Report Column Reference

Note

For a surface-level guide to reading and using the LENS report, see Interpreting the Report. This page provides exhaustive column-by-column documentation for every antigen source.

The LENS workflow concludes by generating a report consisting of predicted pMHCs. The report can be found in the project’s outputs/lens/<DATASET>/<PAT_NAME>/<RUN_NAME>/ directory.

The LENS report, by default, includes information about each predicted pMHC from each antigen source (e.g. SNV, InDel, ERV, etc.). The inclusion of all pMHCs from each antigen source results in many columns not being relevant to each pMHC (for example, a left_gene column intended for a fusion-derived pMHC is not relevant to a SNV-derived pMHC). We have broken down each antigen source’s relevant columns below.

Note

The inclusion of pMHC descriptive columns (e.g. derived from external tools) is conditional upon that tool being specified within the workflow.

Final report semantics

The final *.report.tsv file is the reviewed LENS report. It includes a stable candidate_id for each row and the review scoring columns produced by the review evidence workflow. Intermediate unreviewed reports may be present in sample-level output directories, but the report under outputs/lens is the file intended for downstream review.

The same directory also contains *.run_qc_summary.tsv. This long-format summary records final report row counts, candidate ID integrity checks, candidate counts by antigen source, missingness for important columns, and final-report validation messages. It does not include Nextflow task status counts because trace files are produced after the workflow DAG finishes; use RAFT project status or raft generate-reports to inspect failed or retried tasks from outputs/reports/trace*.txt.

candidate_id values are unique within a report and are assigned in report row order when they are not already present. Evidence JSON files produced during review use the same identifiers, so candidate_id is the preferred key for auditing a report row back to detailed review evidence.

The final report includes these review columns:

Column Name	Description
candidate_id	Stable row identifier used to join report rows, review scores, and review evidence JSON.
alignment_confidence_score	Review score summarizing alignment and read-level confidence evidence.
final_tier	Review tier assigned to the candidate, such as PASS, REVIEW, or FAIL.
reasons	Semicolon-delimited review flags or explanations that contributed to the score or tier. This field can be empty for candidates without triggered review flags.

Missing and non-applicable values

Because the report combines candidates from several antigen sources, many columns only apply to one source. For example, fusion breakpoint columns are expected to be populated only for fusion-derived pMHCs, and InDel allele columns are expected to be populated only for InDel-derived pMHCs.

LENS uses explicit values where possible:

Value	Meaning
NOT_APPLICABLE	The field does not apply to the candidate’s antigen source or context.
NOT_COMPUTED	The computation did not run or the required input was unavailable.
NO_DETECTED_MUTATION	A mutation scan ran and did not detect a mutation in the requested gene.
NO_MATCHED_WT	A matched wildtype peptide or sequence could not be identified for the candidate.
NO_LOHHLA_RESULT_FOR_ALLELE	LOHHLA ran, but did not report a p-value for the candidate’s presented allele.
NA	Legacy or tool-derived missing value. Check the column and antigen source before interpreting it.

Agretopicity and CCF-aware priority scores are most meaningful for variant sources where a matched wildtype sequence and tumor context are available. For non-variant sources, and for variant rows without a matched wildtype peptide or CCF input, these fields can be missing or marked as not computed. Use priority_score_recommended as the primary cross-source sorting score. The companion priority_score_basis column records which source score was selected for that row.

LOHHLA p-values are allele-level annotations. Use lohhla_allele_loss_status to distinguish an available p-value from an allele that did not have a LOHHLA result. Missing p-values should not be interpreted as evidence against HLA loss.

Somatic Single Nucleotide Variants (SNVs)

