The development of advanced molecular technologies has ushered in the era of ‘omics' science, including transcriptomics, proteomics, and genomics. Genomics, or whole genome approach, has become the most comprehensive investigative method to identify new gene mutations, signal pathways and drug targets for cancers. The purpose of this review is to summarize current second generation sequencing techniques in applied genomics, and to analyze the advantages and/or problems associated with each of the various sequencing platforms. Our understanding of molecular factors associated with tumorigenesis is no longer limited to the mutation of well-known cancer related genes, but may involve a broader range of factors involved in tumor development, including novel somatic mutations, gene fusions, long non-coding RNAs, microRNAs, copy number variations, methylation, and genomic structural variations. Furthermore, these new methods are not limited to analyses of single genetic or epigenetic factor, but offer comprehensive molecule profiling as a more critical and powerful approach to decoding the mystery of tumor development and identifying more reliable cancer biomarkers.