Variable gene expression and reduced penetrance in familial adenomatous polyposis Rohlin A* 1, Wernersson J 1, Björk J 2, and Nordling M 1 Dept of Clinical Genetics, Sahlgrenska University Hospital, Gothenburg, 2) The Swedish Polyposis Registry, Department of Gastroenterology and Hepatology, Karolinska University Hospital, Solna. Introduction In our material, 96 unrelated FAP patients from the Swedish polyposis register were screened for mutations in the APC and MUTYH genes. 61 different mutations in the APC gene were found in 81 of the families and 6 additional families were found to have biallelic MUTYH mutations. A disease-causing mutation was found in all except one of the patients with a classical phenotype (Kanter-Smoler et al. 2008). In AFAP the genetic cause remains undetected in up to 70–80% of the patients. The one patient with classical FAP without any identified mutation belongs to a large kindred including 150 individuals of whom 57 are affected. Two individuals from this family were analysed with TaqMan quantitative RT-PCR analysis. A lower APC expression was detected, but no deletion or methylation of the promoter region has been found so far. The Exon- and SNP arrays from Affymetrix were used in order to reveal the genetic cause of the AFAP cases without identified mutations in the APC or MUTYH genes. Further we used the exon-arrays to investigate the lower APC gene expression in cases with classical FAP and with the SNP arrays we verified the extension of larger deletions of the APC region previous found with mlpa. The exon-arrays reveal the expression levels and the differences in isoforms generated by alternative splicing events. Additionally, we used this platform to investigate if expression of different isoforms might in part explain the variable penetrance of FAP observed within families and between families with the same mutation. Material and Methods Five patients with AFAP from two families and two patients with classical FAP from one family were analysed with the 1.0HuEx arrays from affymetrix. The arrays include over 40 probes for each gene and four probes (one probeset) for every exon for all well annotated genes. The robust multi-array analysis (RMA) algorithm was used for probeset (gene-level) and (exon-level) intensity analysis. This generates a core gene list with transcripts for analysis regarding expression and alternative splicing events. Five patients having a deletions including at least the entire APC region previously found with mlpa were analyzed using the 250K and the 6.0 SNP arrays to reveal the extension of the deletions. Conclusions A combination of exon-arrays and SNP-arrays can be used in order to get a more detailed picture of copy number changes and its correlation with differentially expressed/alternative spliced transcripts. This will give valuable information about regulation of genes and add information regarding new mutational mechanisms. Results The exonarrays were analyzed as follows; subsequent to ANOVA analysis a threshold cutoff was set to p-values less than and at least a 2-fold geometric change in gene-level expression between controls and patients. For the AFAP cases two examples of two different spliced gene are shown i fig1a and fig1b. In the classical FAP cases the APC gene showed a difference in expression and splicepattern. 1A 1B A microarray (Affymetrix 250K) analysis of a patient previously identified with mlpa, shows that the deletion extends at least 5 genes 5´ of the APC gene and includes a region of 7.7Mb (fig2a and fig2b). 2A 2B