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scientific_writer/.claude/skills/clinical-reports/references/clinical_trial_reporting.md

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+# Clinical Trial Reporting Standards
+
+## ICH-E3: Structure and Content of Clinical Study Reports
+
+The International Council for Harmonisation (ICH) E3 guideline defines the structure and content of clinical study reports (CSRs) for regulatory submission.
+
+### CSR Overview
+
+**Purpose:**
+- Provide comprehensive description of study design, conduct, and results
+- Support regulatory decision-making
+- Document evidence of safety and efficacy
+
+**Audience:**
+- Regulatory authorities (FDA, EMA, PMDA, etc.)
+- Medical reviewers
+- Statistical reviewers
+- Clinical pharmacology reviewers
+
+**Length:** Typically 50-300 pages (main text), with extensive appendices
+
+### Main Sections of ICH-E3 CSR
+
+#### Section 1: Title Page
+
+**Required elements:**
+- Full study title
+- Protocol number and version
+- Sponsor name and address
+- Compound/drug name and code
+- Study phase
+- Indication
+- Report date and version number
+- Report authors
+- Confidentiality statement
+
+#### Section 2: Synopsis
+
+**Length:** 5-15 pages
+
+**Content:**
+- Brief summary of entire CSR
+- Must be understandable as standalone document
+- Cover all major sections
+
+**Standard synopsis elements:**
+1. Study identifier and title
+2. Study objectives
+3. Methodology:
+   - Study design
+   - Number and description of patients
+   - Diagnosis and main criteria for inclusion
+   - Study treatments
+   - Duration of treatment
+   - Criteria for evaluation
+   - Statistical methods
+4. Results:
+   - Number of patients enrolled, completed, discontinued
+   - Efficacy results
+   - Safety results
+5. Conclusions
+
+#### Section 3: Ethics
+
+**3.1 Independent Ethics Committee/Institutional Review Board**
+- Names and locations of all IRBs
+- Dates of initial approval
+- Dates of protocol amendment approvals
+- Documentation of continuing review
+
+**3.2 Ethical Conduct of Study**
+- Statement of compliance with GCP and Declaration of Helsinki
+- Protocol adherence
+- Informed consent process
+
+**3.3 Patient Information and Consent**
+- Description of informed consent procedures
+- Consent form versions used
+- Process for re-consent if applicable
+
+#### Section 4: Investigators and Study Administrative Structure
+
+**4.1 Investigators**
+- List of principal investigators by site
+- Site addresses and enrollment
+- Coordinating investigator (if applicable)
+
+**4.2 Administrative Structure**
+- Sponsor personnel and roles
+- CRO involvement (if applicable)
+- Monitoring procedures
+- Data management organization
+- Statistical analysis organization
+
+**4.3 Study Monitoring and Quality Assurance**
+- Monitoring procedures and frequency
+- Source document verification
+- Quality control procedures
+- Audits performed
+
+#### Section 5: Introduction
+
+**5.1 Background**
+- Disease or condition being studied
+- Current treatment landscape
+- Unmet medical need
+
+**5.2 Investigational Product**
+- Pharmacology and mechanism of action
+- Nonclinical findings
+- Prior clinical experience
+- Known safety profile
+
+**5.3 Non-Investigational Therapy**
+- Comparator drugs or placebo
+- Concomitant medications allowed/prohibited
+
+#### Section 6: Study Objectives
+
+**6.1 Primary Objective**
+- Main research question
+- Clearly stated and specific
+- Example: "To evaluate the efficacy of Drug X compared to placebo in reducing HbA1c in patients with type 2 diabetes mellitus over 24 weeks of treatment"
+
+**6.2 Secondary Objectives**
+- Additional research questions
+- Supportive efficacy endpoints
+- Safety objectives
+- Exploratory objectives
+
+**6.3 Endpoints**
+- Primary endpoint definition and measurement
+- Secondary endpoints
+- Safety endpoints
+- Pharmacokinetic endpoints (if applicable)
+- Biomarker endpoints (if applicable)
+
+#### Section 7: Investigational Plan
+
+**7.1 Overall Study Design and Plan**
+- Study design type (parallel, crossover, factorial, etc.)
