Transcriptomic landscape of breast cancers through mRNA sequencing. Eswaran, J., Cyanam, D., Mudvari, P., Reddy, S. D. N., Pakala, S. B, Nair, S. S, Florea, L., Fuqua, S. A W, Godbole, S., & Kumar, R. Scientific reports, 2:264, January, 2012.
Transcriptomic landscape of breast cancers through mRNA sequencing. [link]Paper  doi  abstract   bibtex   
Breast cancer is a heterogeneous disease with a poorly defined genetic landscape, which poses a major challenge in diagnosis and treatment. By massively parallel mRNA sequencing, we obtained 1.2 billion reads from 17 individual human tissues belonging to TNBC, Non-TNBC, and HER2-positive breast cancers and defined their comprehensive digital transcriptome for the first time. Surprisingly, we identified a high number of novel and unannotated transcripts, revealing the global breast cancer transcriptomic adaptations. Comparative transcriptomic analyses elucidated differentially expressed transcripts between the three breast cancer groups, identifying several new modulators of breast cancer. Our study also identified common transcriptional regulatory elements, such as highly abundant primary transcripts, including osteonectin, RACK1, calnexin, calreticulin, FTL, and B2M, and "genomic hotspots" enriched in primary transcripts between the three groups. Thus, our study opens previously unexplored niches that could enable a better understanding of the disease and the development of potential intervention strategies.
@article{eswaran_transcriptomic_2012,
	title = {Transcriptomic landscape of breast cancers through {mRNA} sequencing.},
	volume = {2},
	issn = {2045-2322},
	url = {http://www.nature.com/srep/2012/120214/srep00264/full/srep00264.html?WT.ec_id=SREP-631-20120301},
	doi = {10.1038/srep00264},
	abstract = {Breast cancer is a heterogeneous disease with a poorly defined genetic landscape, which poses a major challenge in diagnosis and treatment. By massively parallel mRNA sequencing, we obtained 1.2 billion reads from 17 individual human tissues belonging to TNBC, Non-TNBC, and HER2-positive breast cancers and defined their comprehensive digital transcriptome for the first time. Surprisingly, we identified a high number of novel and unannotated transcripts, revealing the global breast cancer transcriptomic adaptations. Comparative transcriptomic analyses elucidated differentially expressed transcripts between the three breast cancer groups, identifying several new modulators of breast cancer. Our study also identified common transcriptional regulatory elements, such as highly abundant primary transcripts, including osteonectin, RACK1, calnexin, calreticulin, FTL, and B2M, and "genomic hotspots" enriched in primary transcripts between the three groups. Thus, our study opens previously unexplored niches that could enable a better understanding of the disease and the development of potential intervention strategies.},
	language = {en},
	journal = {Scientific reports},
	author = {Eswaran, Jeyanthy and Cyanam, Dinesh and Mudvari, Prakriti and Reddy, Sirigiri Divijendra Natha and Pakala, Suresh B and Nair, Sujit S and Florea, Liliana and Fuqua, Suzanne A W and Godbole, Sucheta and Kumar, Rakesh},
	month = jan,
	year = {2012},
	pmid = {22355776},
	keywords = {Breast Neoplasms, Breast Neoplasms: genetics, Breast Neoplasms: pathology, Female, Gene Expression Profiling, Humans, Messenger, Messenger: genetics, Nucleic Acid, Polymerase Chain Reaction, RNA, Regulatory Sequences, Transcriptome},
	pages = {264}
}
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