Column Name	Description
allele	Relevant HLA allele
peptide	Peptide sequence
mhcflurry_2.1.1.aff	Binding affinity from MHCflurry
mhcflurry_2.1.1.aff_perc	Binding affinity percent from MHCflurry
mhcflurry_2.1.1.proc_score	Processing score from MHCflurry
mhcflurry_2.1.1.pres_score	Presentation score from MHCflurry
mhcflurry_2.1.1.pres_perc	Presentation score percent from MHCflurry
antigen_source	Antigen source (“SNV” for somatic single nucleotide variant pMHCs)
variant_callers	Variant callers which detected variant
variant_effect	Variant’s effect on protein
mut_aa_pos	Mutated amino acid position index within peptide sequence (0-indexed)
nt_context	Nucleotide sequence context around the coding variant (includes coding variant)
pep_context	Peptide sequence context around the variant amino acid (includes variant amino acid)
snv_alt_allele	Coding variant allele
snv_ref_allele	Reference allele
snv_type	SNV type (“missense” for relevant SNVs)
transcript_id	Ensembl transcript identifier
variant_coords	Genomic coordinates of coding variant
variant_position_in_cds	Where, within the transcript coding sequence, the variant occurs (0-index)
n_flank	The N flank protein sequence upstream of peptide
c_flank	The C flank protein sequence downstream of peptide
hlapollo_train_allele	Whether the pMHC’s allele is within HLApollo’s training set or not
hlapollo_mhc_pred_0	Logit score for the input example, higher numbers indicate more likely binding/presentation
hlapollo_mhc_pred_0_rank	Percentile Rank for the input example, lower numbers indicate more likely binding/presentation
pepsickle_0.2.1_max_pep_aa_cleav_score	The maximum cleavage score among the amino acids within the peptide of interest
pepsickle_0.2.1_plus1_aa_cleav_score	The cleavage score of the amino acid immediately downstream of peptide of interest
pepsickle_0.2.1_score	pepsickle_0.2.1_plus1_aa_cleav_score * (1 - pepsickle.0.2.1_plus1_aa_cleav_score) – higher is better
rna_reads_covering_genomic_origin	Number of RNA tumor reads covering genomic origin of pMHC
rna_reads_covering_genomic_origin_with_peptide_cds	Number of RNA tumor reads covering genomic origin of pMHC with coding sequence of pMHC
primary_aln_rna_reads_covering_genomic_origin_with_peptide_cds	Number of primary alignment RNA tumor reads covering genomic origin of pMHC with coding sequence of pMHC
proportion_rna_reads_covering_genomic_origin_with_peptide_cds	rna_reads_covering_genomic_origin_with_peptide_cds/proportion_rna_reads_covering_genomic_origin_with_peptide_cds
mhcflurry_agretopicity	Agretopicity calculated by MHCflurry using BLASTP-derived nearest Wildtype sequence
mhcflurry_agretopicity_status	Status for MHCflurry agretopicity calculation: WT_MATCH_FOUND, NO_WT_MATCH, or WT_TOOL_SCORE_MISSING
vaf	Variant allele frequency
totcopynum	Total copy number of the variant allele
multiplicity	Multiplicity value used for cancer cell fraction (CCF) calculations
ccf	Cancer cell fraction (clonality)
gene_name	Gene symbol
gene_id	Ensembl gene identifier
mean_mtec_tpm	Mean expression (in TPM) of SNV-harboriing transcript in mTEC cells
median_mtec_tpm	Median expression (in TPM) of SNV-harboring transcript in mTEC cells
stdev_mtec_tpm	Standard deviation of expression (in TPM) of SNV-harboring transcript in mTEC cells
mean_mtec_num_reads	Mean count of RNA-seq reads for SNV-harboring transcript in mTEC cells
median_mtec_num_reads	Median count of RNA-seq reads for SNV-harboring transcript in mTEC cells
stdev_mtec_num_reads	Standard deviation of count of RNA-seq reads for SNV-harboring transcript in mTEC cells
gene_detectable_normal_tissues	Normal tissues with detectable expression of SNV-harboring transcript (likely irrelevant for pMHC prioritization)
gene_main_subcellular_location	Subcellular location of SNV-harboring transcript
origin_descriptor	Generic identifier
tpm	Transcripts per million (Salmon by default)
priority_score_mhcflurry	Prioritization score of pMHC using MHCflurry binding affinity
priority_score_mhcflurry_no_ccf using MHCflurry binding affinity	Prioritization score of pMHC (calculated without CCF) using MHCflurry binding affinity
priority_score_mhcflurry_prim_alns	Prioritization score of pMHC using MHCflurry binding affinity and RNA tumor primary alignments for quantification
priority_score_mhcflurry_no_ccf_prim_alns	Prioritization score of pMHC (calculated without CCF) using MHCflurry binding affinity and RNA tumor primary alignments for quantification
priority_score_recommended	Recommended priority score for cross-source ranking, selected from the best available priority score column for the row
priority_score_basis	Basis for priority_score_recommended, such as MHCFLURRY_PRIMARY_ALIGNMENTS_WITH_CCF, MHCFLURRY_WITH_CCF, MHCFLURRY_PRIMARY_ALIGNMENTS_NO_CCF, MHCFLURRY_NO_CCF, NETMHCPAN_PRIMARY_ALIGNMENTS_WITH_CCF, NETMHCPAN_WITH_CCF, NETMHCPAN_PRIMARY_ALIGNMENTS_NO_CCF, NETMHCPAN_NO_CCF, MAXIMUM_AVAILABLE_PRIORITY_SCORE, or NOT_COMPUTED