+- Randomization and blinding
+- Study phases or periods
+- Duration of treatment and follow-up
+- Dosing regimen
+- Study flow diagram (patient flowchart)
+
+**7.2 Sample Size**
+- Target enrollment
+- Sample size justification
+- Power calculation assumptions:
+  - Expected effect size
+  - Variability estimates
+  - Type I error (alpha)
+  - Power (1 - beta)
+  - Drop-out rate assumptions
+
+**7.3 Statistical Methods**
+- Analysis populations (ITT, PP, safety)
+- Handling of missing data
+- Interim analyses (if planned)
+- Multiplicity adjustments
+- Subgroup analyses
+- Sensitivity analyses
+
+**7.4 Changes to Protocol**
+- Protocol amendments and rationale
+- Impact on study conduct and analysis
+
+#### Section 8: Study Patients
+
+**8.1 Inclusion and Exclusion Criteria**
+- Key inclusion criteria
+- Key exclusion criteria
+- Rationale for criteria
+
+**8.2 Demographic and Baseline Characteristics**
+- Age, sex, race/ethnicity
+- Disease severity or stage
+- Prior therapies
+- Baseline values of key endpoints
+- Comparability across treatment groups
+
+**8.3 Patient Disposition**
+- Number screened
+- Number randomized
+- Number completing study
+- Number withdrawn (by reason)
+- Number lost to follow-up
+- CONSORT flow diagram
+
+**8.4 Protocol Deviations**
+- Major protocol deviations
+- Minor protocol deviations
+- Impact on efficacy and safety analyses
+- Corrective actions taken
+
+**8.5 Demographic and Other Baseline Characteristics**
+- Detailed demographic tables
+- Baseline disease characteristics
+- Stratification factors
+- Medical history
+- Prior/concomitant medications
+
+#### Section 9: Efficacy Evaluation
+
+**9.1 Data Sets Analyzed**
+- Intent-to-treat (ITT) population
+- Per-protocol (PP) population
+- Modified ITT
+- Other analysis sets
+- Justification for population definitions
+
+**9.2 Demographic and Baseline Characteristics**
+- Demographics by analysis population
+- Baseline comparability
+
+**9.3 Measurements of Treatment Compliance**
+- Drug accountability
+- Pill counts or diary compliance
+- Plasma drug levels (if measured)
+- Percent of planned dose received
+
+**9.4 Efficacy Results**
+
+**9.4.1 Primary Endpoint**
+- Results for primary endpoint
+- Statistical analysis
+- Effect size and confidence intervals
+- P-values
+- Subgroup analyses
+
+**9.4.2 Secondary Endpoints**
+- Results for each secondary endpoint
+- Statistical analyses
+- Hierarchy of testing (if applicable)
+
+**9.4.3 Other Efficacy Endpoints**
+- Exploratory endpoints
+- Post-hoc analyses
+- Responder analyses
+
+**9.5 Dropouts and Missing Data**
+- Patterns of missing data
+- Reasons for dropout
+- Sensitivity analyses for missing data
+
+#### Section 10: Safety Evaluation
+
+**10.1 Extent of Exposure**
+- Duration of exposure
+- Dose intensity
+- Dose delays or reductions
+- Treatment discontinuations due to adverse events
+
+**10.2 Adverse Events**
+
+**10.2.1 Overview of Adverse Events**
+- Summary tables (any AE, treatment-related, serious, leading to discontinuation)
+- Percentage of patients with AEs
+- Comparison across treatment groups
+
+**10.2.2 Common Adverse Events**
+- AEs occurring in ≥5% or ≥10% of patients
+- Sorted by frequency
+- Preferred terms and system organ class (MedDRA)
+
+**10.2.3 Serious Adverse Events**
+- Definition of SAE
+- Summary table of SAEs
+- Individual narratives for each SAE
+- Causality assessment
+- Outcome
+
+**10.2.4 Adverse Events Leading to Discontinuation**
+- AEs leading to study drug discontinuation
+- Frequency and type
+- Relationship to study drug
+
+**10.2.5 Deaths**
+- All deaths during study and follow-up
+- Detailed narratives for each death
+- Relationship to study drug
+- Autopsy findings (if available)
+
+**10.3 Clinical Laboratory Evaluations**
+- Laboratory abnormalities
+- Shift tables (normal to abnormal, abnormal to normal)
+- Mean changes from baseline
+- Laboratory values meeting protocol-defined criteria
+- Hepatotoxicity monitoring (if applicable)
+
+**10.4 Vital Signs and Physical Findings**
+- Vital signs (BP, HR, temperature, respiratory rate)
+- Mean changes from baseline
+- Clinically significant changes
+- Physical examination findings
+
+**10.5 ECG Evaluation**
+- QTc interval changes
+- Other ECG abnormalities
+- Clinically significant ECG findings
+
+**10.6 Special Safety Evaluations**
+- Immunogenicity (for biologics)
+- Pregnancy outcomes (if applicable)
+- Abuse potential (if applicable)
+- Withdrawal or rebound effects
+- Dependency potential
+
+#### Section 11: Discussion and Overall Conclusions
+
+**11.1 Efficacy Discussion**
+- Interpretation of efficacy results
+- Clinical significance of findings
+- Consistency with prior studies
+- Limitations
+
+**11.2 Safety Discussion**
+- Safety profile overview
+- Notable safety findings
+- Comparison to known safety profile
+- Risk-benefit assessment
+
+**11.3 Benefit-Risk Assessment**
+- Overall benefit-risk conclusion
+- Subpopulations with favorable/unfavorable benefit-risk
+- Implications for dosing or patient selection
+
+**11.4 Clinical Implications**
+- Place in therapy
+- Target patient population
+- Comparison to existing therapies
+
+#### Section 12: Tables, Figures, and Graphs
+
+Comprehensive set of tables and figures for efficacy and safety data.
