Assessment of common regions and specific footprints of DNA copy number aberrations across multiple affymetrix SNP mapping arrays

Roberta Spinelli, Ingrid Cifola, Stefano Ferrero, Luca Beltrame, Paolo Mocarelli, Cristina Battaglia

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

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.

Original languageEnglish
Title of host publicationLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Pages674-681
Number of pages8
Volume4578 LNAI
Publication statusPublished - 2007
Event7th International Workshop on Fuzzy Logic and Applications, WILF 2007 - Camogli, Italy
Duration: Jul 7 2007Jul 10 2007

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume4578 LNAI
ISSN (Print)03029743
ISSN (Electronic)16113349

Other

Other7th International Workshop on Fuzzy Logic and Applications, WILF 2007
CountryItaly
CityCamogli
Period7/7/077/10/07

Keywords

  • Aberration
  • Copy number
  • SNP
  • SNP mapping array

ASJC Scopus subject areas

  • Computer Science(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Theoretical Computer Science

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