Somatic Insertions and Deletions (InDels)

Column Name	Description
allele	Relevant HLA allele
peptide	Peptide sequence
mhcflurry_2.1.1.aff	Binding affinity from MHCflurry
mhcflurry_2.1.1.aff_perc	Binding affinity percent from MHCflurry
mhcflurry_2.1.1.proc_score	Processing score from MHCflurry
mhcflurry_2.1.1.pres_score	Presentation score from MHCflurry
mhcflurry_2.1.1.pres_perc	Presentation score percent from MHCflurry
antigen_source	Antigen source (“INDEL” for somatic insertion and deletion pMHCs)
variant_callers	Variant callers which detected variant
variant_effect	Variant’s effect on protein
indel_alt_allele	Coding variant allele
indel_ref_allele	Reference allele
indel_type	Insertion or deletion type
nt_context	Nucleotide sequence context around the coding variant (includes coding variant)
pep_context	Peptide sequence context around the variant amino acid (includes variant amino acid)
transcript_id	Ensembl transcript identifier
valid_ref_orf	Confirms translated reading frame is correct
variant_coords	Genomic coordinates of coding variant
n_flank	The N flank protein sequence upstream of peptide
c_flank	The C flank protein sequence downstream of peptide
hlapollo_train_allele	Whether the pMHC’s allele is within HLApollo’s training set or not
hlapollo_mhc_pred_0	Logit score for the input example, higher numbers indicate more likely binding/presentation
hlapollo_mhc_pred_0_rank	Percentile Rank for the input example, lower numbers indicate more likely binding/presentation
pepsickle_0.2.1_max_pep_aa_cleav_score	The maximum cleavage score among the amino acids within the peptide of interest
pepsickle_0.2.1_plus1_aa_cleav_score	The cleavage score of the amino acid immediately downstream of peptide of interest
pepsickle_0.2.1_score	pepsickle_0.2.1_plus1_aa_cleav_score * (1 - pepsickle.0.2.1_plus1_aa_cleav_score) – higher is better
rna_reads_covering_genomic_origin	Number of RNA tumor reads covering genomic origin of pMHC
rna_reads_covering_genomic_origin_with_peptide_cds	Number of RNA tumor reads covering genomic origin of pMHC with coding sequence of pMHC
proportion_rna_reads_covering_genomic_origin_with_peptide_cds	rna_reads_covering_genomic_origin_with_peptide_cds/proportion_rna_reads_covering_genomic_origin_with_peptide_cds
primary_aln_rna_reads_covering_genomic_origin_with_peptide_cds	Number of primary alignment RNA tumor reads covering genomic origin of pMHC with coding sequence of pMHC
mhcflurry_agretopicity	Agretopicity calculated by MHCflurry using BLASTP-derived nearest Wildtype sequence
mhcflurry_agretopicity_status	Status for MHCflurry agretopicity calculation: WT_MATCH_FOUND, NO_WT_MATCH, or WT_TOOL_SCORE_MISSING
vaf	Variant allele frequency
totcopynum	Total copy number of the variant allele
multiplicity	Multiplicity value used for cancer cell fraction (CCF) calculations
ccf	Cancer cell fraction (clonality)
gene_name	Gene symbol
gene_id	Ensembl gene identifier
mean_mtec_tpm	Mean expression (in TPM) of InDel-harboriing transcript in mTEC cells
median_mtec_tpm	Median expression (in TPM) of InDel-harboring transcript in mTEC cells
stdev_mtec_tpm	Standard deviation of expression (in TPM) of InDel-harboring transcript in mTEC cells
mean_mtec_num_reads	Mean count of RNA-seq reads for InDel-harboring transcript in mTEC cells
median_mtec_num_reads	Median count of RNA-seq reads for InDel-harboring transcript in mTEC cells
stdev_mtec_num_reads	Standard deviation of count of RNA-seq reads for InDel-harboring transcript in mTEC cells
gene_detectable_normal_tissues	Normal tissues with detectable expression of InDel-harboring transcript (likely irrelevant for pMHC prioritization)
gene_main_subcellular_location	Subcellular location of InDel-harboring transcript
origin_descriptor	Generic identifier
tpm	Transcripts per million (Salmon by default)
priority_score_mhcflurry	Prioritization score of pMHC using MHCflurry binding affinity
priority_score_mhcflurry_no_ccf using MHCflurry binding affinity	Prioritization score of pMHC (calculated without CCF) using MHCflurry binding affinity
priority_score_mhcflurry_prim_alns	Prioritization score of pMHC using MHCflurry binding affinity and RNA tumor primary alignments for quantification
priority_score_mhcflurry_no_ccf_prim_alns	Prioritization score of pMHC (calculated without CCF) using MHCflurry binding affinity and RNA tumor primary alignments for quantification

