---
title: Interpreting oncology analytics outputs
description: >-
  TMB values, MSI status, MHC binding predictions, and neoantigen rankings.
tags:
  - oncology
  - outputs
---

> **Retired tools**

> `hrd_score`, `liquid_biopsy_ctdna` and `tumor_fraction_estimate` are retired and can no longer be run, so their outputs are no longer produced. Use an allele-specific copy-number HRD caller such as scarHRD for HRD, ichorCNA on low-pass WGS for tumor fraction, and a dedicated ctDNA/MRD pipeline for ctDNA.

These tools return TMB values and MSI status, MHC binding predictions, and ranked neoantigens against clinical thresholds — letting you assess checkpoint inhibitor eligibility and feed the readouts into therapy selection and trial matching.

## TMB/MSI Calculate output

| Field | Type | Description |
|-------|------|-------------|
| `tmb` | number | Tumor mutational burden (mutations per megabase) |
| `tmb_status` | string | `"high"` (>= 10) or `"low"` (< 10) |
| `total_mutations` | number | Total somatic mutations detected |
| `coding_mutations` | number | Mutations in coding regions |
| `synonymous_count` | number | Synonymous (silent) mutations |
| `nonsynonymous_count` | number | Nonsynonymous mutations |
| `panel_size_mb` | number | Effective panel size used for TMB calculation |
| `msi_score` | number | Percentage of unstable microsatellite sites |
| `msi_status` | string | `"MSS"`, `"MSI-L"`, or `"MSI-H"` |
| `unstable_sites` | number | Number of unstable microsatellite loci |
| `total_sites_evaluated` | number | Total microsatellite loci assessed |
| `mutation_spectrum` | object | Counts of each mutation type (C>A, C>G, C>T, T>A, T>C, T>G) |

### TMB interpretation by tumor type

| Tumor Type | Median TMB (mut/Mb) | TMB-High Threshold |
|-----------|---------------------|-------------------|
| Melanoma | 13.5 | &ge; 10 |
| NSCLC | 7.2 | &ge; 10 |
| Colorectal (MSS) | 3.8 | &ge; 10 |
| Colorectal (MSI-H) | 45.2 | &ge; 10 |
| Breast | 2.6 | &ge; 10 |
| Pancreatic | 1.7 | &ge; 10 |

### MSI status interpretation

| Status | Unstable Sites | Clinical Implication |
|--------|---------------|---------------------|
| MSI-H | &ge; 30% | Checkpoint inhibitor eligible (pembrolizumab) |
| MSI-L | 10-30% | Not considered MSI-H; standard treatment |
| MSS | &lt; 10% | Microsatellite stable; standard treatment |

## MHC Binding Predict output

| Field | Type | Description |
|-------|------|-------------|
| `predictions` | array | Binding predictions for each peptide-allele pair |
| `total_predictions` | number | Number of peptide-allele combinations evaluated |
| `strong_binders` | number | Predictions with IC50 &lt; 50 nM |
| `weak_binders` | number | Predictions with IC50 50-500 nM |
| `method` | string | Prediction method used |

### Prediction fields

| Field | Type | Description |
|-------|------|-------------|
| `peptide` | string | Input peptide sequence |
| `hla_allele` | string | HLA allele evaluated |
| `ic50_nm` | number | Predicted binding affinity in nanomolar |
| `percentile_rank` | number | Percentile rank (lower = stronger binding) |
| `classification` | string | `"strong_binder"`, `"weak_binder"`, or `"non_binder"` |
| `core_peptide` | string | Predicted binding core (for class II) |

### Binding affinity interpretation

| IC50 (nM) | Percentile Rank | Classification | Immunological Relevance |
|-----------|----------------|----------------|------------------------|
| &lt; 50 | &lt; 0.5% | Strong binder | High likelihood of immune recognition |
| 50-500 | 0.5-2% | Weak binder | Possible immune recognition |
| 500-5000 | 2-10% | Marginal | Unlikely to elicit response |
| &gt; 5000 | &gt; 10% | Non-binder | No binding expected |

## Neoantigen Predict output

| Field | Type | Description |
|-------|------|-------------|
| `neoantigens` | array | Ranked neoantigen candidates |
| `total_candidates` | number | Total neoantigens passing filters |
| `strong_candidates` | number | Candidates with IC50 &lt; 50 nM |
| `mutations_processed` | number | Input mutations evaluated |
| `peptides_generated` | number | Total peptides generated from mutations |

### Neoantigen candidate fields

| Field | Type | Description |
|-------|------|-------------|
| `rank` | integer | Overall ranking (1 = best candidate) |
| `gene` | string | Mutated gene symbol |
| `mutation` | string | Protein-level mutation (e.g., `G12D`) |
| `mutant_peptide` | string | Neoantigen peptide sequence |
| `wildtype_peptide` | string | Corresponding wildtype peptide |
| `hla_allele` | string | Best-binding HLA allele |
| `mutant_ic50` | number | Mutant peptide binding affinity (nM) |
| `wildtype_ic50` | number | Wildtype peptide binding affinity (nM) |
| `agretopicity` | number | Ratio of wildtype to mutant IC50 (higher = more tumor-specific) |
| `expression_tpm` | number | Gene expression level (TPM, if provided) |
| `clonality` | string | `"clonal"` or `"subclonal"` (if available) |
| `composite_score` | number | Weighted ranking score (0-1) |

### Neoantigen prioritization

| Priority | Criteria |
|----------|----------|
| Tier 1 | IC50 &lt; 50 nM, expression &gt; 10 TPM, clonal, agretopicity &gt; 10 |
| Tier 2 | IC50 &lt; 50 nM, expression &gt; 1 TPM, any clonality |
| Tier 3 | IC50 &lt; 500 nM, expression &gt; 1 TPM |
| Tier 4 | IC50 &lt; 500 nM, no expression data |

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