<!-- # COPYRIGHT NOTICE # This file is part of the "Universal Biomedical Skills" project. # Copyright (c) 2026 MD BABU MIA, PhD <md.babu.mia@mssm.edu> # All Rights Reserved. # # This code is proprietary and confidential. # Unauthorized copying of this file, via any medium is strictly prohibited. # # Provenance: Authenticated by MD BABU MIA -->

---

name: 'tumor-heterogeneity-agent' description: 'AI-powered intratumor heterogeneity analysis for clonal architecture reconstruction, subclonal evolution tracking, and therapy resistance prediction using multi-region and longitudinal sequencing.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools:

• read_file
• run_shell_command

---

Tumor Heterogeneity Agent

The Tumor Heterogeneity Agent provides comprehensive analysis of intratumor heterogeneity (ITH) for understanding clonal architecture, tracking subclonal evolution, and predicting therapy resistance. It integrates multi-region sequencing, single-cell data, and longitudinal samples to reconstruct tumor phylogenies and identify actionable subclones.

When to Use This Skill

• When analyzing multi-region tumor sequencing for clonal architecture.
• For tracking clonal evolution under treatment pressure.
• To predict resistance emergence from subclonal populations.
• When assessing tumor heterogeneity impact on treatment response.
• For integrating single-cell and bulk sequencing for ITH analysis.

Core Capabilities

1. Clonal Deconvolution: Infer clonal populations and their frequencies.

2. Phylogeny Reconstruction: Build tumor evolutionary trees from variants.

3. Subclonal Tracking: Monitor subclone dynamics over time.

4. Resistance Prediction: Identify pre-existing resistant subclones.

5. Multi-Region Integration: Combine spatial heterogeneity data.

6. Single-Cell ITH: Integrate scDNA-seq for ground-truth clones.

Heterogeneity Metrics

Metric	Definition	Clinical Relevance
MATH Score	Mutant-allele tumor heterogeneity	ITH quantification
Shannon Index	Clonal diversity	Evolutionary potential
Clone Count	Number of distinct clones	Complexity
Truncal Fraction	% truncal mutations	Targetability
ITH Score	Composite heterogeneity	Prognosis

Workflow

1. Input: Multi-region/longitudinal WES/WGS, copy number, tumor purity.

2. Preprocessing: Variant calling, CNV calling, purity estimation.

3. CCF Estimation: Calculate cancer cell fraction for each mutation.

4. Clustering: Group mutations into clonal populations.

5. Phylogeny: Reconstruct evolutionary tree.

6. Temporal Analysis: Track clone dynamics over time.

7. Output: Clone structures, phylogenies, heterogeneity metrics.

Example Usage

User: "Analyze the clonal architecture of this multi-region lung tumor sequencing to understand heterogeneity and identify resistant subclones."

Agent Action:

python3 Skills/Oncology/Tumor_Heterogeneity_Agent/ith_analysis.py \
    --multi_region_vcfs region1.vcf,region2.vcf,region3.vcf \
    --cnv_segments cnv_calls.seg \
    --purity 0.7,0.65,0.72 \
    --sample_names Primary,Met1,Met2 \
    --method pyclone-vi \
    --phylogeny_method citup \
    --output ith_analysis/

Deconvolution Methods

Method	Approach	Best For
PyClone-VI	Variational inference	Large datasets
SciClone	Kernel density	High purity
EXPANDS	Probabilistic	Multi-region
Canopy	EM algorithm	CNV integration
Clonevol	Phylogeny-aware	Longitudinal
CITUP	Integer programming	Tree optimization

Input Requirements

Input	Format	Required
Somatic Variants	VCF with depth	Yes
Copy Number	SEG file	Yes
Tumor Purity	Float (0-1)	Yes
Sample Metadata	TSV	Yes
Normal BAM	BAM	Recommended

Output Components

Output	Description	Format
Clone Assignments	Mutation-to-clone mapping	.csv
Clone Frequencies	Per-sample clone fractions	.csv
Phylogenetic Tree	Newick and visualization	.nwk, .pdf
ITH Metrics	Heterogeneity scores	.json
Subclone Variants	Clone-specific mutations	.vcf
Evolution Plot	Clone dynamics over time	.png
Actionable Subclones	Druggable clone mutations	.csv

Clonal Classification

Clone Type	Definition	Implications
Truncal	Present in all samples	Ideal targets
Branch	Present in subset	Regional targets
Private	Single sample only	Local significance
Resistant	Expand under therapy	Resistance mechanism

AI/ML Components

Clone Inference:

• Variational autoencoders for CCF estimation
• Dirichlet process mixture models
• Graph neural networks for phylogeny

Resistance Prediction:

• Time-series models for clone trajectories
• Classification of resistant signatures
• Drug-clone interaction prediction

Multi-Region Integration:

• Multi-task learning across regions
• Spatial models for regional patterns
• Transfer learning across cancers

Clinical Applications

Application	ITH Insight	Clinical Action
Treatment Selection	Truncal vs branch targets	Prioritize truncal targets
Resistance Monitoring	Pre-existing resistant clones	Early combination therapy
Prognosis	ITH score	Risk stratification
Biomarker Development	Clonal biomarkers	Robust biomarker selection

Cancer-Specific Patterns

Cancer Type	Typical ITH	Key Drivers
Lung (NSCLC)	High	EGFR, KRAS subclonal
Breast	Moderate-High	PIK3CA, ESR1 evolution
Colorectal	Moderate	KRAS, BRAF clonal
Renal	Very High	VHL truncal, diverse branches
Melanoma	High	BRAF/NRAS truncal

Prerequisites

• Python 3.10+
• PyClone-VI, SciClone
• CITUP, Clonevol
• CNVkit/FACETS for CNV
• R with clonal evolution packages

Related Skills

• ctDNA_Dynamics_MRD_Agent - Liquid biopsy tracking
• Single_Cell_CNV_Agent - scDNA-seq analysis
• HRD_Analysis_Agent - Genomic instability
• Pan_Cancer_MultiOmics_Agent - Multi-omic integration

Phylogeny Visualization

View Type	Shows	Best For
Fish Plot	Clone dynamics over time	Longitudinal
Tree Diagram	Branching evolution	Multi-region
Muller Plot	Population dynamics	Treatment response
Clone Map	Spatial distribution	Multi-region spatial

Special Considerations

1. Sampling Bias: Multi-region captures more heterogeneity
2. Purity Effects: Low purity reduces clone resolution
3. CNV Complexity: High CNV burden complicates CCF
4. Single-Cell Validation: Ground truth from scDNA-seq
5. Temporal Resolution: Frequent sampling improves tracking

Resistance Mechanisms

Mechanism	Detection	Intervention
Pre-existing resistant clone	Subclonal at baseline	Combination therapy
Acquired resistance	New clone emerges	Switch therapy
Phenotypic plasticity	Expression change	Monitor phenotype
Microenvironment	TME evolution	Immunotherapy

Author

AI Group - Biomedical AI Platform

<!-- AUTHOR_SIGNATURE: 9a7f3c2e-MD-BABU-MIA-2026-MSSM-SECURE -->