title: CGH arrays compared for DNA isolated from formalin-fixed, paraffin-embedded material.
abstract: Formalin-fixed, paraffin-embedded (FFPE) archival tissue is an important source of DNA material. The most commonly used technique to identify copy number aberrations from chromosomal DNA in tumorigenesis is array comparative genomic hybridization (aCGH). Although copy number analysis using DNA from FFPE archival tissue is challenging, several research groups have reported high quality and reproducible DNA copy number results using aCGH. Aim of this study is to compare the commercially available aCGH platforms suitable for high-resolution copy number analysis using FFPE-derived DNA. Two dual channel aCGH platforms (Agilent and NimbleGen) and a single channel SNP-based platform (Affymetrix) were evaluated using seven FFPE colon cancer samples, and median absolute deviation (MAD), deflection, signal-to-noise ratio, and DNA input requirements were used as quality criteria. Large differences were observed between platforms; Agilent and NimbleGen showed better MAD values (0.13 for both) compared with Affymetrix (0.22). On the contrary, Affymetrix showed a better deflection of 0.94, followed by 0.71 for Agilent and 0.51 for NimbleGen. This resulted in signal-to-nose ratios that were comparable between the three commercially available platforms. Interestingly, DNA input amounts from FFPE material lower than recommended still yielded high quality profiles on all platforms. Copy number analysis using DNA derived from FFPE archival material is feasible using all three high-resolution copy number platforms and shows reproducible results, also with DNA input amounts lower than recommended.
authors.affiliation: Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands.
authors.forename: Oscar
authors.initials: O
authors.lastname: Krijgsman
authors.forename: Danielle
authors.initials: D
authors.lastname: Israeli
authors.forename: Josien C
authors.initials: JC
authors.lastname: Haan
authors.forename: Hendrik F
authors.initials: HF
authors.lastname: van Essen
authors.forename: Serge J
authors.initials: SJ
authors.lastname: Smeets
authors.forename: Paul P
authors.initials: PP
authors.lastname: Eijk
authors.forename: Renske D M
authors.initials: RD
authors.lastname: Steenbergen
authors.forename: Klaas
authors.initials: K
authors.lastname: Kok
authors.forename: Sabine
authors.initials: S
authors.lastname: Tejpar
authors.forename: Gerrit A
authors.initials: GA
authors.lastname: Meijer
authors.forename: Bauke
authors.initials: B
authors.lastname: Ylstra
mesh_terms: D003110:Colonic Neoplasms / Q000235:genetics*; D055028:Comparative Genomic Hybridization / Q000379:methods*; D004247:DNA / Q000235:genetics* / Q000302:isolation & purification; D056915:DNA Copy Number Variations; D004273:DNA, Neoplasm / Q000235:genetics; D005557:Formaldehyde; D006801:Humans; D016612:Paraffin Embedding; D059629:Signal-To-Noise Ratio; D014021:Tissue Preservation / Q000379:methods*
chemical_list: D004273:DNA, Neoplasm; D005557:Formaldehyde; D004247:DNA