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Development of a Database for Array Comparative Genomic Hybridization

Authors: André Santos

Supervisors: Joana Barbosa de Melo, Helmut Wolters, João Carvalho

MSc thesis, Universidade de Coimbra (2015)

Abstract: Microarray Comparative Genomic Hybridization (arrayCGH) allowed a significant advance on the diagnose of unexplained development disorders by detecting genomic copy number variations (CNVs) that were previously undetectable by other types of cytogenetic technologies. Well characterized genetic syndromes are detected and also new genomic disorders and diseases causing CNVs are being discovered through the utilization of this technique. The pathogenicity assessment of the CNVs detected by arrayCGH are directly or indirectly related with a query of previously recorded and classified CNVs. When a CNV that has not been observed before appears, clinicians have to interpret the variant of uncertain clinical significance (VOUS), which can be very challenging for them. However, sharing classified CNVs between laboratories can be helpful when facing a VOUS in order to help its classification as benign or pathogenic. Easily recording, querying and sharing information about CNVs is very important for clinicians and laboratories in order to accomplish the right diagnostic for their patients. In this work is presented the development of a database, using a LAMP technology (Linux, Apache, MySQL and PHP), to store array CGH records and of an interface that laboratory clinicians can use for querying and management of CNVs.