Main . Previous genomic analyses of HCC in Chinese individuals are limited in cohort size and focus mainly on the exome11 , 12 , 13 , 14, precluding detailed investigations at the whole-genome level. Recently, the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium analysed the genomic complexity of cancer at a considerable scale4 , 5 , 6 , 7 , 8. Nevertheless, the relatively shallow sequencing depth could not fully resolve the subclonal structure of the HCC...