Array comparative genomic hybridization analysis in patients with anophthalmia, microphthalmia, and coloboma

Abstract

Purpose: The goal of our study was to determine whether genomic copy number abnormalities (deletions and duplications) affecting genes involved in eye development contributed to the etiology of anophthalmia, microphthalmia, and coloboma.

Methods: The affected individuals were evaluated for the presence of deletions and duplications in genomic DNA by a very high-resolution array comparative genomic hybridization.

Results: Array analysis of 32 patients detected one case with a deletion encompassing the renal-coloboma syndrome associated gene PAX2. Nonpolymorphic copy number changes were also observed at several candidate chromosomal regions, including 6p12.3, 8q23.1q23.2, 13q31.3, 15q11.2q13.1, 16p13.13, and 20q13.13.

Conclusions: This study identified the first patient with the typical phenotype of the renal-coloboma syndrome caused by a submicroscopic deletion of the coding region of the PAX2 gene. The finding suggests that PAX2 deletion testing should be performed in addition to gene sequencing as a part of molecular evaluation for the renal-coloboma syndrome. Array comparative genomic hybridization testing of 32 affected individuals showed that genomic deletions and duplications are not a common cause of nonsyndromic anophthalmia, microphthalmia, or coloboma but undoubtedly contribute to the etiology of these eye anomalies. Therefore, array comparative genomic hybridization testing represents an important and valuable addition to candidate gene sequencing in research and diagnostics of ocular birth defects.

Figure 1

A) Array CGH profile of the 10q24.31 deletion affecting the PAX2 gene in the patient with Renal-coloboma (Papillorenal) syndrome; panel A (top) is showing the close view of the deleted segment from the OneClick CGH software. B) A screenshot from the UCSC genome browser showing the deleted region at cytogenetic location 10q24.31, from 102,437,000 to 102,677,000 based on the Human Genome March 2006 (hg18) assembly.