LENS Report
The LENS workflow concludes by generating a report consistent of predicted pMHCs. The report can be found in the project’s outputs/lens/<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.
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 |
nt_context |
Nucleotide sequence context around the coding variant (includes coding variant) |
pep_context |
Peptide sequence context around the varinat 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) |
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 |
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 |
allele_raw_read_aligned_count |
Raw count of reads aligned to HLA allele (seq2HLA) |
allele_proportion_rna_tumor_reads |
Proportion of total RNA tumor sample reads aligned to HLA allele (seq2HLA) |
allele_proportion_hla_rna_tumor_reads |
Proportion of HLA-aligned RNA tumor sample reads aligned to HLA allele (seq2HLA) |
origin_descriptor |
Generic identifier |
tpm |
Transcripts per million (Salmon by default) |
priority_score |
Prioritization score of pMHC |
priority_score_no_ccf |
Prioritization score of pMHC (calculated without CCF) |
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 varinat 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 |
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 |
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 |
allele_raw_read_aligned_count |
Raw count of reads aligned to HLA allele (seq2HLA) |
allele_proportion_rna_tumor_reads |
Proportion of total RNA tumor sample reads aligned to HLA allele (seq2HLA) |
allele_proportion_hla_rna_tumor_reads |
Proportion of HLA-aligned RNA tumor sample reads aligned to HLA allele (seq2HLA) |
origin_descriptor |
Generic identifier |
tpm |
Transcripts per million (Salmon by default) |
priority_score |
Prioritization score of pMHC |
priority_score_no_ccf |
Prioritization score of pMHC (calculated without CCF) |
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) |
allele_raw_read_aligned_count |
Raw count of reads aligned to HLA allele (seq2HLA) |
allele_proportion_rna_tumor_reads |
Proportion of total RNA tumor sample reads aligned to HLA allele (seq2HLA) |
allele_proportion_hla_rna_tumor_reads |
Proportion of HLA-aligned RNA tumor sample reads aligned to HLA allele (seq2HLA) |
origin_descriptor |
Generic identifier |
tpm |
Transcripts per million (Salmon by default) |
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 varinat amino acid (includes variant amino acid) |
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 |
allele_raw_read_aligned_count |
Raw count of reads aligned to HLA allele (seq2HLA) |
allele_proportion_rna_tumor_reads |
Proportion of total RNA tumor sample reads aligned to HLA allele (seq2HLA) |
allele_proportion_hla_rna_tumor_reads |
Proportion of HLA-aligned RNA tumor sample reads aligned to HLA allele (seq2HLA) |
origin_descriptor |
Generic identifier |
tpm |
Transcripts per million (Salmon by default) |
priority_score_no_ccf |
Prioritization score of pMHC (calculated without CCF) |
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 varinat amino acid (includes variant amino acid) |
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]) |
allele_raw_read_aligned_count |
Raw count of reads aligned to HLA allele (seq2HLA) |
allele_proportion_rna_tumor_reads |
Proportion of total RNA tumor sample reads aligned to HLA allele (seq2HLA) |
allele_proportion_hla_rna_tumor_reads |
Proportion of HLA-aligned RNA tumor sample reads aligned to HLA allele (seq2HLA) |
origin_descriptor |
Generic identifier |
tpm |
Transcripts per million (Salmon by default) |
priority_score_no_ccf |
Prioritization score of pMHC (calculated without CCF) |
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) |
allele_raw_read_aligned_count |
Raw count of reads aligned to HLA allele (seq2HLA) |
allele_proportion_rna_tumor_reads |
Proportion of total RNA tumor sample reads aligned to HLA allele (seq2HLA) |
allele_proportion_hla_rna_tumor_reads |
Proportion of HLA-aligned RNA tumor sample reads aligned to HLA allele (seq2HLA) |
Cancer-testis Antigens and Self-antigens
Tumor-level Metrics
Column Name |
Description |
|---|---|
b2m_mutations |
List of any B2M mutations |
b2m_tpm |
B2M gene-level TPM in RNA tumor sample |
tap1_mutations |
List of any TAP1 mutations |
tap1_tpm |
TAP1 gene-level TPM in RNA tumor sample |
tap2_mutations |
List of any TAP2 mutations |
tap2_tpm |
TAP2 gene-level TPM in RNA tumor sample |
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 |
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.
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 |