Poster presentation, P45

Official XXIst International Pigment Cell Conference website - 21-24 Sept 2011, Bordeaux - France | updated: September 04 2011

Bioinformatics tools to predict splicing mutation effect in genetic diagnosis of oculocutaneous albinism

BACKGROUND: Oculocutaneous albinism (OCA) is an autosomal recessive disease of skin, hair and eye hypopigmentation caused by a deficiency in melanin biosynthesis. Four genes respectively responsible for the four types (1 to 4) of OCA have been identified: TYR, OCA2, TYRP1 and SLC45A2. Molecular analysis is essential for precise diagnostic of the different forms of OCA. We found mutations affecting splicing in the different genes leading to OCA. We sought to highlight the major role of bioinformatics resources in helping to evaluate the consequence of variants on splicing. METHODS: We analyzed the whole coding region of the four OCA genes, including intron-exon boundaries and searched for deletions/duplications. Intronic variants were analysed using the Alamut 2.0 software (Interactive Biosoftware, Rouen, France) which gives access to several algorithms like Human splicing Finder and Max Ent Scan. RESULTS: We identified 3 new intronic variants in TYR, eight in OCA2, one in SLC45A2 and one in TYRP1 potentially affecting splicing. The splicing variant c.1037-7T > A in the TYR gene was already known as a frequent mutation. We found several variants which occurred in the splicing consensus region of the acceptor site (at position -1). As expected all of these variants were predicted to disrupt splice site signalling. Then we analysed the deleterious effect of the variants located at position between +3 and +7 from the donor splice site, and -3 to -10 and beyond from the acceptor splice site for which these algorithms are most useful to predict pathogenic effect. For some of the tested variants, the algorithms provided splice scores indicating that splicing was altered. CONCLUSION: Bioinformatics resources play a major role in helping diagnostic laboratories to evaluate the consequence of mutations on splicing (exon skipping, partial exonic deletion, intronic retention) especially because most genetic tests use DNA samples and not RNA samples. RNA studies in albino patients are rendered difficult by the fact that expression of the OCA genes is restricted to specific cells such as melanocytes. Results of analyses specifically focused on splice sites should however be taken with caution, since features other than splice sites are also involved in the splicing process.

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