Twenty-eight years after Frederick Sanger made his first attempts to sequence small pieces of DNA, the National Human Genome Research Institute (NHGRI) announced the completion of the Human Genome Project [1
]. After 13 years of international collaborative effort at a cost of $3 billion, an essentially complete human genome sequence was finished and the world was ushered into a “genomic” era. In 2007, less than 4 years later, the first genome sequence of a single individual, James Watson, was deciphered in only 2 months at a cost of less than $2 million. Project “Jim” was initiated by a private company in collaboration with the Baylor College of Medicine-Human Genome Sequencing Center (BCM-HGSC) [4
]. This project demonstrated the feasibility of characterizing virtually all of the small scale variation in a single individual using a next generation sequencing technology thereby advancing the “personalized” genomic medicine model one step closer to a reality.
Cancer has long been recognized as fundamentally driven by genetic mutations [6
]. Although opinions vary as to whether a comprehensive inventory of the genetic changes in tumor cells can lead to fundamental new insights that will further the diagnosis and treatment of this cancer, pilots for large-scale projects already have been initiated [8
]. Sjöblom et al
have shown that the somatic mutations playing a role in the multistep progression of carcinogenesis are far from completely identified, even in the most studied cancer types (breast and colon) [11
]. The Tumor Sequencing Project Consortium (TSPC), formed between the NHGRI funded Genome Centers at BCM, Washington University, and the Broad Institute has initiated a pre-pilot project on non-small cell lung cancer (1,000 genes) to demonstrate the potential of a systemic approach to tumor genotyping by DNA sequencing [12
]. The benefit of this large-scale project already has been proven by the identification of a novel candidate proto-oncogene [13
]. The Cancer Genome Atlas pilot project (TCGA), launched by the National Cancer Institute (NCI) and NHGRI, is now attempting the identification of all genomic alterations significantly associated with cancer. This includes detecting genomic loss or amplification, mutations in coding regions, chromosomal rearrangements, aberrant methylations, and expression profiles. Three tumor types (glioblastoma multiforme, squamous cell carcinoma of the lung, and ovarian carcinoma) have been selected initially by TCGA, with the scope of expanding to all major cancer types [14
Some success in cancer care has already been obtained with the targeting of specific genetic alterations. Among the first effective applications of targeted therapy was the use of imatinib to inhibit the tyrosine kinase activity of the Bcr-Abl fusion protein formed by the chromosomal t(9:22) translocation in chronic myeloid leukemia [15
], and the use of transtuzumab, a recombinant monoclonal antibody against HER2
, in women with metastatic breast cancer with HER2
amplification and overexpression [16
]. Other breakthroughs in personalized therapies include the treatment of gastrointestinal stromal cell tumors, in which mutations in KIT
were found to predict a response to imatinib [15
]. Additionally, mutations in EGFR
predicted a response to gefitinib and erlotinib in lung adenocarcinoma [18
]. The fact that specific mutations in multiple loci are a major determinant of the response to targeted therapies suggests that DNA sequencing is likely to provide an effective diagnostic and therapeutic approach to cancer in the future.
This review focuses on the requisites to identify, validate, and confirm mutations, as well as the possible applications the discovery of new DNA changes can have for the characterization and treatment of the disease. Some technical information is provided for those who may be interested in initiating similar projects, and some examples of preliminary attempts to apply current knowledge in a clinical setting are given with the goal of attracting new clinical investigators to bridge the gap between genomics and its application to everyday patient care.