Introduction

LENS

Landscape of Effective Neoantigen Software (LENS) is a tumor antigen discovery workflow capable of identifying potential therapeutic cancer immunotherapy targets from seven antigen sources. More information on LENS can be found in the LENS publication.

LENS predicts peptide-MHCs (pMHCs) from seven antigen sources:

• Somatic Nucleotide Variants (SNVs)

• Somatic Insertion and Deletion Variants (InDels)

• Splice Variants

• Fusion Events

• Endogenous Retroviruses (ERVs)

• Viruses

• Cancer-testis Antigens (CTAs)

Note

Ready to get started? See Quick Start to install RAFT and run a demonstration.

Sample Prerequisites

LENS can be run on multiple patients simultaneously and there are benefits to running multiple patients (such as shared tumor splice variant detection with SNAF and improved CNA detection with CNVKit), but only one patient worth of samples is required.

It is strongly recommended to run LENS with the following sample types (per patient) for the best experience:

• DNA tumor

• DNA normal

• RNA tumor

Alternatively, the following sample types (per patient) can be used to get fusion, splice, ERV, viral, and CTA pMHCs:

• RNA tumor

Additionally, users should provide a tissue-matched normal RNA sample (e.g. GTEx or Fagerberg et al., 2014).

More information on running multiple sample sets per patient (e.g. primary vs. metastasis, pre-treatment vs. post-treatment, multiple timepoints, etc.) can be found in the Preparing Your Samples section.