inst/markdown/methods/pMHC-SNV.markdown

In CRI-iAtlas/iatlas-app: What the Package Does (One Line, Title Case)

Title: Neoantigen Prediction from SNVs

Description: Potential neoantigenic peptides were identified using NetMHCpan v3.0 (Nielsen and Andreatta, 2016), based on HLA types derived from RNA-seq using OptiType. In brief, using the HLA calls from OptiType, for each sample, all pairs of MHC and minimal mutant peptide were input into NetMHCpan v3.0 using default settings. NetMHCpan will automatically extract all 8-11mer peptides from a minimal peptide sequence and predict binding for each peptide-MHC pair. After computation, the results were parsed to only retain peptides which included the mutated position. Peptides containing amino acid mutations were identified as potential antigens on the basis of a predicted binding to autologous MHC (IC50 < 500 nM) and detectable gene expression meeting an empirically determined threshold of 1.6 transcripts-per-million (TPM). This threshold was selected in order to divide the bimodal distribution in the expression data.

Specifically, somatic nonsynonymous coding single nucleotide variants were extracted from the MC3 variant file (mc3.v0.2.8.CONTROLLED.maf) with the following filters: FILTER in PASS, wga, native_wga_mix; NCALLERS > 1; barcode in whitelist where do_not_use = False; Variant_Classification = Missense_Mutation; and Variant_Type = SNP. For each SNV, the Ensembl protein reference sequence was obtained, and the minimal peptide encompassing the mutation site plus 10 amino acids up and downstream of the mutation site was extracted (21 aa long peptide). If the mutation occurred within 10 amino acids of the N- or C-terminal end of the protein, all available sequence between the mutation and start/end of the protein was taken, resulting in a minimal peptide shorter than 21 aa. The variant position within the minimal peptide was recorded, and the mutation was applied to the minimal peptide, resulting in a mutant minimal peptide. Variation in sequencing coverage and tumor purity require careful consideration in order to mitigate the risk of impacting mutation calls and on pMHC, and prior to pMHC calling, sequencing data was subjected to rigorous harmonization efforts, performed by the PanCancer MC3 Consortium(Ellrott et al., 2018).

Reference List

Contributors: Scott D. Brown, Robert A. Holt

CRI-iAtlas/iatlas-app documentation built on Feb. 7, 2025, 9:02 p.m.