Splice variants

Column Name	Description
allele	Relevant HLA allele
peptide	Peptide sequence
mhcflurry_2.1.1.aff	Binding affinity from MHCflurry
mhcflurry_2.1.1.aff_perc	Binding affinity percent from MHCflurry
mhcflurry_2.1.1.proc_score	Processing score from MHCflurry
mhcflurry_2.1.1.pres_score	Presentation score from MHCflurry
mhcflurry_2.1.1.pres_perc	Presentation score percent from MHCflurry
antigen_source	Antigen source (“SPLICE” for splice variant pMHCs)
coding_sequence	Nucleotide coding sequence for peptide of interest
pep_context	Peptide sequence context around the variant amino acid (includes variant amino acid)
splice_coords	Coordinates of the splice event
splice_description	Description of the splice event (see SNAF documentation)
n_flank	The N flank protein sequence upstream of peptide
c_flank	The C flank protein sequence downstream of peptide
hlapollo_train_allele	Whether the pMHC’s allele is within HLApollo’s training set or not
hlapollo_mhc_pred_0	Logit score for the input example, higher numbers indicate more likely binding/presentation
hlapollo_mhc_pred_0_rank	Percentile Rank for the input example, lower numbers indicate more likely binding/presentation
pepsickle_0.2.1_max_pep_aa_cleav_score	The maximum cleavage score among the amino acids within the peptide of interest
pepsickle_0.2.1_plus1_aa_cleav_score	The cleavage score of the amino acid immediately downstream of peptide of interest
pepsickle_0.2.1_score	pepsickle_0.2.1_plus1_aa_cleav_score * (1 - pepsickle.0.2.1_plus1_aa_cleav_score) – higher is better
rna_reads_covering_genomic_origin_with_peptide_cds	Number of RNA tumor reads covering genomic origin of pMHC with coding sequence of pMHC
primary_aln_rna_reads_covering_genomic_origin_with_peptide_cds	Number of primary alignment RNA tumor reads covering genomic origin of pMHC with coding sequence of pMHC
gene_id	Ensembl gene identifier
origin_descriptor	Generic identifier
priority_score_mhcflurry	Prioritization score of pMHC using MHCflurry binding affinity
priority_score_mhcflurry_no_ccf using MHCflurry binding affinity	Prioritization score of pMHC (calculated without CCF) using MHCflurry binding affinity
priority_score_mhcflurry_prim_alns	Prioritization score of pMHC using MHCflurry binding affinity and RNA tumor primary alignments for quantification
priority_score_mhcflurry_no_ccf_prim_alns	Prioritization score of pMHC (calculated without CCF) using MHCflurry binding affinity and RNA tumor primary alignments for quantification

