Figure 4

Effect of hybridization time (a) and temperature (b) in conditions of b,b type homozygosity (HLA-A*2091 labeled with Cy5 vs HLA-A*0101 labeled with Cy3). b) _LogRatio for Va (HLA-A*2901-specific) oligos (red), k-oligos (yellow) and CO-oligos. c) Test for labeling bias and reproducibility in conditions of a,a homozygosity and b,c heterozygosity: gene pix image. d) Scatter plot of Cy3 and Cy5 fluorescence intensity in conditions of a,a homozygosity. In red are portrayed Va oligos; in green k and consensus oligos. A cluster of consensus oligos with poor hybridization kinetics due to high CG content (average of 75%) is portrayed in light blue. Reproducibility was tested in conditions of b,b homozygosity (HLA-A*0201 vs HLA-A*0101) and a,b heterozygosity (HLA-A*0101, 2901 vs HLA-A*0101) by reciprocally labeling test and reference targets in duplicate experiments as shown by the clusterogram. In spite of variable hybridization kinetics, differential hybridization could be observed consistently among Va and corresponding consensus oligos. Only HLA-A*0201-specific and relevant homologous consensus oligos (solid red and green bar respectively) or HLA-A*2901-specific oligos (dashed red line) are shown.