Microarray for DNA & RNA Mosa Alzowelei BME 11/12/2014

Agenda Introduction History Mechanisms Clinical Application Future Improvement References

Introduction DNA Microarray –“a grid of DNA segments of known sequence that is used to test and map DNA fragments, antibodies, or proteins” Affymetrix –Pioneer in breakthrough tools Driving genomic revolution Discovery, exploration, validation and genetic testing –Revolutionizing scientific and medical communities Investigating Parkinson’s disease, cancer, malaria etc

History Affymetrix’ GeneChip technology –Invented in 1980 Semiconductor manufacturing technique along with combinatorial chemistry Biological data on a small glass chip Growth via acquisitions –From 1994 to 2008 Major customers –Biotech, pharmaceutical, agrichemical etc –Academic and government institutions

Mechanism

Clinical Application Cytogenetics – Tools and resources Cancer research –Genomic Parameter at various complexities Whole-genome to single gene –Translational work flow Discovery to test development

Future Improvements CytoScan HD Array –Blood Tumor DNA Somatic mutation and allelic ratio detection GeeChip miRNA 2.0 array –Gene regulation profiling OncoScan FFPE Express Services –Solid Tumor DNA Copy number aberration and allelic ratio detection

References Irizarry, Rafael A et al. "Summaries of Affymetrix GeneChip probe level data." Nucleic acids research 31.4(2003): e15­e15 Cheadle, Chris et al. "Application of z­score transformation to Affymetrix data." Applied bioinformatics 2.4(2003): van de Goor, Tom A. "A history of DNA microarrays." (2005) rizarry, Rafael A et al. "Summaries of Affymetrix GeneChip probe level data." Nucleic acids research 31.4(2003): e15­e15 Ragoussis, Jiannis, and Gareth Elvidge. "Affymetrix GeneChip® system: moving from research to the clinic." Expert review of molecular diagnostics 6.2 (2006): 145­152. Mikhailovich, Vladimir et al. "DNA microarrays in the clinic: infectious diseases." Bioessays 30.7 (2008) 673­682