Table 1 Juxtaposition of conventional CGH- and SNP-array techniques to the combined approach chosen in this study
|  | Conventional aCGH | Conventional SNP-array | Novel CGH + SNP-array |
|---|---|---|---|
Array design | One target consists of one 60mer oligonucleotide | Allele-specific 60mer olionucleotide targets, arranged in quartets differing in a single base each are arranged for SNP-detection | CGH + SNP-arrays contain both kinds of probes |
Type of aberrations targeted | Copy number aberrations | Copy number and copy number neutral deviations (LOH) | Copy number and copy number neutral deviations (LOH) |
Mode of hybridization | Comparative hybridization with a reference sample | Sample hybridization only | Comparative hybridization with a reference sample |
Mode of detection/ algorithm settings | Copy number determination by comparison with a diploid reference sample | Determination of heterozygosity status by measuring of A- and B-alleles and in silico comparison to reference sample sets, deduction of copy number status from that | Combined detection: Only one allele is measured, the total number of alleles at given loci are estimated from CGH-probe signals |