Bio Immunoinformatics Neoantigen Prediction

Version Compatibility

Reference examples tested with: Ensembl VEP 111+, MHCflurry 2.1+, pVACtools 4.1+, pandas 2.2+

Before using code patterns, verify installed versions match. If versions differ:

• Python: pip show <package> then help(module.function) to check signatures
• CLI: <tool> --version then <tool> --help to confirm flags

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Neoantigen Prediction

"Identify neoantigens from my tumor mutations" → Predict mutant peptides from somatic variants that bind patient HLA alleles and may elicit T-cell responses for personalized cancer immunotherapy.

• CLI: pvacseq run with VEP-annotated VCF and patient HLA types (pVACtools)

pVACtools Pipeline (Ensembl VEP 111+)

Goal: Install pVACtools and its IEDB prediction engine dependencies.

Approach: Install via pip (optionally in a dedicated conda environment) and download IEDB tools for binding prediction.

# Install pVACtools
pip install pvactools

# Or use conda for dependencies
conda create -n pvactools python=3.8
conda activate pvactools
pip install pvactools

# Download IEDB tools
pvactools download_iedb_tools

pVACseq Workflow (Ensembl VEP 111+)

Goal: Run the full pVACseq neoantigen prediction pipeline on a VEP-annotated VCF.

Approach: Provide annotated VCF with patient HLA alleles and select binding prediction algorithms; pVACseq generates mutant peptides and predicts MHC binding.

# Run pVACseq on annotated VCF
pvacseq run \
    annotated.vcf \
    sample_name \
    "HLA-A*02:01,HLA-A*24:02,HLA-B*07:02,HLA-B*44:02" \
    MHCflurry MHCnuggetsI \
    output_dir \
    -e1 8,9,10,11 \
    --iedb-install-directory /path/to/iedb

# Key parameters:
# -e1: Epitope lengths for MHC-I (8-11)
# -e2: Epitope lengths for MHC-II (15)
# --binding-threshold: IC50 cutoff (default 500)
# --percentile-threshold: Alternative cutoff

VCF Annotation Requirements (Ensembl VEP 111+)

Goal: Annotate somatic VCF with transcript consequences and amino acid changes required by pVACseq.

Approach: Run Ensembl VEP with Downstream and Wildtype plugins to produce a VCF containing protein-level mutation annotations.

# pVACseq requires VEP-annotated VCF
# Must include transcript and amino acid changes

# Run VEP first
vep -i somatic.vcf -o annotated.vcf \
    --cache --offline \
    --format vcf --vcf \
    --plugin Downstream \
    --plugin Wildtype \
    --terms SO \
    --symbol

Parse pVACseq Results

Goal: Parse pVACseq output and calculate the differential agretopicity index (DAI) for candidate neoantigens.

Approach: Load TSV results, filter by binding threshold, and compute WT/MT binding ratio to identify mutations that create new epitopes.

import pandas as pd

def parse_pvacseq_results(results_file):
    '''Parse pVACseq output

    Key columns:
    - Mutation: Gene and amino acid change
    - HLA Allele: Patient HLA presenting this peptide
    - MT Epitope Seq: Mutant peptide sequence
    - WT Epitope Seq: Wild-type peptide sequence
    - Median MT Score: Binding affinity (nM)
    - Median WT Score: WT binding (for agretopicity)
    - Tumor DNA VAF: Variant allele frequency
    - Gene Expression: If RNA-seq available
    '''
    df = pd.read_csv(results_file, sep='\t')

    # Filter by binding threshold
    strong_binders = df[df['Median MT Score'] < 500]

    return strong_binders


def calculate_agretopicity(df):
    '''Calculate agretopicity (DAI) score

    Agretopicity = ratio of WT to MT binding
    Higher agretopicity means MT binds better than WT
    indicating mutation creates new epitope

    DAI (Differential Agretopicity Index):
    - >1: Mutant binds better (favorable)
    - ~1: Similar binding (less likely immunogenic)
    - <1: WT binds better (unfavorable)
    '''
    df = df.copy()
    df['agretopicity'] = df['Median WT Score'] / df['Median MT Score']

    # High agretopicity = mutation improves binding
    df['dai_favorable'] = df['agretopicity'] > 1

    return df

Prioritize Neoantigens (Ensembl VEP 111+)

Goal: Rank neoantigen candidates for vaccine design by combining binding, clonality, and expression evidence.