Fusions

Column Name	Description
allele	Relevant HLA allele
peptide	Peptide sequence
mhcflurry_2.1.1.aff	Binding affinity from MHCflurry
mhcflurry_2.1.1.aff_perc	Binding affinity percent from MHCflurry
mhcflurry_2.1.1.proc_score	Processing score from MHCflurry
mhcflurry_2.1.1.pres_score	Presentation score from MHCflurry
mhcflurry_2.1.1.pres_perc	Presentation score percent from MHCflurry
antigen_source	Antigen source (“FUSION” for fusion-derived pMHCs)
fusion_annotation	Annotation information about the fusion event
fusion_id	Fusion identifier
fusion_left_breakpoint	Fusion’s left breakpoint
fusion_left_gene	Fusion’s left gene symbol
fusion_left_transcript	Fusion’s left ensembl transcript identifier
fusion_right_breakpoint	Fusion’s right breakpoint
fusion_right_gene	Fusion’s right gene symbol
fusion_right_transcript	Fusion’s right ensembl transcript identifier
fusion_type	Type of fusion
nt_context	Nucleotide sequence context around the coding variant (includes coding variant)
pep_context	Peptide sequence context around the variant amino acid (includes variant amino acid)
n_flank	The N flank protein sequence upstream of peptide
c_flank	The C flank protein sequence downstream of peptide
hlapollo_train_allele	Whether the pMHC’s allele is within HLApollo’s training set or not
hlapollo_mhc_pred_0	Logit score for the input example, higher numbers indicate more likely binding/presentation
hlapollo_mhc_pred_0_rank	Percentile Rank for the input example, lower numbers indicate more likely binding/presentation
pepsickle_0.2.1_max_pep_aa_cleav_score	The maximum cleavage score among the amino acids within the peptide of interest
pepsickle_0.2.1_plus1_aa_cleav_score	The cleavage score of the amino acid immediately downstream of peptide of interest
pepsickle_0.2.1_score	pepsickle_0.2.1_plus1_aa_cleav_score * (1 - pepsickle.0.2.1_plus1_aa_cleav_score) – higher is better
rna_reads_covering_genomic_origin_with_peptide_cds	Number of RNA tumor reads covering genomic origin of pMHC with coding sequence of pMHC
primary_aln_rna_reads_covering_genomic_origin_with_peptide_cds	Number of primary alignment RNA tumor reads covering genomic origin of pMHC with coding sequence of pMHC
mhcflurry_agretopicity	Agretopicity calculated by MHCflurry using BLASTP-derived nearest Wildtype sequence
mhcflurry_agretopicity_status	Status for MHCflurry agretopicity calculation: WT_MATCH_FOUND, NO_WT_MATCH, or WT_TOOL_SCORE_MISSING
origin_descriptor	Generic identifier
tpm	Transcripts per million (Salmon by default; TPMs listed separately for each original transcript)
priority_score_mhcflurry	Prioritization score of pMHC using MHCflurry binding affinity
priority_score_mhcflurry_no_ccf using MHCflurry binding affinity	Prioritization score of pMHC (calculated without CCF) using MHCflurry binding affinity
priority_score_mhcflurry_prim_alns	Prioritization score of pMHC using MHCflurry binding affinity and RNA tumor primary alignments for quantification
priority_score_mhcflurry_no_ccf_prim_alns	Prioritization score of pMHC (calculated without CCF) using MHCflurry binding affinity and RNA tumor primary alignments for quantification

