Era of Comprehensive Cancer Genome Analyses

摘要: The dramatic responses seen in patients with advanced solid tumors bearing kinase mutations who receive inhibitors have shifted the therapeutic paradigm to approaches that are based on molecular characteristics of a given cancer. As an example, testing for somatic genetic alterations affecting genes encoding epidermal growth factor receptor (EGFR) or anaplastic lymphoma (ALK) has become diagnostic routine lung Unfortunately, however, acquired resistance initial inhibitor will eventually develop during course treatment, thus necessitating drugs can overcome resistance. Accordingly, several next-generation EGFR and ALK been developed, impressive early signs clinical activity. Thus, addition genomic diagnosis, precise determination actual mechanism is key requirement provide optimal care throughout different lines therapy. Although rearrangements already reached general routine, additional pairs cancer response new currently development (eg, ROS1, BRAF, FGFR2, RET, NTRK1). consequence, requirements comprehensive diagnosis growing at pace, number need be tested increasing steadily. In addition, major types therapeutically relevant genome gene mutations, amplifications deletions, fusions) pose entirely challenges their detection. Finally, contrast these demands, most samples non–small-cell small, minimal tumor content, it often difficult obtain larger tissue because location patient comorbidity. technical address this complexity grossly subdivided into three generations (Table 1): one, conventional Sanger sequencing (for mutation detection) plus microscopy coupled fluorescence situ hybridization (FISH; detection amplifications, rearrangements, fusions); two, multiplex panel FISH; three, capture-based massively parallel sequencing. advantage low associated costs, technique typically lacks sensitivity identification heterogeneous specimens those content) therefore not ideally suited application. Several simultaneous (ie, multiplex) developed over past years, goal providing view mutational pattern tumor. These use various underlying analytic methods, ranging from mass-spectrometric genotyping real-time polymerase chain reaction (PCR) PCR-based All common enhanced occurring frequencies broad coverage mutations. sequencing-based inherent disadvantage individual must prespecified; is, rare same residue protein, but which part panel, missed. secondgeneration all fusions still require by FISH. contrast, third-generation analysis methods similarly sequencing, they involve hybrid shotgun libraries prepared formalin-fixed tissue. such approach lies possibility covering sites recurrent high capability reliably identifying (mutations, single assay.