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clinical-decision-support Generate professional clinical decision support (CDS) documents for pharmaceutical and clinical research settings, including patient cohort analyses (biomarker-stratified with outcomes) and treatment recommendation reports (evidence-based guidelines with decision algorithms). Supports GRADE evidence grading, statistical analysis (hazard ratios, survival curves, waterfall plots), biomarker integration, and regulatory compliance. Outputs publication-ready LaTeX/PDF format optimized for drug development, clinical research, and evidence synthesis.
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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:

  1. Patient Cohort Analysis - Biomarker-stratified group analyses with statistical outcome comparisons
  2. 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

When creating documents with this skill, always consider adding scientific diagrams and schematics to enhance visual communication.

If your document does not already contain schematics or diagrams:

  • 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

For new documents: Scientific schematics should be generated by default to visually represent key concepts, workflows, architectures, or relationships described in the text.

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):

  1. Document Title and Type

    • Main title (e.g., "Biomarker-Stratified Cohort Analysis" or "Evidence-Based Treatment Recommendations")
    • Subtitle with disease state and focus

  2. 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

  3. 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:

  1. Report Information Box: Disease state, guideline version/date, target population
  2. Key Recommendations Box (green): Top 3-5 GRADE-graded recommendations by line of therapy
  3. Biomarker Decision Criteria Box (blue): Key molecular markers influencing treatment selection
  4. Evidence Summary Box (gray): Major trials supporting recommendations (e.g., KEYNOTE-189, FLAURA)
  5. 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

  1. Patient Selection Transparency: Clearly document inclusion/exclusion criteria, patient flow, and reasons for exclusions
  2. Biomarker Clarity: Specify assay methods, platforms (e.g., FoundationOne, Caris), cut-points, and validation status
  3. 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
  4. Outcome Definitions: Use standard criteria:
    • Response: RECIST 1.1, iRECIST for immunotherapy
    • Adverse events: CTCAE version 5.0
    • Performance status: ECOG or Karnofsky
  5. 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
  6. Subgroup Analyses: Pre-specify subgroups; clearly label exploratory vs pre-planned analyses
  7. Data Completeness: Report missing data and how it was handled

For Treatment Recommendation Reports

  1. 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)
  2. 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)
  3. Biomarker-Guided Recommendations:
    • Link specific biomarkers to therapy recommendations
    • Specify testing methods and validated assays
    • Include FDA/EMA approval status for companion diagnostics
  4. Clinical Actionability: Every recommendation should have clear implementation guidance
  5. Decision Algorithm Clarity: TikZ flowcharts should be unambiguous with clear yes/no decision points
  6. Special Populations: Address elderly, renal/hepatic impairment, pregnancy, drug interactions
  7. Monitoring Guidance: Specify safety labs, imaging, and frequency
  8. Update Frequency: Date recommendations and plan for periodic updates

General Best Practices

  1. 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
  2. De-identification: Remove all 18 HIPAA identifiers before document generation (Safe Harbor method)
  3. Regulatory Compliance: Include confidentiality notices for proprietary pharmaceutical data
  4. Publication-Ready Formatting: Use 0.5in margins, professional fonts, color-coded sections
  5. Reproducibility: Document all statistical methods to enable replication
  6. Conflict of Interest: Disclose pharmaceutical funding or relationships when applicable
  7. 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
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