In total, validation results confirmed 11 events of differential splicing in NSCLC.
In total, 12 events of differential splicing were confirmed in AdCa.
Four events of differential splicing could not be confirmed in AdCa (ANTXR1, CTNND1-CE-3', intron retention event in KIAA1217, MYH14).
Four events of differential splicing were not confirmed with qRT-PCR in SCC (CTNND1-CE-3', intron retention event in KIAA1217, MYH14, SYNE2).
In order to assess the improvements by the new chip definition, we investigated whether events of differential splicing can be reliably identified.
Since the probes on the BeadChip mainly covered CpGs in promoter regions, it is not surprising that only limited events of differential methylation were detected in gene-poor regions (Fig. 3).
For the remaining 13 candidate genes, we hypothesise 10 cassette exon events, two events of an alternative transcription start site, one event of intron retention, one event of an alternative 5'-splice site, and two events of mutually exclusive exons (in total 16 events of differential splicing, see Table 1).
In order to identify events of differential splicing we developed a workflow that essentially consists of three components: (1) filtering of probe sets whose signals are not significantly above background signal, (2) re-definition of probe sets according to most up-to-date transcript annotations from public databases, and (3) statistical evaluation using a MLM ANOVA and SI.
To explore potential effects of unobserved clinical events because of differential follow-up, sensitivity analyses were performed including different ages at first examination (range less than 4 months to any age) and examination intervals (less than 2 to 6 months).
According to the interchangeable model (I-model), or function-sharing model, alternative isoforms that were originally coded within a single gene may separate into different genes after a GD event by means of differential retention of AS patterns in each duplicate gene.
