title: Genome-wide copy number alterations detection in fresh frozen and matched FFPE samples using SNP 6.0 arrays.
abstract: SNP arrays offer the opportunity to get a genome-wide view on copy number alterations and are increasingly used in oncology. DNA from formalin-fixed paraffin-embedded material (FFPE) is partially degraded which limits the application of those technologies for retrospective studies. We present the use of Affymetrix GeneChip SNP6.0 for identification of copy number alterations in fresh frozen (FF) and matched FFPE samples. Fifteen pairs of adenocarcinomas with both frozen and FFPE embedded material were analyzed. We present an optimization of the sample preparation and show the importance of correcting the measured intensities for fragment length and GC-content when using FFPE samples. The absence of GC content correction results in a chromosome specific "wave pattern" which may lead to the misclassification of genomic regions as being altered. The highest concordance between FFPE and matched FF were found in samples with the highest call rates. Nineteen of the 23 high level amplifications (83%) seen using FF samples were also detected in the corresponding FFPE material. For limiting the rate of "false positive" alterations, we have chosen a conservative False Discovery Rate (FDR). We observed better results using SNP probes than CNV probes for copy number analysis of FFPE material. This is the first report on the detection of copy number alterations in FFPE samples using Affymetrix GeneChip SNP6.0.
authors.affiliation: JE2492 Department, Faculté de Médecine Paris-Sud, IFR69, Villejuif, France. tuefferd@vjf.inserm.fr
authors.forename: Marianne
authors.initials: M
authors.lastname: Tuefferd
authors.forename: An
authors.initials: A
authors.lastname: De Bondt
authors.forename: Ilse
authors.initials: I
authors.lastname: Van Den Wyngaert
authors.forename: Willem
authors.initials: W
authors.lastname: Talloen
authors.forename: Tobias
authors.initials: T
authors.lastname: Verbeke
authors.forename: Benilton
authors.initials: B
authors.lastname: Carvalho
authors.forename: Djork-Arne
authors.initials: DA
authors.lastname: Clevert
authors.forename: Marco
authors.initials: M
authors.lastname: Alifano
authors.forename: Nandini
authors.initials: N
authors.lastname: Raghavan
authors.forename: Dhammika
authors.initials: D
authors.lastname: Amaratunga
authors.forename: Hinrich
authors.initials: H
authors.lastname: Göhlmann
authors.forename: Philippe
authors.initials: P
authors.lastname: Broët
authors.forename: Sophie
authors.initials: S
authors.lastname: Camilleri-Broët
mesh_terms: D004273:DNA, Neoplasm / Q000032:analysis; D005557:Formaldehyde / Q000737:chemistry; D018628:Gene Dosage; D015894:Genome, Human; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D016612:Paraffin Embedding / Q000379:methods; D020641:Polymorphism, Single Nucleotide
chemical_list: D004273:DNA, Neoplasm; D005557:Formaldehyde