-quality evidence 2B: Weak recommendation, moderate-quality evidence 2C: Weak recommendation, low-quality evidence
Recommendation Strength
Strong: Benefits clearly outweigh risks Conditional: Trade-offs exist, patient values important Research: Insufficient evidence, clinical trials needed Best Practices For Cohort Analyses Patient Selection Transparency: Clearly document inclusion/exclusion criteria, patient flow, and reasons for exclusions Biomarker Clarity: Specify assay methods, platforms (e.g., FoundationOne, Caris), cut-points, and validation status Statistical Rigor: Report hazard ratios with 95% confidence intervals, not just p-values Include median follow-up time for survival analyses Specify statistical tests used (log-rank, Cox regression, Fisher's exact) Account for multiple comparisons when appropriate Outcome Definitions: Use standard criteria: Response: RECIST 1.1, iRECIST for immunotherapy Adverse events: CTCAE version 5.0 Performance status: ECOG or Karnofsky Survival Data Presentation: Median OS/PFS with 95% CI Landmark survival rates (6-month, 12-month, 24-month) Number at risk tables below Kaplan-Meier curves Censoring clearly indicated Subgroup Analyses: Pre-specify subgroups; clearly label exploratory vs pre-planned analyses Data Completeness: Report missing data and how it was handled For Treatment Recommendation Reports Evidence Grading Transparency: Use GRADE system consistently (1A, 1B, 2A, 2B, 2C) Document rationale for each grade Clearly state quality of evidence (high, moderate, low, very low) Comprehensive Evidence Review: Include phase 3 randomized trials as primary evidence Supplement with phase 2 data for emerging therapies Note real-world evidence and meta-analyses Cite trial names (e.g., KEYNOTE-189, CheckMate-227) Biomarker-Guided Recommendations: Link specific biomarkers to therapy recommendations Specify testing methods and validated assays Include FDA/EMA approval status for companion diagnostics Clinical Actionability: Every recommendation should have clear implementation guidance Decision Algorithm Clarity: TikZ flowcharts should be unambiguous with clear yes/no decision points Special Populations: Address elderly, renal/hepatic impairment, pregnancy, drug interactions Monitoring Guidance: Specify safety labs, imaging, and frequency Update Frequency: Date recommendations and plan for periodic updates General Best Practices First Page Executive Summary (MANDATORY): ALWAYS create a complete executive summary on page 1 that spans the entire first page Use 3-5 colored tcolorbox elements to highlight key findings No table of contents or detailed sections on page 1 Use \thispagestyle{empty} and end with \newpage This is the single most important page - it should be scannable in 60 seconds De-identification: Remove all 18 HIPAA identifiers before document generation (Safe Harbor method) Regulatory Compliance: Include confidentiality notices for proprietary pharmaceutical data Publication-Ready Formatting: Use 0.5in margins, professional fonts, color-coded sections Reproducibility: Document all statistical methods to enable replication Conflict of Interest: Disclose pharmaceutical funding or relationships when applicable Visual Hierarchy: Use colored boxes consistently (blue=data, green=biomarkers, yellow/orange=recommendations, red=warnings) References
See the references/ directory for detailed guidance on:
Patient cohort analysis and stratification methods Treatment recommendation development Clinical decision algorithms Biomarker classification and interpretation Outcome analysis and statistical methods Evidence synthesis and grading systems Templates
See the assets/ directory for LaTeX templates:
cohort_analysis_template.tex - Biomarker-stratified patient cohort analysis with statistical comparisons treatment_recommendation_template.tex - Evidence-based clinical practice guidelines with GRADE grading clinical_pathway_template.tex - TikZ decision algorithm flowcharts for treatment sequencing biomarker_report_template.tex - Molecular subtype classification and genomic profile reports evidence_synthesis_template.tex - Systematic evidence review and meta-analysis summaries
Template Features:
0.5in margins for compact presentation Color-coded recommendation boxes Professional tables for demographics, biomarkers, outcomes Built-in support for Kaplan-Meier curves, waterfall plots, forest plots GRADE evidence grading tables Confidentiality headers for pharmaceutical documents Scripts
See the scripts/ directory for analysis and visualization tools:
generate_survival_analysis.py - Kaplan-Meier curve generation with log-rank tests, hazard ratios, 95% CI create_waterfall_plot.py - Best response visualization for cohort analyses create_forest_plot.py - Subgroup analysis visualization with confidence intervals create_cohort_tables.py - Demographics, biomarker frequency, and outcomes tables build_decision_tree.py - TikZ flowchart generation for treatment algorithms biomarker_classifier.py - Patient stratification algorithms by molecular subtype calculate_statistics.py - Hazard ratios, Cox regression, log-rank tests, Fisher's exact validate_cds_document.py - Quality and compliance checks (HIPAA, statistical reporting standards) grade_evidence.py - Automated GRADE assessment helper for treatment recommendations