ERVs

Column Name	Description
allele	Relevant HLA allele
peptide	Peptide sequence
mhcflurry_2.1.1.aff	Binding affinity from MHCflurry
mhcflurry_2.1.1.aff_perc	Binding affinity percent from MHCflurry
mhcflurry_2.1.1.proc_score	Processing score from MHCflurry
mhcflurry_2.1.1.pres_score	Presentation score from MHCflurry
mhcflurry_2.1.1.pres_perc	Presentation score percent from MHCflurry
antigen_source	Antigen source (“ERV” for ERV-derived pMHCs)
erv_norm_cpm	ERV counts per million (normal RNA sample)
erv_orf_id	ERV open reading frame identifier (from gEVE)
erv_orf_raw_read_count	ERV open reading frame raw read count (tumor RNA sample)
erv_orf_tpm	ERV open reading frame transcripts per million
erv_tumor_cpm	ERV counts per million (tumor RNA sample)
erv_tumor_cpm_to_norm_cpm_delta	Difference between tumor CPM and normal CPM (log(tumor cpm + 1) - log(normal cpm + 1))
pep_context	Peptide sequence context around the variant amino acid (includes variant amino acid)
n_flank	The N flank protein sequence upstream of peptide
c_flank	The C flank protein sequence downstream of peptide
hlapollo_train_allele	Whether the pMHC’s allele is within HLApollo’s training set or not
hlapollo_mhc_pred_0	Logit score for the input example, higher numbers indicate more likely binding/presentation
hlapollo_mhc_pred_0_rank	Percentile Rank for the input example, lower numbers indicate more likely binding/presentation
pepsickle_0.2.1_max_pep_aa_cleav_score	The maximum cleavage score among the amino acids within the peptide of interest
pepsickle_0.2.1_plus1_aa_cleav_score	The cleavage score of the amino acid immediately downstream of peptide of interest
pepsickle_0.2.1_score	pepsickle_0.2.1_plus1_aa_cleav_score * (1 - pepsickle.0.2.1_plus1_aa_cleav_score) – higher is better
rna_reads_covering_genomic_origin_with_peptide_cds	Number of RNA tumor reads covering genomic origin of pMHC with coding sequence of pMHC
primary_aln_rna_reads_covering_genomic_origin_with_peptide_cds	Number of primary alignment RNA tumor reads covering genomic origin of pMHC with coding sequence of pMHC
erv_hervq_region	ERV open read frame’s hERVQuant region (if any)
erv_geve_annot	ERV open reading frame gEVE annotation
erv_ribo_cov_mean	ERV open reading frame ribo-seq mean coverage (external references)
erv_ribo_probe_count	ERV open reading frame ribo-seq probe count (external references)
erv_hervq_region_total_erv_orf_count	Total number of ERV open reading frames in corresponding hERVQuant region (if any) – more is better
erv_hervq_region_ribo_covd_erv_orf_count	Total number of ERV open reading frames in corresponding hERVQuant region with ribo-seq coverage (if any) – More is better
erv_mtec_exp_status	Whether ERV open reading frame expression in mTEC cells (no expression is better)
erv_norm_exp_status	Whether ERV open reading frame expression in normal cells (no expression is better)
erv_hervq_region_proteins_list	List of ERV proteins within ERV open reading frame’s corresponding hERVQuant region
erv_hervq_region_erv_uniq_proteins_count	Number of ERV proteins within ERV open reading frame’s corresponding hERVQuant region
erv_hervq_region_avg_exp_corr	Average expression correlation among ERV open reading frames within corresponding hERVQuant region (external references)
erv_hervq_region_pairwise_corr_count	Number of pairwise ERV open reading frame expression correlations used to calculate average expression correlation (external references)
erv_hervq_region_score	Score used for calculating ERV confidence score (1 if in hERVQuant region; 0 otherwise)
erv_annot_score	Score used for calculating ERV confidence score (1 if valid ERV protein; 0 otherwise)
erv_ribo_cov_mean_score	Score used for calculating ERV confidence score (1 if ribo-seq coverage; 0 otherwise)
erv_total_erv_count_score	Score used for calculating ERV confidence score (1 if >1 ERV ORFs in hERVQuant region; 0 otherwise)
erv_ribo_covd_erv_count_score	Score used for calculating ERV confidence score (1 if >1 ERV ORFs with ribo-seq coverage; 0 otherwise)
erv_mtec_exp_status_score	Score used for calculating ERV confidence score (1 if not expressed in mTECs; 0 otherwise)
erv_norm_exp_status_score	Score used for calculating ERV confidence score (1 if not expressed in normal tissues; 0 otherwise)
erv_uniq_proteins_count_score	Score used for calculating ERV confidence score (0 if no ERV proteins, 0.25 if one unique ERV protein in hERVQuant region; 0.5 if two unique ERV proteins in hERVQuant region; 0.75 if three unique ERV proteins in hERVQuant region; 1.0 if four unique ERV proteins in hERVQuant region)
erv_avg_exp_corr_within_hervq_region_score	Score used for calculating ERV confidence score (bound between [0, 1]; expression correlation value)
erv_raw_erv_orf_confidence_score	Raw ERV score
erv_normd_erv_orf_confidence_score	Normalized ERV score (bound between [0, 1])
origin_descriptor	Generic identifier
tpm	Transcripts per million (Salmon by default)
priority_score_mhcflurry	Prioritization score of pMHC using MHCflurry binding affinity
priority_score_mhcflurry_no_ccf using MHCflurry binding affinity	Prioritization score of pMHC (calculated without CCF) using MHCflurry binding affinity
priority_score_mhcflurry_prim_alns	Prioritization score of pMHC using MHCflurry binding affinity and RNA tumor primary alignments for quantification
priority_score_mhcflurry_no_ccf_prim_alns	Prioritization score of pMHC (calculated without CCF) using MHCflurry binding affinity and RNA tumor primary alignments for quantification

Viruses

Column Name	Description
allele	Relevant HLA allele
peptide	Peptide sequence
mhcflurry_2.1.1.aff	Binding affinity from MHCflurry
mhcflurry_2.1.1.aff_perc	Binding affinity percent from MHCflurry
mhcflurry_2.1.1.proc_score	Processing score from MHCflurry
mhcflurry_2.1.1.pres_score	Presentation score from MHCflurry
mhcflurry_2.1.1.pres_perc	Presentation score percent from MHCflurry
antigen_source	Antigen source (“VIRUS” for viral pMHCs)
pep_context	Sequence context around peptide of interest
virus_id	Viral identifier
rna_reads_covering_genomic_origin	Number of RNA tumor reads covering genomic origin of pMHC
rna_reads_covering_genomic_origin_with_peptide_cds	Number of RNA tumor reads covering genomic origin of pMHC with coding sequence of pMHC
origin_descriptor	Generic identifier
priority_score_mhcflurry	Prioritization score of pMHC using MHCflurry binding affinity
priority_score_mhcflurry_no_ccf using MHCflurry binding affinity	Prioritization score of pMHC (calculated without CCF) using MHCflurry binding affinity
priority_score_mhcflurry_prim_alns	Prioritization score of pMHC using MHCflurry binding affinity and RNA tumor primary alignments for quantification
priority_score_mhcflurry_no_ccf_prim_alns	Prioritization score of pMHC (calculated without CCF) using MHCflurry binding affinity and RNA tumor primary alignments for quantification

