Whole genome amplification; array-comparative genomic hybridization; copy-number changes; copy-number neutral loss of heterozygosity; genotyping

Whole genome amplification (WGA) is an approach designed to overcome small amounts of DNA for genome-wide genetic tests used in many clinical applications. Various strategies of WGA have been developed; however, none of them can guarantee the absence of amplification bias. In this study, a total of four multiple displacement amplification (MDA)-based and two PCR-based WGA kits were compared in their effect on segmental copy-number (CN) changes and copy-number neutral loss of heterozygosity (cnnLOH) detection by three microarray platforms: CGH/4x44K (Agilent), CGH+SNP/4x180K (Agilent) and CGH+SNP/4x180K (OGT). Genomic imbalances-rich myeloma cell line U266 was used as material. The main outcomes are as follows: 1) MDA-based WGAs showed higher tendency to generate false positive imbalances in contrast to PCR-based WGAs with higher risk of false negativity; 2) the specific risk of false positivity and/or negativity increased with decreasing CN segments size; 3) single-cell WGAs showed significantly worse effect on results in comparison to WGAs with nanogram level of DNA as input; 4) PCR-based WGAs were incompatible with cnnLOH analysis based on SNP in restriction digestion sites and also showed higher risk of cnnLOH false negativity when combined with analysis based on simple hybridization. In conclusion, the results of this study help to choose WGA according to individual user requirements and options. Moreover, we have shown a strategy to verify and validate segmental CN changes detection by DNA array protocol including any WGA for any purpose to attain the highest efficiency without an unnecessary WGA bias.