iatlas-app: What the Package Does (One Line, Title Case)

Title: Prediction of Neoantigens

Description: Neoantigens were predicted using the Landscape of Effective Neoantigens Software (LENS) workflow (Vensko 2023). LENS is a bioinformatic workflow for predicting tumor-specific and tumor-associated antigens across a variety of tumor antigen sources.

The classes of neoantigens predicted by LENS are:

Somatic SNVs: Somatic single-nucleotide variants (SNVs), or variants present within tumor tissue but absent from germline tissue. These peptides may be a direct result of a somatic variant or may be a downstream coding consequence of the variant.
Somatic InDels: Somatic insertion/deletion variants (InDels), or variants present within tumor tissue but absent from germline tissue. These peptides may be a direct result of a somatic variant or may be a downstream coding consequence of the variant.
Fusion Events: Scenarios in which a translocation, deletion, or inversion causes two previously genomically distant loci to become neighboring sequences or “fuse” within the genome are also of interest as sources of tumor antigens.
Splice Variants: Aberrant splicing events create tumor-specific transcripts through intron retention, exon skipping, or altered splice targeting.
CTAs and Self-antigens: These antigens are non-mutated self-antigens that may be overexpressed within a tumor. Antigens derived from these transcripts are commonly referred to as cancer testis antigens (CTAs).
Virus: Some viruses, such as human papillomavirus, Epstein–Barr virus, human T cell leukemia/lymphoma virus type 1, and hepatitis C virus, are associated with development of cancers in the tissues they infect earning them the label of oncogenic viruses.
ERVs: Aberrantly expressed endogenous retroviruses (ERVs).