A Robust Whole Genome Amplification Method for Agilent Array-based Comparative Genome Hybridization Analysis

Genomic instability is a classic hallmark of cancer and genetic disorders. The Agilent Oligonucleotide array-based Comparative Genomic Hybridization (aCGH) platform lets you profile DNA copy number variations on a highthroughput and genome-wide scale. We have developed a rapid, low-input whole genome amplification (WGA) method for aCGH analysis that pairs the Sigma GenomePlex WGA Kit with Agilent’s established high-performance aCGH microarrays. In addition, aCGH results were validated using the Stratagene Mx3000P QPCR System. Using this powerful system, nanogram quantities of starting genomic DNA can generate robust and precise aCGH data. Introduction Array-based Comparative Genomic Hybridization (aCGH) is currently used to determine chromosomal changes in various sample types (Barrett, M.T. et al., 2004). This evolving technology requires DNA inputs of typically 0.5 μg per sample to process one aCGH array (Agilent Application note, 5989-5048EN). However, certain precious samples such as laser capture microdissected (LCM) cells or needle biopsies do not provide enough DNA for labeling and hybridization to an array. Whole genome amplification (WGA) methods are routinely used on genomic DNA for genotyping and sequence analysis when the amount of starting template is extremely low (Kuivaniemi, H.S. et al., 2002; Hosono, S. et al., 2002). Two commonly used WGA strategies are i) primer extension pre-amplification (PEP), a Taq DNA polymerase PCR-based reaction (Zhang, L.X. et al., 1992), and ii) multiple displacement amplification (MDA), an isothermal genome amplification using Phi29 DNA polymerase (Dean, F.B. et al., 2002). In PEP-PCR, due to the usage of completely degenerate primers, shorter products are generated with each cycle. We found that the Phi29 polymerase-based MDA method often produces high noise Further research highlights can be found in the publication “Oligonucleotide Array CGH Analysis of a Robust Whole Genome Amplification Method” (Brueck, C. et al.) from Biotechniques (2007) 42(2):230-233. 1 Recently, Agilent Technologies acquired Stratagene in an effort to accelerate growth in life sciences through a complementary product portfolio.