Translating Cancer 'omics' to Improved Outcomes

Overview

Journal Genome Res

Specialty Genetics

Date 2012 Feb 4

PMID 22301133

Citations 48

Authors

Emily A Vucic

Kelsie L Thu

Keith Robison

Leszek A Rybaczyk

Raj Chari

Carlos E Alvarez

Wan L Lam

Affiliations

Soon will be listed here.

Abstract

The genomics era has yielded great advances in the understanding of cancer biology. At the same time, the immense complexity of the cancer genome has been revealed, as well as a striking heterogeneity at the whole-genome (or omics) level that exists between even histologically similar tumors. The vast accrual and public availability of multi-omics databases with associated clinical annotation including tumor histology, patient response, and outcome are a rich resource that has the potential to lead to rapid translation of high-throughput omics to improved overall survival. We focus on the unique advantages of a multidimensional approach to genomic analysis in this new high-throughput omics age and discuss the implications of the changing cancer demographic to translational omics research.

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References

Aberle D, Adams A, Berg C, Black W, Clapp J, Fagerstrom R . Reduced lung-cancer mortality with low-dose computed tomographic screening. N Engl J Med. 2011; 365(5):395-409. PMC: 4356534. DOI: 10.1056/NEJMoa1102873. View

Fischer A, Greenman C, Mustonen V . Germline fitness-based scoring of cancer mutations. Genetics. 2011; 188(2):383-93. PMC: 3122307. DOI: 10.1534/genetics.111.127480. View

Greenman C, Wooster R, Futreal P, Stratton M, Easton D . Statistical analysis of pathogenicity of somatic mutations in cancer. Genetics. 2006; 173(4):2187-98. PMC: 1569711. DOI: 10.1534/genetics.105.044677. View

Sawyers C . The cancer biomarker problem. Nature. 2008; 452(7187):548-52. DOI: 10.1038/nature06913. View

Boyko A, Quignon P, Li L, Schoenebeck J, Degenhardt J, Lohmueller K . A simple genetic architecture underlies morphological variation in dogs. PLoS Biol. 2010; 8(8):e1000451. PMC: 2919785. DOI: 10.1371/journal.pbio.1000451. View

Weitzel J, Blazer K, MacDonald D, Culver J, Offit K . Genetics, genomics, and cancer risk assessment: State of the Art and Future Directions in the Era of Personalized Medicine. CA Cancer J Clin. 2011; 61(5):327-59. PMC: 3346864. DOI: 10.3322/caac.20128. View

Sengupta S, Chakrabarti S, Roy A, Panda C, Roychoudhury S . Inactivation of human mutL homolog 1 and mutS homolog 2 genes in head and neck squamous cell carcinoma tumors and leukoplakia samples by promoter hypermethylation and its relation with microsatellite instability phenotype. Cancer. 2007; 109(4):703-12. DOI: 10.1002/cncr.22430. View

Poste G . Bring on the biomarkers. Nature. 2011; 469(7329):156-7. DOI: 10.1038/469156a. View

Stephens P, McBride D, Lin M, Varela I, Pleasance E, Simpson J . Complex landscapes of somatic rearrangement in human breast cancer genomes. Nature. 2009; 462(7276):1005-10. PMC: 3398135. DOI: 10.1038/nature08645. View

10.

Jones S, Laskin J, Li Y, Griffith O, An J, Bilenky M . Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors. Genome Biol. 2010; 11(8):R82. PMC: 2945784. DOI: 10.1186/gb-2010-11-8-r82. View

11.

Bernstein B, Stamatoyannopoulos J, Costello J, Ren B, Milosavljevic A, Meissner A . The NIH Roadmap Epigenomics Mapping Consortium. Nat Biotechnol. 2010; 28(10):1045-8. PMC: 3607281. DOI: 10.1038/nbt1010-1045. View

12.

Flaherty K, Puzanov I, Kim K, Ribas A, McArthur G, Sosman J . Inhibition of mutated, activated BRAF in metastatic melanoma. N Engl J Med. 2010; 363(9):809-19. PMC: 3724529. DOI: 10.1056/NEJMoa1002011. View

13.

Chen W, Swartz J, Rush L, Alvarez C . Mapping DNA structural variation in dogs. Genome Res. 2008; 19(3):500-9. PMC: 2661804. DOI: 10.1101/gr.083741.108. View

14.

Haber D, Gray N, Baselga J . The evolving war on cancer. Cell. 2011; 145(1):19-24. DOI: 10.1016/j.cell.2011.03.026. View

15.

Modrek B, Ge L, Pandita A, Lin E, Mohan S, Yue P . Oncogenic activating mutations are associated with local copy gain. Mol Cancer Res. 2009; 7(8):1244-52. DOI: 10.1158/1541-7786.MCR-08-0532. View

16.

Lee W, Jiang Z, Liu J, Haverty P, Guan Y, Stinson J . The mutation spectrum revealed by paired genome sequences from a lung cancer patient. Nature. 2010; 465(7297):473-7. DOI: 10.1038/nature09004. View

17.

Druker B, Guilhot F, OBrien S, Gathmann I, Kantarjian H, Gattermann N . Five-year follow-up of patients receiving imatinib for chronic myeloid leukemia. N Engl J Med. 2006; 355(23):2408-17. DOI: 10.1056/NEJMoa062867. View

18.

Karapetis C, Khambata-Ford S, Jonker D, OCallaghan C, Tu D, Tebbutt N . K-ras mutations and benefit from cetuximab in advanced colorectal cancer. N Engl J Med. 2008; 359(17):1757-65. DOI: 10.1056/NEJMoa0804385. View

19.

Lussier Y, Chen J . The emergence of genome-based drug repositioning. Sci Transl Med. 2011; 3(96):96ps35. PMC: 4262402. DOI: 10.1126/scitranslmed.3001512. View

20.

Bignell G, Santarius T, Pole J, Butler A, Perry J, Pleasance E . Architectures of somatic genomic rearrangement in human cancer amplicons at sequence-level resolution. Genome Res. 2007; 17(9):1296-303. PMC: 1950898. DOI: 10.1101/gr.6522707. View