+
+**Common tables:**
+- Demographic and baseline characteristics
+- Patient disposition
+- Extent of exposure
+- Efficacy results (primary and secondary endpoints)
+- Adverse event summary
+- Common adverse events
+- Serious adverse events
+- Deaths
+- Laboratory abnormalities
+- Vital signs
+
+**Common figures:**
+- Study design schematic
+- Patient disposition flowchart (CONSORT)
+- Kaplan-Meier curves (survival, time to event)
+- Forest plots (subgroup analyses)
+- Mean change over time plots
+
+#### Section 13: References
+
+- Publications cited in CSR
+- Relevant literature
+- Regulatory guidelines
+- Prior study reports
+
+#### Section 14: Appendices
+
+**Required appendices:**
+- Study protocol and amendments
+- Sample case report forms
+- Investigator list with IRB information
+- Patient information and informed consent forms
+- List of patients receiving study drug
+- Randomization scheme
+- Audit certificates (if applicable)
+- Documentation of statistical methods
+- Publications based on study
+
+**Optional appendices:**
+- Individual patient data listings
+- SAE narratives
+- Laboratory normals and conversion factors
+- Investigator signatures
+
+### Statistical Analysis Plan (SAP)
+
+**SAP Components:**
+- Analysis populations
+- Handling of missing data
+- Statistical tests to be used
+- Adjustment for multiplicity
+- Interim analysis plan
+- Subgroup analyses
+- Sensitivity analyses
+- Safety analyses
+
+**SAP Timing:**
+- Finalized before database lock
+- Amendments documented with rationale
+
+## CONSORT (Consolidated Standards of Reporting Trials)
+
+CONSORT guidelines promote transparent and complete reporting of randomized controlled trials.
+
+### CONSORT 2010 Checklist
+
+#### Title and Abstract
+- **1a. Title**: Identification as randomized trial in title
+- **1b. Abstract**: Structured summary covering trial design, methods, results, conclusions
+
+#### Introduction
+- **2a. Background**: Scientific background and explanation of rationale
+- **2b. Objectives**: Specific objectives or hypotheses
+
+#### Methods - Participants
+- **3a. Eligibility**: Eligibility criteria for participants
+- **3b. Settings**: Settings and locations of data collection
+
+#### Methods - Interventions
+- **4a. Interventions**: Details of interventions for each group
+- **4b. Details**: Sufficient details to allow replication
+
+#### Methods - Outcomes
+- **5. Outcomes**: Clearly defined primary and secondary outcome measures
+- **6a. Sample size**: How sample size was determined
+- **6b. Interim analyses**: When applicable, explanation of interim analyses
+
+#### Methods - Randomization
+- **7a. Sequence generation**: Method of random sequence generation
+- **7b. Allocation concealment**: Mechanism of allocation concealment
+- **8a. Implementation**: Who generated allocation, enrolled, and assigned participants
+- **8b. Blinding**: Whether participants, care providers, outcome assessors were blinded
+
+#### Methods - Statistical
+- **9. Statistical methods**: Methods for primary and secondary outcomes
+- **10. Additional analyses**: Subgroup or adjusted analyses
+
+#### Results - Participant Flow
+- **11a. Enrollment**: Numbers screened, randomized, allocated
+- **11b. Losses and exclusions**: For each group, losses and exclusions after randomization
+- **12. Recruitment**: Dates defining recruitment and follow-up periods
+- **13a. Baseline**: Baseline demographic and clinical characteristics
+- **13b. Baseline comparability**: Numbers analyzed in each group
+
+#### Results - Outcomes and Estimation
+- **14a. Outcomes**: For primary and secondary outcomes, results for each group
+- **14b. Binary outcomes**: For binary outcomes, effect sizes and confidence intervals
+- **15. Ancillary analyses**: Results of other analyses performed
+
+#### Results - Harms
+- **16. Harms**: All important harms or unintended effects in each group
+
+#### Discussion
+- **17a. Limitations**: Trial limitations, addressing biases, imprecision
+- **17b. Generalizability**: Generalizability (external validity) of trial findings
+- **18. Interpretation**: Interpretation consistent with results, balancing benefits and harms
+- **19. Registration**: Registration number and name of trial registry
+- **20. Protocol**: Where full trial protocol can be accessed
+- **21. Funding**: Sources of funding, role of funders
+
+### CONSORT Flow Diagram
+
