Details of the exon array results and the laboratory validation results for ADD3. (a) Exon structure and known transcript variants of ADD3 (introns not to scale; green: Ensembl transcripts; red: RefSeq entries; purple: Genscan predictions). (b) Position of probe sets in the new exon array chip definition (grey: absent probe sets; blue: present probe sets). (c) Exon expression in the NSCLC data set suggests higher inclusion of a cassette exon (arrow) in tumour compared to normal adjacent tissue (NAT) (red graph: exon expression in NSCLC; blue graph: exon expression in NAT). (d) Splicing indices for exons in the NSCLC data set (logarithmic scale). (e) Verification of RT-PCR product sizes generated from paired samples of adenocarcinoma of NSCLC and NAT of six patients (ø: no template control). In tumour, exon inclusion was observed in all cases analysed. Sequencing of representative products confirmed the expected exon-exon junctions (data not shown). (f) Quantification of gene expression (G) and transcript variant expression (CE: cassette exon; ES: exon skipping) in adenocarcinoma of NSCLC compared to NAT as measured by qRT-PCR. Median values based on six sample pairs are shown (values for each patient shown as dots), error bars indicate one standard deviation, significance was determined using a paired t-test. FC: Fold-change of over-expression in adenocarcinoma of NSCLC versus NAT. SI: Splicing index. (g) Quantification of gene expression and transcript variant expression in squamous cell carcinoma of NSCLC compared to NAT as measured by qRT-PCR. Median values based on four sample pairs are shown.
Langer et al. BMC Genomics 2010 11:676 doi:10.1186/1471-2164-11-676