Progress Determining the Mechanism of Segmental Duplication and Deletion in Axenfeld Rieger Phenotypes

Abstract

Purpose:: To identify the cause(s) of chromosome 6p25 segmental duplication and deletion, which result in a spectrum of Axenfeld Rieger phenotypes.

Methods:: Array Comparative Genome Hybridization (CGH) was undertaken to refine the location of breakpoints in segmental deletion (n=1) and duplication (n=5) pedigrees. Subsequently, long range PCR was performed to amplify breakpoint-spanning junctional fragments with sequencing and in silico analysis used to determine the genomic architecture of the junctional fragment and the region flanking the breakpoints.

Results:: CGH accurately defined the extent of 6p25 segmental anomalies [deletion 1216 kb; duplications 474, 477.5 and 492kb]. A 1.2kb junctional fragment amplified in the deletion pedigree (n=5 affected) segregated with the clinical phenotype. The breakpoints lie within simple repeats with 368bp of novel sequence, comprising two 100% homologous motifs in head to tail orientation, inserted between them separated by a 13bp insert. Analyses of the segmental duplications are commencing.

Conclusions:: Array CGH represents a powerful technique to define the extent of chromosomal anomalies and facilitate analysis of the mechanism(s) that cause glaucoma-associated segmental duplications and deletions. The segmental deletion exhibits features of both homologous recombination and non-homologous end joining with an unusually large insert of DNA at the breakpoint. The variation in segmental duplication size indicates existence of a common causative mechanism and elucidation of this will clarify the etiology of a proportion of Axenfeld Rieger syndrome cases.

Keywords: genetics • development