Abstract
Purpose :
Infantile nystagmus (IN) is a genetically heterogeneous disorder that can arise as a result of mutations in genes expressed in the developing retina and brain. We aimed to develop and assess the utility of a next generation sequencing (NGS) panel to enhance the diagnosis of IN.
Methods :
A total of 140 nystagmus associated genes were selected based on OMIM records and previous literature. We designed a NimbleGen Custom array to target all the coding sequences and splice junctions. Sequencing was performed using Illumina HiSeq 2000 with a mean coverage of 100x.
Experiment 1: We aimed to assess the sensitivity and specificity of the NGS panel. The reference sample (NA12878) was obtained from National Institute of Standards and Technology (NIST). We assessed the variants detected using our NGS panel against previously published gold standard variants for this sample.
Experiment 2: We aimed to assess the clinical utility of the panel. We performed sequence analysis on 15 patients. The inclusion criteria were: (1) IN and (2) family history of nystagmus (at least one additional family member affected). Authors MGT and GDEM were blinded to the clinical diagnoses and performed the sequence analysis.
Results :
The validation experiment revealed that the panel has a sensitivity of 98.5% and specificity of 99.9%. In the blinded analysis, we were able to determine the genetic diagnosis in 10/15 patients. We identified mutations of FRMD7 (n=2), CACNA1F (n=2), TYR (n=5) and COL11A1 (n=1) resulting in IN. This was consistent with the clinical diagnosis in 8/10 patients, in the remaining 2 patients the results from the genetic diagnoses (COL11A1 and TYR mutation) were used to revise the clinical diagnoses. In 5/15 patients we were unable to determine a genetic diagnosis. In one patient with X-linked Idiopathic IN we did not identify any FRMD7 mutations using the panel. However copy number variation analysis revealed an FRMD7 deletion of exons 2-12.
Conclusions :
This is the first study establishing the clinical utility of a diagnostic NGS panel for IN. Using reference material from the NIST we were able to show that the panel had very high sensitivity and specificity. The genetic information from the panel will not only lead to personalised diagnosis and management of IN but also enable accurate genetic counselling. Establishing genotype-phenotype correlations is important in understanding the molecular mechanisms of IN.
This is an abstract that was submitted for the 2016 ARVO Annual Meeting, held in Seattle, Wash., May 1-5, 2016.