2.1. Primary Tumors and Pair-End RNA Sequencing

Ten formalin fixed paraffin embedded (FFPE) NPC samples were retrieved from the Department of Pathology of Sun Yat-sen University Cancer Center (SYSUCC, Guangzhou, China). All tumor samples were reviewed by two experienced pathologists. Total RNA were extracted from ten FFPE tissues with RNeasy FFPE Kit (QIANGEN, Hilden, Germany) according to the manufacturer's instructions for RNA sequencing. cDNA libraries were prepared according to the standard protocol provided by the mRNA-seq sample Pre Kit (Illumina Inc, California, USA) and sequenced (90 nt paired-end) on the Illumina Hi-seq 2000. To identify fusion genes from paired-end RNA sequencing, the data were analyzed by the computational pipeline called SOAPfusion, which uses clusters of discordant paired-end alignments to inform a split-read alignment analysis for finding fusion boundaries [15]. The UCSC H. sapiens reference genome (build hg19) was used for alignments. The written informed consent was obtained from each patient and this study was approved by Ethics Committee and Institutional Review Board of SYSUCC.