NeoPredPipe: high-throughput neoantigen prediction and recognition potential pipeline

BMC Bioinformatics

Alexander R.A. Anderson¹  Chandler Gatenbee¹  Ryan O. Schenck²  Eszter Lakatos³  Trevor A. Graham³ 

[1] 0000 0000 9891 5233, grid.468198.a, Integrated Mathematical Oncology, Moffitt Cancer Center, 33612, Tampa, FL, USA;0000 0000 9891 5233, grid.468198.a, Integrated Mathematical Oncology, Moffitt Cancer Center, 33612, Tampa, FL, USA;0000 0004 0641 4511, grid.270683.8, Wellcome Centre for Human Genetics, University of Oxford, OX3 7BN, Oxford, UK;0000 0001 2171 1133, grid.4868.2, Evolution and Cancer Laboratory, Barts Cancer Institute, Queen Mary University of London, EC1M, London, UK;

关键词: Neoantigens;    Cancer;    Evolution;    Heterogeneity;    Next-generation sequencing;   

DOI  :  10.1186/s12859-019-2876-4

来源: publisher

【 摘 要 】

BackgroundNext generation sequencing has yielded an unparalleled means of quickly determining the molecular make-up of patient tumors. In conjunction with emerging, effective immunotherapeutics for a number of cancers, this rapid data generation necessitates a paired high-throughput means of predicting and assessing neoantigens from tumor variants that may stimulate immune response.ResultsHere we offer NeoPredPipe (Neoantigen Prediction Pipeline) as a contiguous means of predicting putative neoantigens and their corresponding recognition potentials for both single and multi-region tumor samples. NeoPredPipe is able to quickly provide summary information for researchers, and clinicians alike, on predicted neoantigen burdens while providing high-level insights into tumor heterogeneity given somatic mutation calls and, optionally, patient HLA haplotypes. Given an example dataset we show how NeoPredPipe is able to rapidly provide insights into neoantigen heterogeneity, burden, and immune stimulation potential.ConclusionsThrough the integration of widely adopted tools for neoantigen discovery NeoPredPipe offers a contiguous means of processing single and multi-region sequence data. NeoPredPipe is user-friendly and adaptable for high-throughput performance. NeoPredPipe is freely available at https://github.com/MathOnco/NeoPredPipe.

【 授权许可】

CC BY