SNP characterization and RT-PCR analysis of 3q gains in FA. (A) SNP array characterization of 3q gains in all FA bone marrow harvests. SNP array data are visualized using CNAG 3.0 software. Analysis of call intensity was conducted using standard Affymetrix analysis software algorithms provided in GCOS and GTYPE 4.0. Chromosomal aberrations were analyzed using Copy Number Analyzer for Affymetrix GeneChip Mapping arrays (CNAG) 3.0 software employing the AsCNAR algorithm. In 4 patients with 3q gain, the extension of aberration is depicted using red bars and the position coordinates are shown on the right side. Position of EVI1 is indicated. (B-I) qRT-PCR analysis of selected genes as indicated (B: EVI1; C: TERC; D: PAK2; E: SKIL; F: PIK3CA; G: EIF-4G1; H: FXR1; I: DCUN1D1) in FA bone marrow samples with 3q-gains (darker-shaded right 4 columns) and without (brighter-shaded left 2 columns). Transcripts levels are shown as 2^−ΔΔCt normalized to normal BM (*P below graph) using β-actin and SDHA as housekeeper genes. Comparison also between mean transcript levels of FA marrows with and without 3q gains (t test).