@article {1132,
	title = {Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection.},
	journal = {Nature methods},
	year = {2015},
	month = {2015 May 18},
	abstract = {The detection of somatic mutations from cancer genome sequences is key to understanding the genetic basis of disease progression, patient survival and response to therapy. Benchmarking is needed for tool assessment and improvement but is complicated by a lack of gold standards, by extensive resource requirements and by difficulties in sharing personal genomic information. To resolve these issues, we launched the ICGC-TCGA DREAM Somatic Mutation Calling Challenge, a crowdsourced benchmark of somatic mutation detection algorithms. Here we report the BAMSurgeon tool for simulating cancer genomes and the results of 248 analyses of three in silico tumors created with it. Different algorithms exhibit characteristic error profiles, and, intriguingly, false positives show a trinucleotide profile very similar to one found in human tumors. Although the three simulated tumors differ in sequence contamination (deviation from normal cell sequence) and in subclonality, an ensemble of pipelines outperforms the best individual pipeline in all cases. BAMSurgeon is available at https://github.com/adamewing/bamsurgeon/.},
	keywords = {cancer, NGS, variant calling},
	issn = {1548-7105},
	doi = {10.1038/nmeth.3407},
	url = {http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.3407.html},
	author = {Ewing, Adam D and Houlahan, Kathleen E and Hu, Yin and Ellrott, Kyle and Caloian, Cristian and Yamaguchi, Takafumi N and Bare, J Christopher and P{\textquoteright}ng, Christine and Waggott, Daryl and Sabelnykova, Veronica Y and Kellen, Michael R and Norman, Thea C and Haussler, David and Friend, Stephen H and Stolovitzky, Gustavo and Margolin, Adam A and Stuart, Joshua M and Boutros, Paul C},
	editor = {ICGC-TCGA DREAM Somatic Mutation Calling Challenge participants and Liu Xi and Ninad Dewal and Yu Fan and Wenyi Wang and David Wheeler and Andreas Wilm and Grace Hui Ting and Chenhao Li and Denis Bertrand and Niranjan Nagarajan and Qing-Rong Chen and Chih-Hao Hsu and Ying Hu and Chunhua Yan and Warren Kibbe and Daoud Meerzaman and Kristian Cibulskis and Mara Rosenberg and Louis Bergelson and Adam Kiezun and Amie Radenbaugh and Anne-Sophie Sertier and Anthony Ferrari and Laurie Tonton and Kunal Bhutani and Nancy F Hansen and Difei Wang and Lei Song and Zhongwu Lai and Liao, Yang and Shi, Wei and Carbonell-Caballero, Jos{\'e} and Joaqu{\'\i}n Dopazo and Cheryl C K Lau and Justin Guinney}
}
@article {19127482,
	title = {Analysis of chronic lymphotic leukemia transcriptomic profile: differences between molecular subgroups},
	journal = {Leuk Lymphoma},
	volume = {50},
	number = {1},
	year = {2009},
	note = {<p>Jantus Lewintre, Eloisa Reinoso Martin, Cristina Montaner, David Marin, Miguel Jose Terol, Maria Farras, Rosa Benet, Isabel Calvete, Juan J Dopazo, Joaquin Garcia-Conde, Javier Research Support, Non-U.S. Gov{\textquoteright}t England Leukemia \&amp; lymphoma Leuk Lymphoma. 2009 Jan;50(1):68-79.</p>},
	pages = {68-79},
	abstract = {<p>B cell chronic lymphocytic leukemia (CLL) is a lymphoproliferative disorder with a variable clinical course. Patients with unmutated IgV(H) gene show a shorter progression-free and overall survival than patients with immunoglobulin heavy chain variable regions (IgV(H)) gene mutated. In addition, BCL6 mutations identify a subgroup of patients with high risk of progression. Gene expression was analysed in 36 early-stage patients using high-density microarrays. Around 150 genes differentially expressed were found according to IgV(H) mutations, whereas no difference was found according to BCL6 mutations. Functional profiling methods allowed us to distinguish KEGG and gene ontology terms showing coordinated gene expression changes across subgroups of CLL. We validated a set of differentially expressed genes according to IgV(H) status, scoring them as putative prognostic markers in CLL. Among them, CRY1, LPL, CD82 and DUSP22 are the ones with at least equal or superior performance to ZAP70 which is actually the most used surrogate marker of IgV(H) status.</p>},
	keywords = {cancer, microarray data analysis},
	url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=PubMed\&dopt=Citation\&list_uids=19127482},
	author = {Jantus Lewintre, E. and Reinoso Martin, C. and Montaner, D. and Marin, M. and Jose Terol, M. and Farras, R. and Benet, I. and Calvete, J. J. and Dopazo, J. and Garcia-Conde, J.}
}