Approach: Apply sequential filters (binding affinity, VAF, expression) and compute a composite priority score weighting inverse IC50, VAF, and agretopicity.

def prioritize_neoantigens(df, vaf_threshold=0.1, expression_threshold=1.0):
    '''Prioritize neoantigens for vaccine design

    Criteria for good neoantigen candidates:
    1. Strong MHC binding (IC50 < 500nM, ideally < 50nM)
    2. High agretopicity (MT binds better than WT)
    3. High tumor VAF (clonal, present in most tumor cells)
    4. Expressed in tumor (if RNA-seq available)
    5. Not in tolerogenic region (self-similarity check)

    Typical pipeline returns 10-50 candidates per patient
    '''
    candidates = df.copy()

    # Filter by binding
    candidates = candidates[candidates['Median MT Score'] < 500]

    # Filter by VAF (clonal mutations preferred)
    if 'Tumor DNA VAF' in candidates.columns:
        candidates = candidates[candidates['Tumor DNA VAF'] >= vaf_threshold]

    # Filter by expression
    if 'Gene Expression' in candidates.columns:
        candidates = candidates[candidates['Gene Expression'] >= expression_threshold]

    # Calculate priority score
    # Lower binding affinity = better
    # Higher VAF = better
    # Higher agretopicity = better
    candidates['priority_score'] = (
        (1 / candidates['Median MT Score']) *
        candidates.get('Tumor DNA VAF', 1) *
        candidates.get('agretopicity', 1)
    )

    return candidates.sort_values('priority_score', ascending=False)

Alternative: Manual Neoantigen Pipeline (Ensembl VEP 111+)

Goal: Predict neoantigens without pVACtools by directly extracting mutant peptides from an annotated VCF and predicting MHC binding.

Approach: Parse VEP annotations from VCF via cyvcf2, generate mutant peptides around each coding mutation, and predict binding with MHCflurry.

def manual_neoantigen_pipeline(vcf_file, hla_alleles, reference_fasta):
    '''Simplified neoantigen prediction without pVACtools

    Steps:
    1. Extract coding mutations from VCF
    2. Generate mutant protein sequences
    3. Extract peptides around mutation
    4. Predict MHC binding
    '''
    from cyvcf2 import VCF
    from mhcflurry import Class1PresentationPredictor

    vcf = VCF(vcf_file)
    predictor = Class1PresentationPredictor.load()

    neoantigens = []

    for variant in vcf:
        # Get amino acid change from VEP annotation
        if 'CSQ' not in variant.INFO:
            continue

        # Parse consequence and extract mutant peptides
        # ... (implementation depends on annotation format)

        # For each mutant peptide, predict binding
        for peptide in mutant_peptides:
            for allele in hla_alleles:
                pred = predictor.predict(peptides=[peptide], alleles=[allele])
                if pred['mhcflurry_affinity'].values[0] < 500:
                    neoantigens.append({
                        'variant': f'{variant.CHROM}:{variant.POS}',
                        'peptide': peptide,
                        'allele': allele,
                        'affinity': pred['mhcflurry_affinity'].values[0]
                    })

    return neoantigens

Neoantigen Quality Metrics (Ensembl VEP 111+)

Goal: Assess neoantigen quality across multiple dimensions and produce a composite confidence score.

Approach: Normalize binding affinity, agretopicity, clonality, and expression to 0-1 scales and combine with domain-informed weights.

def assess_neoantigen_quality(neoantigen):
    '''Assess multiple quality metrics for neoantigen

    Returns composite quality score considering:
    - Binding affinity
    - Agretopicity
    - Clonality (VAF)
    - Expression
    - Self-similarity
    '''
    scores = {}

    # Binding (0-1, lower IC50 = higher score)
    ic50 = neoantigen.get('Median MT Score', 500)
    scores['binding'] = 1 - min(ic50 / 5000, 1)

    # Agretopicity (0-1)
    dai = neoantigen.get('agretopicity', 1)
    scores['agretopicity'] = min(dai / 10, 1)

    # Clonality (0-1)
    vaf = neoantigen.get('Tumor DNA VAF', 0.5)
    scores['clonality'] = vaf

    # Expression (0-1, log scale)
    import math
    expr = neoantigen.get('Gene Expression', 1)
    scores['expression'] = min(math.log10(expr + 1) / 3, 1)

    # Composite score
    weights = {'binding': 0.3, 'agretopicity': 0.3, 'clonality': 0.2, 'expression': 0.2}
    composite = sum(scores[k] * weights[k] for k in weights)

    return composite, scores

Related Skills

• immunoinformatics/mhc-binding-prediction - MHC binding details
• immunoinformatics/immunogenicity-scoring - Prioritization
• variant-calling/variant-calling - Input somatic mutations