Array Comparative Genomic Hybridization (aCGH)

Platform

DNA was labeled with Cy3 or Cy5 fluorochromes using the Enzo Agilent aCGH labelling kit (Enzo Life Sciences, Raamsdonksveer, the Netherlands) according to manufacturer’s instructions. DNA was hybridized to Nimblegen 12x135K arrays (Roche Nimblegen) according to manufacturer’s instructions, with labeled Human genomic female DNA (Promega, Leiden, the Netherlands) as reference DNA. Arrays were scanned using an Agilent scanner, and analyzed using the Nimblescan software program.

Analysis

Logratio’s were transformed into calls with the R-package CGHcall.