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	≥ 10
NSCLC	7.2	≥ 10
Colorectal (MSS)	3.8	≥ 10
Colorectal (MSI-H)	45.2	≥ 10
Breast	2.6	≥ 10
Pancreatic	1.7	≥ 10

MSI status interpretation

Status	Unstable Sites	Clinical Implication
MSI-H	≥ 30%	Checkpoint inhibitor eligible (pembrolizumab)
MSI-L	10-30%	Not considered MSI-H; standard treatment
MSS	< 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 < 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
< 50	< 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
> 5000	> 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 < 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 < 50 nM, expression > 10 TPM, clonal, agretopicity > 10
Tier 2	IC50 < 50 nM, expression > 1 TPM, any clonality
Tier 3	IC50 < 500 nM, expression > 1 TPM
Tier 4	IC50 < 500 nM, no expression data

Interpreting oncology analytics outputs