Considering this, unbiased sequencing surveys of tumor transcriptomes or genomes are expected to reveal mutations in these commonly affected cancer genes as well as many novel mutations in genes with no previous implication in cancer. Next-generation sequencing (NGS) technology (Shendure and Ji, 2008) has now emerged as a practical, high-throughput and low-cost sequencing method enabling the full and rapid interrogation of the genomes and transcriptomes of individual tumors for mutations. As such, NGS has presented an unprecedented opportunity for SNV discovery in cancer. Recent studies involving deeply sequencing the tumor genomes from acute myeloid leukemia patients (Ley et al., 2008; Mardis et al., 2009) and a lobular breast cancer patient (Shah et al., 2009b) have revealed numerous novel somatic mutations in genes that had not been previously reported to harbor abnormalities. In addition, sequencing the transcriptomes of ovarian cancers with RNA-seq (Marioni et al., 2008; Morin et al., 2008; Mortazavi et al., 2008) led to the discovery of a defining mutation in the FOXL2 gene (previously not implicated in cancer) in granulosa cell tumors of the ovary (Shah et al., 2009a).
