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Translating Cancer Genomes and Transcriptomes for Precision Oncology


Translating Cancer Genomes and Transcriptomes for Precision Oncology

Sameek Roychowdhury et al. CA Cancer J Clin.


Understanding the molecular landscape of cancer has facilitated the development of diagnostic, prognostic, and predictive biomarkers for clinical oncology. Developments in next-generation DNA sequencing technologies have increased the speed and reduced the cost of sequencing the nucleic acids of cancer cells. This has unlocked opportunities to characterize the genomic and transcriptomic landscapes of cancer for basic science research through projects like The Cancer Genome Atlas. The cancer genome includes DNA-based alterations, such as point mutations or gene duplications. The cancer transcriptome involves RNA-based alterations, including changes in messenger RNAs. Together, the genome and transcriptome can provide a comprehensive view of an individual patient's cancer that is beginning to impact real-time clinical decision-making. The authors discuss several opportunities for translating this basic science knowledge into clinical practice, including a molecular classification of cancer, heritable risk of cancer, eligibility for targeted therapies, and the development of innovative, genomic-based clinical trials. In this review, key applications and new directions are outlined for translating the cancer genome and transcriptome into patient care in the clinic.

Keywords: gene fusion; genomics; neoplasm; patient care; transcriptome.


Figure 1
Figure 1. Mutational heterogeneity with and across cancer
(Adapted from Lawrence, Nature 2013, Figure 1). Authors assessed over 3000 cases of cancer from The Cancer Genome Atlas and plotted the number of mutations identified, patterns of mutations, and grouped them by tumor tissue-of-origin. The plot illustrates that variation of point mutation burden across different cancer types and also within a given cancer type such head and neck cancers, and the importance of performing personalized genomic testing. Further, some cancers appear to be hyper-mutated with 100s of mutations such as lung and melanoma cancers, while others such as acute myeloid leukemia have few point mutations.
Figure 2
Figure 2. Strategies for integrative clinical tumor sequencing
(Adapted from Roychowdhury, Science Translational Medicine 2011, Figure 1C, 1D). This pilot study for clinical tumor sequencing demonstrated the feasibility and the need for multi-disciplinary collaboration. A, Shows a clinical relevant timeline that is dependent collaboration with oncologists, radiologists, pathologists, genetics labs, and bioinformaticians. B, Several strategies for sequencing tumor DNA and RNA can contribute to characterizing the landscape of alterations in an individual’s cancer. Whole genome, whole exome, and transcriptome sequencing can be integrated to evaluate for point mutations, copy number alterations, gene fusions, and gene expression.
Figure 3
Figure 3. Research and clinical opportunities for precision cancer medicine through genomic and transcriptome sequencing
A systematic framework for implementing precision cancer medicine through genome and transcriptome sequencing can support multiple clinical and research efforts. Genomics can support the development of molecular diagnostics, drug target discovery, innovative genomics-based trials, evaluation of exceptional responders, and study of mechanisms of acquired resistance.

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