Functional copy-number alterations in cancer. Export

@article{citeulike:3246042, abstract = {Understanding the molecular basis of cancer requires characterization of its genetic defects. DNA microarray technologies can provide detailed raw data about chromosomal aberrations in tumor samples. Computational analysis is needed (1) to deduce from raw array data actual amplification or deletion events for chromosomal fragments and (2) to distinguish causal chromosomal alterations from functionally neutral ones. We present a comprehensive computational approach, RAE, designed to robustly map chromosomal alterations in tumor samples and assess their functional importance in cancer. To demonstrate the methodology, we experimentally profile copy number changes in a clinically aggressive subtype of soft-tissue sarcoma, pleomorphic liposarcoma, and computationally derive a portrait of candidate oncogenic alterations and their target genes. Many affected genes are known to be involved in sarcomagenesis; others are novel, including mediators of adipocyte differentiation, and may include valuable therapeutic targets. Taken together, we present a statistically robust methodology applicable to high-resolution genomic data to assess the extent and function of copy-number alterations in cancer.}, address = {Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America.}, author = {Taylor, Barry S. and Barretina, Jordi and Socci, Nicholas D. and Decarolis, Penelope and Ladanyi, Marc and Meyerson, Matthew and Singer, Samuel and Sander, Chris}, citeulike-article-id = {3246042}, citeulike-linkout-0 = {http://dx.doi.org/10.1371/journal.pone.0003179}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/18784837}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=18784837}, day = {11}, doi = {10.1371/journal.pone.0003179}, issn = {1932-6203}, journal = {PloS one}, keywords = {acgh, algorithm, cancer, copynumber, rae}, month = {September}, number = {9}, pages = {e3179+}, posted-at = {2009-08-17 17:57:29}, priority = {2}, publisher = {Public Library of Science}, title = {Functional copy-number alterations in cancer.}, url = {http://dx.doi.org/10.1371/journal.pone.0003179}, volume = {3}, year = {2008} }

TY - JOUR ID - citeulike:3246042 L3 - citeulike-article-id:3246042 N2 - Understanding the molecular basis of cancer requires characterization of its genetic defects. DNA microarray technologies can provide detailed raw data about chromosomal aberrations in tumor samples. Computational analysis is needed (1) to deduce from raw array data actual amplification or deletion events for chromosomal fragments and (2) to distinguish causal chromosomal alterations from functionally neutral ones. We present a comprehensive computational approach, RAE, designed to robustly map chromosomal alterations in tumor samples and assess their functional importance in cancer. To demonstrate the methodology, we experimentally profile copy number changes in a clinically aggressive subtype of soft-tissue sarcoma, pleomorphic liposarcoma, and computationally derive a portrait of candidate oncogenic alterations and their target genes. Many affected genes are known to be involved in sarcomagenesis; others are novel, including mediators of adipocyte differentiation, and may include valuable therapeutic targets. Taken together, we present a statistically robust methodology applicable to high-resolution genomic data to assess the extent and function of copy-number alterations in cancer. IS - 9 JF - PloS one SN - 1932-6203 AD - Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America. TI - Functional copy-number alterations in cancer. PB - Public Library of Science VL - 3 SP - e3179 KW - acgh KW - algorithm KW - cancer KW - copynumber KW - rae AU - Taylor, Barry AU - Barretina, Jordi AU - Socci, Nicholas AU - Decarolis, Penelope AU - Ladanyi, Marc AU - Meyerson, Matthew AU - Singer, Samuel AU - Sander, Chris PY - 2008/09/11/ UR - http://dx.doi.org/10.1371/journal.pone.0003179 ER -