@article{Attig01102019,
author = {Attig, Jan and Young, George R. and Hosie, Louise and Perkins, David and Encheva-Yokoya, Vesela and Stoye, Jonathan P. and Snijders, Ambrosius P. and Ternette, Nicola and Kassiotis, George}, 
title = {LTR retroelement expansion of the human cancer transcriptome and immunopeptidome revealed by de novo transcript assembly},
volume = {29}, 
number = {10}, 
pages = {1578-1590}, 
year = {2019}, 
doi = {10.1101/gr.248922.119}, 
abstract ={Dysregulated endogenous retroelements (EREs) are increasingly implicated in the initiation, progression, and immune surveillance of human cancer. However, incomplete knowledge of ERE activity limits mechanistic studies. By using pan-cancer de novo transcript assembly, we uncover the extent and complexity of ERE transcription. The current assembly doubled the number of previously annotated transcripts overlapping with long-terminal repeat (LTR) elements, several thousand of which were expressed specifically in one or a few related cancer types. Exemplified in melanoma, LTR-overlapping transcripts were highly predictable, disease prognostic, and closely linked with molecularly defined subtypes. They further showed the potential to affect disease-relevant genes, as well as produce novel cancer-specific antigenic peptides. This extended view of LTR elements provides the framework for functional validation of affected genes and targets for cancer immunotherapy.}, 
URL = {http://genome.cshlp.org/content/29/10/1578.abstract}, 
eprint = {http://genome.cshlp.org/content/29/10/1578.full.pdf+html}, 
journal = {Genome Research} 
}