+Standard format showing patient flow through trial:
+```
+Assessed for eligibility (n=)
+    ↓
+Randomized (n=)
+    ├─ Allocated to intervention (n=)
+    │   ├─ Received intervention (n=)
+    │   └─ Did not receive intervention (n=)
+    │       Give reasons
+    ├─ Allocated to control (n=)
+    │   ├─ Received control (n=)
+    │   └─ Did not receive control (n=)
+    │       Give reasons
+    ↓
+Lost to follow-up (n=)
+    Give reasons
+Discontinued intervention (n=)
+    Give reasons
+    ↓
+Analyzed (n=)
+Excluded from analysis (n=)
+    Give reasons
+```
+
+## Serious Adverse Event (SAE) Reporting
+
+### Definition of Serious Adverse Event
+
+An adverse event or suspected adverse reaction is considered serious if it:
+- Results in death
+- Is life-threatening
+- Requires inpatient hospitalization or prolongation of existing hospitalization
+- Results in persistent or significant disability/incapacity
+- Is a congenital anomaly/birth defect
+- Requires intervention to prevent permanent impairment or damage (device-related)
+- Other medically important events (based on medical judgment)
+
+### SAE Report Components
+
+**1. Administrative Information**
+- Report type (initial, follow-up, final)
+- Report number
+- Date of report
+- Reporter information
+- Sponsor information
+- Study identifier (protocol number, NCT number)
+
+**2. Patient Information (De-identified)**
+- Subject ID or randomization number
+- Initials (if permitted)
+- Age or date of birth (year only)
+- Sex
+- Race/ethnicity
+- Weight
+- Height
+
+**3. Study Information**
+- Study phase (I, II, III, IV)
+- Study design (randomized, open-label, etc.)
+- Treatment arm or randomization
+- Date of first study drug
+- Date of last study drug
+
+**4. Event Information**
+- Reported term (verbatim)
+- MedDRA preferred term
+- System organ class
+- Date of onset
+- Time of onset (if relevant)
+- Date of resolution (or ongoing)
+- Duration
+
+**5. Seriousness Criteria**
+- Death: Yes/No
+- Life-threatening: Yes/No
+- Hospitalization required: Yes/No
+- Hospitalization prolonged: Yes/No
+- Disability/incapacity: Yes/No
+- Congenital anomaly: Yes/No
+- Medically significant: Yes/No
+
+**6. Severity**
+- Mild: Noticeable but does not interfere with daily activities
+- Moderate: Interferes with daily activities but manageable
+- Severe: Prevents usual daily activities, requires intervention
+
+Note: Severity ≠ Seriousness
+
+**7. Outcome**
+- Recovered/resolved
+- Recovering/resolving
+- Not recovered/not resolved
+- Recovered/resolved with sequelae
+- Fatal
+- Unknown
+
+**8. Causality Assessment**
+- Relationship to study drug:
+  - Not related
+  - Unlikely related
+  - Possibly related
+  - Probably related
+  - Definitely related
+- Relationship to study procedures
+- Relationship to underlying disease
+- Relationship to concomitant medications
+- Reasoning for determination
+
+**9. Expectedness**
+- Expected (per Investigator's Brochure or protocol)
+- Unexpected (not in IB or more severe than documented)
+
+**10. Action Taken with Study Drug**
+- No change
+- Dose reduced
+- Dose increased
+- Drug interrupted (temporarily held)
+- Drug discontinued
+- Not applicable (event occurred after discontinuation)
+
+**11. Treatments/Interventions for Event**
+- Medications administered
+- Procedures performed
+- Hospitalization details
+- ICU admission
+- Surgical intervention
+
+**12. Event Narrative**
+- Detailed description of event
+- Timeline of events
+- Clinical course
+- Relevant medical history
+- Concomitant medications
+- Diagnostic test results
+- Treatment and response
+- Outcome and current status
+
+**Example narrative:**
+```
+A 58-year-old male (Subject ID: 12345) enrolled in Study XYZ-301, a Phase 3
+randomized trial of Drug X vs. placebo for heart failure. On Day 42 of treatment
+(15-Feb-2024), the patient presented to the emergency department with sudden onset
+severe chest pain, diaphoresis, and dyspnea. ECG showed ST-segment elevation in
+leads V2-V4. Troponin I was elevated at 12.5 ng/mL (normal <0.04). The patient was
+diagnosed with acute ST-elevation myocardial infarction and underwent emergent
+cardiac catheterization revealing 95% occlusion of the left anterior descending
+artery. Percutaneous coronary intervention with drug-eluting stent placement was
+performed successfully. The patient was admitted to the cardiac intensive care unit.
