We collected tumour and matched normal DNA samples from 158 ESCC patients in the Chaoshan District of Guangdong Province, an area of high ESCC prevalence in China, and performed whole-genome sequencing (WGS>30X), whole-exome sequencing (WES>100X), and array comparative genomic hybridization (a-CGH) analyses.

We identified eight significantly mutated genes, of which six are well known tumour-associated genes (TP53, RB1, CDKN2A, PIK3CA, NOTCH1, NFE2L2), and two have not previously been described in ESCC (ADAM29 and FAM135B). Notably, FAM135B is identified as a novel cancer- implicated gene as assayed for its ability to promote malignancy of ESCC cells. Additionally, MIR548K, a microRNA encoded in the amplified 11q13.3-13.4 region, is characterized as a novel oncogene, and functional assays demonstrate that MIR548K enhances malignant phenotypes of ESCC cells. Moreover, we have found that several important histone regulator genes (MLL2 (also called KMT2D) , ASH1L, MLL3 (KMT2C) , SETD1B, CREBBP and EP300) are frequently altered in ESCC. Pathway assessment reveals that somatic aberrations are mainly involved in the Wnt, cell cycle and Notch pathways. Genomic analyses suggest that ESCC and head and neck squamous cell carcinoma share some common pathogenic mechanisms, and ESCC development is associated with alcohol drinking.

This study represents a comprehensive characterization of genomic alterations in ESCC, and provides insights into the genetic mechanism(s) of ESCC tumorigenesis. These findings enable us to determine further the biological and therapeutic significance of the newly discovered mutated and amplified genes, which may ultimately lead to the development of effective diagnostic and therapeutic approaches for ESCC.