TY - GEN
T1 - Assessment of common regions and specific footprints of DNA copy number aberrations across multiple affymetrix SNP mapping arrays
AU - Spinelli, Roberta
AU - Cifola, Ingrid
AU - Ferrero, Stefano
AU - Beltrame, Luca
AU - Mocarelli, Paolo
AU - Battaglia, Cristina
PY - 2007
Y1 - 2007
N2 - The application of genome-wide approaches to the molecular characterization of cancer was investigated, identifying footprints that can potentially assist in the subclassification of tumors in order to contribute to diagnosis and clinical management of patients. High resolution DNA copy number analysis by single nucleotide polymorphism mapping array technology has been widely applied to study copy number aberrations and to distinguish among different loss of heterozigosity mechanisms associated with or without copy number changes in tumors. However, assessment of statistically significant common aberrations across the whole data set or a subset of tumor samples is still an open problem. Therefore, we adapted the recently developed STAC algorithm, previously applied to comparative genomic hybridization data, to identify common copy number aberrations in renal carcinoma samples using Affymetrix 100K SNP arrays. SNP copy number data were processed by a homebrew pipeline implemented in R and analyzed using STAC.
AB - The application of genome-wide approaches to the molecular characterization of cancer was investigated, identifying footprints that can potentially assist in the subclassification of tumors in order to contribute to diagnosis and clinical management of patients. High resolution DNA copy number analysis by single nucleotide polymorphism mapping array technology has been widely applied to study copy number aberrations and to distinguish among different loss of heterozigosity mechanisms associated with or without copy number changes in tumors. However, assessment of statistically significant common aberrations across the whole data set or a subset of tumor samples is still an open problem. Therefore, we adapted the recently developed STAC algorithm, previously applied to comparative genomic hybridization data, to identify common copy number aberrations in renal carcinoma samples using Affymetrix 100K SNP arrays. SNP copy number data were processed by a homebrew pipeline implemented in R and analyzed using STAC.
KW - Aberration
KW - Copy number
KW - SNP
KW - SNP mapping array
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M3 - Conference contribution
AN - SCOPUS:37249058862
SN - 9783540733997
VL - 4578 LNAI
T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
SP - 674
EP - 681
BT - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
T2 - 7th International Workshop on Fuzzy Logic and Applications, WILF 2007
Y2 - 7 July 2007 through 10 July 2007
ER -