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Is AMD a Disease or a Disorder? A Systems Biology Attempt to Subtype AMD on the Basis of Gene Expression

Friday, November 08, 2013 — Poster Session IV

2:00 p.m. – 4:00 p.m.

FAES Academic Center (Upper-Level Terrace)




  • C.C. Chan


Genetic pathways underlying the initiation and progression of age-related macular degeneration (AMD) have not been yet sufficiently revealed, and whether AMD’s phenotypes represent a single disease or a disorder with an assemblage of diseases is still awaiting resolution. We applied the systems biology parsimony phylogenetics to gene expression data of ocular tissues in AMD (Newman 2012). Gene expression data included macular and extra-macular specimens of 55 normal, 13 pre-AMD, and 47 AMD retinas, as well as 96 normal, 21 pre-AMD, and 60 AMD retinal pigment epithelium (RPE)-choroids. Values of retinal and RPE-choroidal specimens were polarized separately against their respective normal specimens, and the new polarized data matrices were processed through MIX, a parsimony program of PHYLIP. Gene lists extracted from the cladograms nodes were processed in Genomatix GePS to generate gene networks. Datasets of retina and RPE produced multiple cladograms indicating heterogeneous gene-expression data. AMD phenotypes were not distinct according to their transcriptome showing more subtypes than the currently recognized phenotypes. Macular and temporal extra-macular tissues of the same patient separated in most of the retinal and RPE sets but others clustered together. Thus, cladograms did not support classical AMD phenotypes as a valid transcriptomal subtype /profile of AMD.

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