Genomic Deletions of RXRA-COL5A1, FAM46A-IBTK, HS3ST3B1-PMP22, and GRIA4 in Familial Keratoconus Patients

Abstract

Purpose: DNA copy number variations (CNVs) have been shown to play an important role in ocular disorders. However, their role still remains unclear in keratoconus (KC). This study is to examine their role in familial KC patients.

Methods: 95 DNA samples from 29 multiplex KC families were genotyped using Illumina HumanOmni2.5-8 BeadChips containing 2.5 million markers. We identified a total of 1,600 CNVs with at least 10 consecutive probes and 5 kb in size using the PennCNV software. We examined the CNVs that are located within or adjacent to over 50 known genes that are reported to be associated with central cornea thickness (CCT), myopia, or KC, in genome-wide association studies.

Results: We detected an average of 18 CNVs per sample with an average size of 42 kb. In 13 samples, we detected 14 homozygous deletions, of which none overlaps or is adjacent to the known candidate genes. In 18 individuals, we identified 20 heterozygous deletions that are located within or adjacent to 4 candidate regions (RXRA-COL5A1, FAM46A-IBTK, HS3ST3B1-PMP22, and GRIA4). Two patients in one family have genomic deletions located in the RXRA-COL5A1 locus, which has been associated with both CCT and KC. Two patients from two families have deletions located within the HS3ST3B1-PMP22 region, which has been associated with CCT. One patient carries a deletion in the upstream of the GRIA4 gene, which has been associated with myopia. Fourteen samples (10 affected and 4 controls) have genomic deletions adjacent to the FAM46A-IBTK locus, which has been associated with CCT. These genomic deletions are rare (< 0.1%) in the general population or have not been documented by the CNV database DGV (Database of Genomic Variants). We noted an incomplete segregation of these heterozygous deletions with KC affection status, probably due to the reported incomplete penetrance of KC. We will further explore these genomic deletions in an independent KC cohort. TaqMan-based realtime PCR reactions will be used to validate these genomic deletions and to further evaluate their segregation with KC in additional families.

Conclusions: We have identified several genomic deletions located within or adjacent to the regions associated with CCT, myopia and KC. These include regions within RXRA-COL5A1, FAM46A-IBTK, HS3ST3B1-PMP22, and GRIA4. In addition, this study provides suggestive evidence for the involvement of CNVs in the pathogenesis of KC.

Keywords: 574 keratoconus • 480 cornea: basic science • 539 genetics