Cancer-testis Antigens and Self-antigens

Column Name	Description
allele	Relevant HLA allele
peptide	Peptide sequence
mhcflurry_2.1.1.aff	Binding affinity from MHCflurry
mhcflurry_2.1.1.aff_perc	Binding affinity percent from MHCflurry
mhcflurry_2.1.1.proc_score	Processing score from MHCflurry
mhcflurry_2.1.1.pres_score	Presentation score from MHCflurry
mhcflurry_2.1.1.pres_perc	Presentation score percent from MHCflurry
antigen_source	Antigen source (“CTA/SELF” for CTA/Self-antigen pMHCs)
pep_context	Sequence context around peptide of interest
transcript_id	Ensembl transcript identifier
n_flank	The N flank protein sequence upstream of peptide
c_flank	The C flank protein sequence downstream of peptide
hlapollo_train_allele	Whether the pMHC’s allele is within HLApollo’s training set or not
hlapollo_mhc_pred_0	Logit score for the input example, higher numbers indicate more likely binding/presentation
hlapollo_mhc_pred_0_rank	Percentile Rank for the input example, lower numbers indicate more likely binding/presentation
pepsickle_0.2.1_max_pep_aa_cleav_score	The maximum cleavage score among the amino acids within the peptide of interest
pepsickle_0.2.1_plus1_aa_cleav_score	The cleavage score of the amino acid immediately downstream of peptide of interest
pepsickle_0.2.1_score	pepsickle_0.2.1_plus1_aa_cleav_score * (1 - pepsickle.0.2.1_plus1_aa_cleav_score) – higher is better
all_transcript_ids_encoding_peptide	All transcript identifiers encoding peptide of interest – useful for ensuring non-CTA transcripts are not encoding the peptide
all_gene_ids_encoding_peptide	All gene identifiers encoding peptide of interest – useful for ensuring non-CTA genes are not encoding the peptide
all_gene_names_encoding_peptide	All gene symbols encoding peptide of interest – useful for ensuring non-CTA genes are not encoding the peptide
rna_reads_covering_genomic_origin	Number of RNA tumor reads covering genomic origin of pMHC
rna_reads_covering_genomic_origin_with_peptide_cds	Number of RNA tumor reads covering genomic origin of pMHC with coding sequence of pMHC
primary_aln_rna_reads_covering_genomic_origin_with_peptide_cds	Number of primary alignment RNA tumor reads covering genomic origin of pMHC with coding sequence of pMHC
proportion_rna_reads_covering_genomic_origin_with_peptide_cds	rna_reads_covering_genomic_origin_with_peptide_cds/proportion_rna_reads_covering_genomic_origin_with_peptide_cds
mhcflurry_agretopicity	Agretopicity calculated by MHCflurry using BLASTP-derived nearest Wildtype sequence
mhcflurry_agretopicity_status	Status for MHCflurry agretopicity calculation: WT_MATCH_FOUND, NO_WT_MATCH, or WT_TOOL_SCORE_MISSING
mean_mtec_tpm	Mean expression (in TPM) of CTA transcript in mTEC cells
median_mtec_tpm	Median expression (in TPM) of CTA transcript in mTEC cells
stdev_mtec_tpm	Standard deviation of expression (in TPM) of CTA transcript in mTEC cells
mean_mtec_num_reads	Mean count of RNA-seq reads for CTA transcript in mTEC cells
median_mtec_num_reads	Median count of RNA-seq reads for CTA transcript in mTEC cells
stdev_mtec_num_reads	Standard deviation of count of RNA-seq reads for CTA transcript in mTEC cells
gene_detectable_normal_tissues	Normal tissues with detectable expression of CTA
gene_main_subcellular_location	Subcellular location of CTA
gene_name	Gene symbol
gene_id	Ensembl gene identifier
origin_descriptor	Generic identifier
tpm	Transcripts per million (Salmon by default)
priority_score_mhcflurry	Prioritization score of pMHC using MHCflurry binding affinity
priority_score_mhcflurry_no_ccf using MHCflurry binding affinity	Prioritization score of pMHC (calculated without CCF) using MHCflurry binding affinity
priority_score_mhcflurry_prim_alns	Prioritization score of pMHC using MHCflurry binding affinity and RNA tumor primary alignments for quantification
priority_score_mhcflurry_no_ccf_prim_alns	Prioritization score of pMHC (calculated without CCF) using MHCflurry binding affinity and RNA tumor primary alignments for quantification

