integrative cancer genomics

Integrating results from diverse experiments is an essential process in our effort to understand the logic of complex systems, such as development, homeostasis and responses to the environment. With the advent of high-throughput methods - including genome-wide association studies (GWAS), chromatin immunoprecipitation followed by sequencing (ChIP-seq) and RNA sequencing (RNA-seq) - acquisition of genome-scale data has never been easier.

Epigenomics, transcriptomics, proteomics and genomics each provide an insightful, and yet one-dimensional, view of genome function; integrative analysis promises a unified, global view.

However, the large amount of information and diverse technology platforms pose multiple challenges for data access and processing.

See also

 data integration
 data management
 next-generation genomics

Review

 Next-generation genomics: an integrative approach. Hawkins RD, Hon GC, Ren B. Nat Rev Genet. 2010 Jun 8;11(7):476-486. PMID: 20531367

References

 Understanding genomic alterations in cancer genomes using an integrative network approach. Wang E. Cancer Lett. 2012 Dec 22. doi : pii: S0304-3835(12)00712-4. 10.1016/j.canlet.2012.11.050 PMID:23266571

 Integrating chromosomal aberrations and gene expression profiles to dissect rectal tumorigenesis. Lips EH, van Eijk R, de Graaf EJ, Oosting J, de Miranda NF, Karsten T, van de Velde CJ, Eilers PH, Tollenaar RA, van Wezel T, Morreau H. BMC Cancer. 2008 Oct 29;8:314. PMID: 18959792 [Free]

 Lindvall C, Furge K, Björkholm M, Guo X, Haab B, Blennow E, Nordenskjöld M, Teh BT. Combined genetic and transcriptional profiling of acute myeloid leukemia with normal and complex karyotypes. Haematologica. 2004 Sep;89(9):1072-81. PMID: 15377468

 Lombardi L, Poretti G, Mattioli M, Fabris S, Agnelli L, Bicciato S, Kwee I, Rinaldi A, Ronchetti D, Verdelli D, Lambertenghi-Deliliers G, Bertoni F, Neri A. Molecular characterization of human multiple myeloma cell lines by integrative genomics: insights into the biology of the disease. Genes Chromosomes Cancer. 2007 Mar;46(3):226-38. PMID: 17171682

 Yang S, Jeung HC, Jeong HJ, Choi YH, Kim JE, Jung JJ, Rha SY, Yang WI, Chung HC. Identification of genes with correlated patterns of variations in DNA copy number and gene expression level in gastric cancer.
Genomics. 2007 Jan 15; PMID: 17229543

 Wang Q, Diskin S, Rappaport E, Attiyeh E, Mosse Y, Shue D, Seiser E, Jagannathan J, Shusterman S, Bansal M, Khazi D, Winter C, Okawa E, Grant G, Cnaan A, Zhao H, Cheung NK, Gerald W, London W, Matthay KK, Brodeur GM, Maris JM. Integrative genomics identifies distinct molecular classes of neuroblastoma and shows that multiple genes are targeted by regional alterations in DNA copy number. Cancer Res. 2006 Jun 15;66(12):6050-62. PMID: 16778177

 Dahia PL, Hao K, Rogus J, Colin C, Pujana MA, Ross K, Magoffin D, Aronin N, Cascon A, Hayashida CY, Li C, Toledo SP, Stiles CD; Familial Pheochromocytoma Consortium. Novel pheochromocytoma susceptibility loci identified by integrative genomics. Cancer Res. 2005 Nov 1;65(21):9651-8. PMID: 16266984

 Zhao H, Kim Y, Wang P, Lapointe J, Tibshirani R, Pollack JR, Brooks JD. Genome-wide characterization of gene expression variations and DNA copy number changes in prostate cancer cell lines. Prostate. 2005 May 1;63(2):187-97. PMID: 15486987

 Guo X, Lui WO, Qian CN, Chen JD, Gray SG, Rhodes D, Haab B, Stanbridge E, Wang H, Hong MH, Min HQ, Larsson C, Teh BT. Identifying cancer-related genes in nasopharyngeal carcinoma cell lines using DNA and mRNA expression profiling analyses. Int J Oncol. 2002 Dec;21(6):1197-204. PMID: 12429968