Firstly, the rams were evaluated for head alterations (i.e., nasal and ocular discharge, corneal opacity and missing teeth).
Splice-site variants were evaluated for putative alteration of regulatory process at the transcriptional or splicing level with NetGene2 (http://www.cbs.dtu.dk/services/NetGene2) [Brunak et al., 1991] and NNSPLICE (http://www.fruitfly.org/seq_tools/splice.html) [Reese et al., 1997].
Somatically mutated genes were then resequenced from another 72 ECs, and evaluated for copy number alterations in all 112 tumors.
All animals were weighed and evaluated daily for alterations in neurological motor function using a clinical assessment scoring system as previously described [ 31] (experiment 1: day -2 through day 21; experiment 2: day -7 through day 43, days 60, 75, and 90).
The ESCC cases studied here were previously evaluated for LOH and copy number alterations using genome-wide arrays [ 5, 6].
Using data from the Affymetrix Nsp arrays, chromosome 13 was evaluated for copy-number and LOH alterations, and analyses compared with samples with and without FLT3 mutations.
Cells of a patient with Turcot's syndrome and of her parents were evaluated for the presence of molecular alterations in the p53 and the Ki-ras gene.
Using Pearson's Chi-Squared test, molecular alterations were evaluated for association with histological tumour characteristics: ER and PR status, HER2 amplification, Ki67 proliferation index.
These defined alterations are currently evaluated for their use as biomarkers for diagnosis, prognosis and prediction of therapy response for different cancers [101].
The genomic alterations were further evaluated for prognostic significance in CC patients, and we did not find any correlation with a number of clinical or histological parameters.
