Three commercial array platforms compared for DNA copy number detection with DNA isolated from FFPE tissue [Agilent]

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 the present study is to compare aCGH platforms suitable for 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, median absolute deviation (MAD), deflection, signal-to-noise ratio (SNR) and DNA

ORGANISM(S): Homo sapiens

SUBMITTER: Oscar Krijgsman 

PROVIDER: E-GEOD-30121 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress