Jones, C;
(2004)
Development of software utilities for CGH-microarray management and data analysis.
Masters thesis , UNSPECIFIED.
Abstract
CGH (Comparative Genome Hybridisation) microarrays are an emerging technology used to detect chromosome copy number changes. Large numbers of genomic DNA segments are accurately printed at high density onto surface-treated glass slides, and competitively hybridised with two DNA samples labelled with different fluorescent dyes. Variations in the genetic content of the two samples are detected as changes in the ratio of the two fluorescent dyes hybridising to individual features of the microarray. CGH microarray technology requires significant bioinformatics input in the manufacturing and analysis processes, in addition to substantial sample-tracking demands from its laboratory use. This thesis describes the design and implementation of integrated software and database utilities for use in the CGH microarray process, using the Perl programming language and a MySQL database. Perl subroutines provide a simple means to identify large numbers of genomic DNA clones from the Ensembl databases, starting with an XML-formatted list of a variety of different genome feature types. The identified genomic DNA clones are collected in a local database which is used as the starting point for the design of the microarray. The database design centres around the use of foreign key constraints and bar-coded laboratory samples to provide consistent and efficient sample tracking throughout the microarray design, manufacture and experimental use. Finally, a Perl script interprets the output from a microarray laser scanning device determining the identifies of each feature on the microarray. It calculates replicate averages and fluorescent ratios at each distinct feature and populates the database with the analysed data. These utilities have been implemented in the laboratory and will continue to be developed to provide a user friendly web-based interface and dynamic microarray layout interpretation
| Type: | Thesis (Masters) |
|---|---|
| Title: | Development of software utilities for CGH-microarray management and data analysis |
| Additional information: | Academic Department: Cranfield Centre for Bioinformatics and I.T. City: Silsoe |
| Keywords: | analysis, Chromosome, DNA, MANAGEMENT, OnCite |
| UCL classification: | UCL > Provost and Vice Provost Offices UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Population Health Sciences > UCL EGA Institute for Womens Health |
| URI: | https://discovery.ucl.ac.uk/id/eprint/94157 |
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