+Study drug was permanently discontinued on Day 42. The patient recovered and was
+discharged on Day 47 (20-Feb-2024) in stable condition. This event was assessed as
+unlikely related to study drug by the investigator, as the patient had significant
+underlying coronary artery disease risk factors including diabetes, hypertension,
+and smoking history.
+```
+
+### Regulatory Reporting Timelines
+
+**FDA IND Safety Reporting (21 CFR 312.32):**
+- **Fatal or life-threatening unexpected SAEs**: 7 calendar days for preliminary report, 15 days for complete report
+- **Other serious unexpected events**: 15 calendar days
+- **Annual safety reports**: Within 60 days of anniversary of IND
+
+**EMA Expedited Reporting:**
+- **Fatal or life-threatening unexpected events**: 7 days initial, 8 additional days for complete report
+- **Other unexpected serious events**: 15 days
+
+**IRB Reporting:**
+- Per institutional policy
+- Typically 5-10 days for serious unexpected events
+- Some institutions require reporting within 24-48 hours
+
+### MedDRA Coding
+
+**MedDRA (Medical Dictionary for Regulatory Activities):**
+- Standardized medical terminology for regulatory communication
+- Hierarchical structure:
+  - SOC (System Organ Class) - highest level
+  - HLGT (High Level Group Term)
+  - HLT (High Level Term)
+  - PT (Preferred Term) - used for coding AEs
+  - LLT (Lowest Level Term) - verbatim terms
+
+**Example:**
+- Verbatim term: "bad headache"
+- LLT: Headache
+- PT: Headache
+- HLT: Headaches NEC
+- HLGT: Neurological disorders NEC
+- SOC: Nervous system disorders
+
+### Causality Assessment Methods
+
+**WHO-UMC Causality Categories:**
+- **Certain**: Event cannot be explained by other factors
+- **Probable/Likely**: Event more likely related to drug than other factors
+- **Possible**: Event could be related to drug, but other factors cannot be ruled out
+- **Unlikely**: Event likely explained by other factors
+- **Conditional/Unclassified**: More data needed
+- **Unassessable/Unclassifiable**: Information insufficient
+
+**Naranjo Algorithm (for ADRs):**
+Scoring system based on 10 questions:
+- Score ≥9: Definite
+- Score 5-8: Probable
+- Score 1-4: Possible
+- Score ≤0: Doubtful
+
+## Data Safety Monitoring Board (DSMB)
+
+**Purpose:**
+- Independent review of safety data
+- Monitoring benefit-risk
+- Recommendations on study continuation
+
+**DSMB Charter Elements:**
+- Membership and qualifications
+- Roles and responsibilities
+- Meeting frequency
+- Data reviewed
+- Decision-making criteria
+- Communication procedures
+- Confidentiality
+
+**DSMB Reports:**
+- Open reports (all parties can see)
+- Closed reports (DSMB and sponsor only)
+- Recommendations: Continue, modify, or terminate study
+
+---
+
+This reference provides comprehensive guidance for clinical trial reporting following ICH-E3 and CONSORT guidelines, as well as SAE reporting requirements. Use these standards when preparing regulatory submissions and trial publications.
+