Tumor-level Metrics

Column Name	Description
b2m_mutations	List of detected B2M mutations, or NO_DETECTED_MUTATION when the mutation scan ran and found none
b2m_tpm	B2M gene-level TPM in RNA tumor sample, or NOT_COMPUTED if expression could not be extracted
tap1_mutations	List of detected TAP1 mutations, or NO_DETECTED_MUTATION when the mutation scan ran and found none
tap1_tpm	TAP1 gene-level TPM in RNA tumor sample, or NOT_COMPUTED if expression could not be extracted
tap2_mutations	List of detected TAP2 mutations, or NO_DETECTED_MUTATION when the mutation scan ran and found none
tap2_tpm	TAP2 gene-level TPM in RNA tumor sample, or NOT_COMPUTED if expression could not be extracted

HLA Allele-level Metrics

Column Name	Description
allele	HLA allele is interest
hla_allele_raw_read_aligned_count	Total number of HLA-aligned RNA tumor reads
hla_allele_proportion_rna_tumor_reads	Proportion of all RNA tumor reads assigned to HLA allele
hla_allele_proportion_hla_rna_tumor_reads	Proportion of HLA-aligned RNA tumor reads assigned to HLA allele
hla_allele_support	Tool-level support for HLA allele
lohhla_allele_loss_pval	LOHHLA allele-specific loss test p-value
lohhla_allele_loss_status	Status for LOHHLA p-value availability: LOH_RESULT_AVAILABLE or NO_LOHHLA_RESULT_FOR_ALLELE

Optional columns

The LENS report may contain additional columns depending upon the tools and references utilized. For example, users with licenses for the NetMHC tool suite that add them to the tools used (see LINK) will see NetMHC-specific columns.

A list of optional columns is listed below.

Optional Columns

Column Name	Description
netmhcpan_4.1b.score_el	Elution score from NetMHCpan
netmhcpan_4.1b.perc_rank_el	Elution percent rank from NetMHCpan
netmhcpan_4.1b.score_ba	Binding affinity score from NetMHCpan
netmhcpan_4.1b.perc_rank_ba	Binding affinity percent rank from NetMHCpan
netmhcpan_4.1b.aff_nm	Binding affinity from NetMHCpan
netmhcstabpan_1.0.stab_pred_score	Binding stability score from NetMHCstabpan
netmhcstabpan_1.0.halflife_hours	Half life in hours from NetMHCstabpan
netmhcstabpan_1.0.perc_rank_stab	Binding stability percent rank from NetMHCstabpan
netmhcpan_agretopicity	Agretopicity calculated by NetMHCpan using BLASTP-derived nearest Wildtype sequence
netmhcpan_agretopicity_status	Status for NetMHCpan agretopicity calculation: WT_MATCH_FOUND, NO_WT_MATCH, or WT_TOOL_SCORE_MISSING
priority_score_netmhcpan	Prioritization score of pMHC using NetMHCpan binding affinity
priority_score_netmhcpan_no_ccf using NetMHCpan binding affinity	Prioritization score of pMHC (calculated without CCF) using NetMHCpan binding affinity
priority_score_netmhcpan_prim_alns	Prioritization score of pMHC using NetMHCpan binding affinity and RNA tumor primary alignments for quantification
priority_score_netmhcpan_no_ccf_prim_alns	Prioritization score of pMHC (calculated without CCF) using NetMHCpan and RNA tumor primary alignments for quantification
priority_score_recommended	Recommended priority score for cross-source ranking, selected from the best available priority score column for the row
priority_score_basis	Basis for priority_score_recommended, such as MHCFLURRY_PRIMARY_ALIGNMENTS_WITH_CCF, MHCFLURRY_WITH_CCF, MHCFLURRY_PRIMARY_ALIGNMENTS_NO_CCF, MHCFLURRY_NO_CCF, NETMHCPAN_PRIMARY_ALIGNMENTS_WITH_CCF, NETMHCPAN_WITH_CCF, NETMHCPAN_PRIMARY_ALIGNMENTS_NO_CCF, NETMHCPAN_NO_CCF, MAXIMUM_AVAILABLE_PRIORITY_SCORE, or NOT_COMPUTED